Surveyor Plus

User Guide for LC Devices

60053-97221 Revision C March 2011

© 2011Thermo Fisher Scientific Inc. All rights reserved.

Surveyor and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States.
The following are registered trademarks in the United States and other countries:
Teflon is a registered trademark of E. I. du Pont de Nemours and Company. Windows, Excel, and XP are
registered trademarks of Microsoft Corporation.
All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.

Software version: Thermo Fisher Scientific provides the Surveyor device drivers on the LC Devices.
software CD. This manual describes Surveyor devices available on the LC Devices 2.2.0 software CD or later.
These drivers are compatible with Xcalibur 2.0 or later and Thermo Foundation 1.0.x or later.

Firmware versions: Installing the Surveyor device drivers also installs the Surveyor Firmware Upgrade Utility
and the firmware files for the Surveyor devices. For the Surveyor PDA Plus Detector, ensure that the firmware
version is 2.02 or later.

Revision history: Revision A, January 2009; Revision B, April 2010; Revision C, March 2011

For Research Use Only. Not for use in diagnostic procedures.

 Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described in the next section or sections by product name.

Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.

This section contains regulatory compliance information for the following devices of the Surveyor Plus family of LC
instruments:

• Surveyor LC Pump Plus • Surveyor PDA Plus Detector

• Surveyor MS Pump Plus • Surveyor UV/Vis Plus Detector
• Surveyor Autosampler Plus

Surveyor LC Pump Plus

When the Surveyor LC Pump Plus is delivered to you, it meets all pertinent electromagnetic compatibility (EMC) and
safety standards as described below.

EMC Directive 89/336/EEC amended by 92/31/EEC and 93/68/EEC

EMC compliance has been evaluated by Underwriters Laboratories Inc.

EN 55011 1998 EN 61000-4-3 2002

EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 EN 61000-4-4 1995, A1; 2001, A2; 2001
IEC 61000-3-2 2000 EN 61000-4-5 1995, A1; 2001
EN 61000-3-3 1995 EN 61000-4-6 1996, A1; 2001
IEC 61000-3-3 1994 EN 61000-4-11 1994, A1; 2001
EN 61326-1 1997
EN 61000-4-2 1995 A1; 1998 A2; 2001 CISPR 11 1999, A1; 1999, A2; 2002
FCC Class A, CFR 47 Part 15 Subpart B: 2004
Low Voltage Safety Compliance
Low voltage safety compliance has been evaluated by TUV Rheinland of North America, Inc. This device complies
with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.

Surveyor MS Pump Plus

When the Surveyor MS Pump Plus is delivered to you, it meets all pertinent electromagnetic compatibility (EMC) and
safety standards as described below.

EMC Directive 89/336/EEC amended by 92/31/EEC and 93/68/EEC

EMC compliance has been evaluated by Underwriters Laboratories Inc.

EN 55011 1998 EN 61000-4-3 2002

EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 EN 61000-4-4 1995, A1; 2001, A2; 2001
IEC 61000-3-2 2000 EN 61000-4-5 1995, A1; 2001
EN 61000-3-3 1995 EN 61000-4-6 1996, A1; 2001
IEC 61000-3-3 1994 EN 61000-4-11 1994, A1; 2001
EN 61326-1 1997
EN 61000-4-2 1995 A1; 1998 A2; 2001 CISPR 11 1999, A1; 1999, A2; 2002
FCC Class A, CFR 47 Part 15 Subpart B: 2004

Low Voltage Safety Compliance

Low voltage safety compliance has been evaluated by TUV Rheinland of North America, Inc.This device complies with
Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
 Surveyor Autosampler Plus
When the Surveyor Autosampler Plus is delivered to you, it meets all pertinent electromagnetic compatibility (EMC)
and safety standards as described below.

EMC Directive 89/336/EEC amended by 92/31/EEC and 93/68/EEC

EMC compliance has been evaluated by Underwriters Laboratories Inc.

EN 55011 1998 EN 61000-4-3 2002

EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 EN 61000-4-4 1995, A1; 2001, A2; 2001
IEC 61000-3-2 2000 EN 61000-4-5 1995, A1; 2001
EN 61000-3-3 1995 EN 61000-4-6 1996, A1; 2001
IEC 61000-3-3 1994 EN 61000-4-11 1994, A1; 2001
EN 61326-1 1997
EN 61000-4-2 1995 A1; 1998 A2; 2001 CISPR 11 1999, A1; 1999, A2; 2002
FCC Class A, CFR 47 Part 15 Subpart B: 2004

Low Voltage Safety Compliance

Low voltage safety compliance has been evaluated by TUV Rheinland of North America, Inc. This device complies
with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
 Surveyor PDA Plus Detector
When the Surveyor PDA Plus Detector is delivered to you, it meets all pertinent electromagnetic compatibility (EMC)
and safety standards as described below.

EMC Directive 89/336/EEC amended by 92/31/EEC and 93/68/EEC

EMC compliance has been evaluated by Underwriters Laboratories Inc.

EN 55011 1998 EN 61000-4-3 2002

EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 EN 61000-4-4 1995, A1; 2001, A2; 2001
IEC 61000-3-2 2000 EN 61000-4-5 1995, A1; 2001
EN 61000-3-3 1995 EN 61000-4-6 1996, A1; 2001
IEC 61000-3-3 1994 EN 61000-4-11 1994, A1; 2001
EN 61326-1 1997
EN 61000-4-2 1995 A1; 1998 A2; 2001 CISPR 11 1999, A1; 1999, A2; 2002
FCC Class A, CFR 47 Part 15 Subpart B: 2003

Low Voltage Safety Compliance

Low voltage safety compliance has been evaluated by TUV Rheinland of North America, Inc.This device complies with
Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
 Surveyor UV/Vis Plus Detector
When the Surveyor UV/Vis Detector is delivered to you, it meets all pertinent electromagnetic compatibility (EMC)
and safety standards as described below.

EMC Directive 89/336/EEC amended by 92/31/EEC and 93/68/EEC

EMC compliance has been evaluated by Underwriters Laboratories Inc.

EN 55011 1998 EN 61000-4-3 2002

EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 EN 61000-4-4 1995, A1; 2001, A2; 2001
IEC 61000-3-2 2000 EN 61000-4-5 1995, A1; 2001
EN 61000-3-3 1995 EN 61000-4-6 1996, A1; 2001
IEC 61000-3-3 1994 EN 61000-4-11 1994, A1; 2001
EN 61326-1 1997
EN 61000-4-2 1995 A1; 1998 A2; 2001 CISPR 11 1999, A1; 1999, A2; 2002
FCC Class A, CFR 47 Part 15 Subpart B: 2004

Low Voltage Safety Compliance

Low voltage safety compliance has been evaluated by TUV Rheinland of North America, Inc.This device complies with
Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.

FCC Compliance Statement

THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.

CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
 Notice on Lifting and Handling of
Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one
person alone to handle safely.

Notice on the Proper Use of

Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.

Notice on the Susceptibility

to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.

For manufacturing location, see the label on the instrument.

 WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE)
Directive 2002/96/EC. It is marked with the following symbol:

Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union
(EU) Member State, and these companies should dispose of or recycle this product. See www.thermo.com/
WEEERoHS for further information on Thermo Fisher Scientific’s compliance with these Directives and the
recyclers in your country.

WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen.
Das Produkt ist durch folgendes Symbol gekennzeichnet:

Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten

getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Mehr Information
über die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific, über die Verwerter, und weitere Hinweise,
die nützlich sind, um die Produkte zu identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter
www.thermo.com/WEEERoHS.
 Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et
Electroniques (DEEE). Il est marqué par le symbole suivant:

Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de
l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage d'informations sur la
conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre pays et les informations sur les
produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont
disponibles sur www.thermo.com/WEEERoHS.
 C

Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xv
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii

Chapter 1 Introduction to the Surveyor Plus LC System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Analytical Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Surveyor MS Pump Plus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Surveyor LC Pump Plus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Tray Compartment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Vial and Well Notation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Injection System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Injection Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Temperature Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
PDA Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
UV/Vis Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Solvent Platform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Communication with the Data System Computer. . . . . . . . . . . . . . . . . . . . . . . 24
Turning Off the Computer’s Energy Saving Features . . . . . . . . . . . . . . . . . . . . 24
Synchronization of the LC Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Status LEDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Surveyor MS Pump Plus LED States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Surveyor LC Pump Plus LED States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Autosampler LED States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
PDA Detector LED States. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
UV-Vis Detector LED States. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Chapter 2 Thermo Foundation Instrument Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41

Checking the Communication Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Opening the Thermo Foundation Instrument Configuration Application. . . . . 43
Adding Devices to the Instrument Configuration . . . . . . . . . . . . . . . . . . . . . . . 44

Thermo Scientific Surveyor Plus User Guide for LC Devices xi

Contents

Specifying the Configuration Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Surveyor Autosampler Plus Configuration Settings . . . . . . . . . . . . . . . . . . . . 45
Surveyor MS Pump Plus Configuration Settings . . . . . . . . . . . . . . . . . . . . . . 61
Surveyor LC Pump Plus Configuration Settings . . . . . . . . . . . . . . . . . . . . . . 63
Surveyor PDA Plus Detector Configuration Settings . . . . . . . . . . . . . . . . . . . 65
Surveyor UV/Vis Plus Detector Configuration Settings. . . . . . . . . . . . . . . . . 66
Closing the Foundation Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Chapter 3 Instrument Method Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67

Opening the Instrument Setup Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Surveyor LC Pump Plus Instrument Method Parameters . . . . . . . . . . . . . . . . . 69
Surveyor LC Pump Plus General Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Surveyor LC Pump Plus Gradient Program Page. . . . . . . . . . . . . . . . . . . . . . 71
Surveyor MS Pump Plus Instrument Method Settings . . . . . . . . . . . . . . . . . . . 74
Specifying the Chromatographic Conditions for a Single-Pump System . . . . 74
Programming the Pumps in a Dual-Pump System. . . . . . . . . . . . . . . . . . . . . 84
Autosampler Instrument Method Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Surveyor AS Method Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Reservoir Content Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Timed Events Page for the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
PDA Detector Instrument Method Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 95
Triggering an External Device with the PDA Detector . . . . . . . . . . . . . . . . . . 104
UV-Vis Detector Instrument Method Parameters . . . . . . . . . . . . . . . . . . . . . . 106
Saving the Instrument Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

Chapter 4 Sample Preparation Routines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113

Opening the Sample Preparation Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Sample Preparation Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Building the Sample Preparation Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Sample Locations for the Sample Preparation Tasks . . . . . . . . . . . . . . . . . . . . 122
Draw, Eject, and Transfer Volumes for Sample Preparation Tasks . . . . . . . . . 123
Syringe Speed Range for Sample Preparation Tasks. . . . . . . . . . . . . . . . . . . . . 124
Syringe Speed for Tasks that Can Use Either Plunger . . . . . . . . . . . . . . . . . 125
Syringe Speed for Tasks that Use the Inner Plunger. . . . . . . . . . . . . . . . . . . 126
Sample Preparation Routine Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

Chapter 5 Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .133

Turning On the Power to Each LC Device . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Initiating Communication with the Data System . . . . . . . . . . . . . . . . . . . . . . 135
Checking the Status of the LC Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Opening the Status Page of the Information View. . . . . . . . . . . . . . . . . . . . 136
Viewing the Status of Each Device . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Turning Devices On, Off, or into Standby from the Info View. . . . . . . . . . . . 154
Filling the Solvent Reservoir Lines with Fresh Solvent. . . . . . . . . . . . . . . . . . . 155
Priming the Pulse Dampener of the Surveyor MS Pump Plus . . . . . . . . . . . . . 156
Accessing the Direct Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158

xii Surveyor Plus User Guide for LC Devices Thermo Scientific

 Contents

Chapter 6 Direct Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .161

PDA Detector Direct Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Turning the Lamps On or Off. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Resetting the Lamp Usage Hours . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Changing the Polarity of the Analog Outputs . . . . . . . . . . . . . . . . . . . . . . . 164
Testing the Analog Outputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Setting the Lamp Startup Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
Checking the Chromatographic Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Viewing, Exporting, and Clearing the Error Log for the PDA Detector. . . . 171
Checking the Firmware Version of the PDA Detector . . . . . . . . . . . . . . . . . 171
Configuration Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Display Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Information Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
UV-Vis Detector Direct Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Pump Direct Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Surveyor LC Pump Plus Direct Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Surveyor MS Pump Plus Direct Controls . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Autosampler Direct Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Applying a Direct Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
Direct Control Commands for the Autosampler . . . . . . . . . . . . . . . . . . . . . 194
Flushing the Autosampler Syringe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Removing and Installing Sample Trays . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Controlling the Tray and Oven Compartment Temperatures . . . . . . . . . . . 199

Chapter 7 Sequence Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .201

Creating a Single Sample Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Opening the Sequence Setup Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Creating the Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Selecting the Vial Locations Interactively. . . . . . . . . . . . . . . . . . . . . . . . . . . 206
Saving the Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Equilibrating the Chromatographic Column . . . . . . . . . . . . . . . . . . . . . . . . . . 209
Loading the Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
Starting Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Working with the Real Time Plot View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Viewing Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Reviewing Real-Time Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Adding Cells to the Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

Chapter 8 Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .219

Opening a Raw Data File in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Working with the Cell Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Cell States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Cursor Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Changing the Font Size of the Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
Viewing a Report of the Instrument Method. . . . . . . . . . . . . . . . . . . . . . . . . . 232

Thermo Scientific Surveyor Plus User Guide for LC Devices xiii

Contents

Creating a Layout for PDA Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233

Specifying the Chromatogram and Spectrum Ranges . . . . . . . . . . . . . . . . . 233
Specifying the Display Options for the Chromatogram and Spectrum
Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
Inserting Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Saving the New Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
Viewing the Spectrum for a Specific Time Point . . . . . . . . . . . . . . . . . . . . . . . 249
Viewing the Chromatogram for a Specific Wavelength . . . . . . . . . . . . . . . . . . 250
Determining Peak Areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Calculating the Purity of the Chromatographic Peaks . . . . . . . . . . . . . . . . . . . 254

Chapter 9 LC Pump Calibration and Record Keeping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .259

Calibrating the Surveyor LC Pump Plus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Accessing the Calibration Options for the Surveyor LC Pump Plus. . . . . . . 260
Calibration Options for the Surveyor LC Pump Plus . . . . . . . . . . . . . . . . . 262
Calibration Procedures for the Surveyor LC Pump Plus . . . . . . . . . . . . . . . 266
Recording Maintenance Information for the Surveyor LC Pump Plus. . . . . . . 270
Firmware Version Information for the Surveyor LC Pump Plus . . . . . . . . . . . 272

Chapter 10 Autosampler Calibration and Record Keeping . . . . . . . . . . . . . . . . . . . . . . . . . . .273

Calibrating the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
Column Oven Air Sensor Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Vial Tray Metal Sensor Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Arm Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
Well Bottom Distance Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
Autosampler Maintenance Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
Autosampler Validation Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311

Chapter 11 PDA Detector Performance Check and Calibration . . . . . . . . . . . . . . . . . . . . . . .313

Verifying the Performance of the PDA Detector . . . . . . . . . . . . . . . . . . . . . . . 313
Creating a Display Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Adjusting the Light Throughput to the Diode Array . . . . . . . . . . . . . . . . . . 315
Calibrating the PDA Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319
Calibration Page for the PDA Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
Performing a Dark Current Calibration. . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Performing a Wavelength Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Creating and Editing a Custom Wavelength Calibration List . . . . . . . . . . . 337

Chapter 12 Making a Single Injection from the Tune Window. . . . . . . . . . . . . . . . . . . . . . . .341

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .345

xiv Surveyor Plus User Guide for LC Devices Thermo Scientific

 P

Preface
This guide describes how to use your Thermo Scientific mass spectrometry application to
control the Surveyor™ Plus high-performance liquid chromatography (HPLC) system.

Contents
• Related Documentation
• Safety and Special Notices
• Contacting Us

Tip Use the Lamp Startup Time feature to preserve the useful lifetime of the deuterium
lamp. The default lamp startup time for the PDA detector is 4:55 PM. For optimal system
performance, reset the lamp startup time to approximately two hours before you plan to
start data acquisition. For information about changing the lamp startup time, see “Setting
the Lamp Startup Time” on page 166.

Tip The default setting for the autosampler maintenance counters is 0. If you turn on the
autosampler maintenance log (see “Communication Page” on page 52) when you specify
the configuration settings for the autosampler and leave the counters at the default setting,
the autosampler status displays Maintenance Due and the data system prevents you from
starting a run. For information about changing the counter settings on the Maintenance
Information page, see “Autosampler Maintenance Information” on page 309.

Thermo Scientific Surveyor Plus User Guide for LC Devices xv

Preface

Related Documentation
In addition to Help that you can access from the data system, these manuals are provided with
LC Devices as PDF files for the Surveyor Plus family of high-performance LC instruments:
• Surveyor Plus User Guide for LC Devices (formerly entitled Surveyor Plus User Guide for the
Xcalibur Data System)
• Surveyor Plus Preinstallation Requirements Guide
• Surveyor Plus Getting Connected Guide
• Surveyor Autosampler Plus Hardware Manual
• Surveyor LC Pump Plus Hardware Manual
• Surveyor MS Pump Plus Hardware Manual
• Surveyor PDA Plus Detector Hardware Manual
• Surveyor UV/Vis Plus Detector Hardware Manual

 To view manuals for your Surveyor Plus LC devices

Go to Start > Programs > Thermo Instruments > Manuals > LC Devices > Surveyor >.

 To open Help

• From the Instrument Setup window, choose Help >product name Help.
• If available for a specific window or dialog box, click Help or press F1 for
information about setting parameters.

For more information, visit www.thermoscientific.com.

xvi Surveyor Plus User Guide for LC Devices Thermo Scientific

 Preface

Safety and Special Notices

Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.

Safety and special notices include the following:

CAUTION Highlights hazards to humans, property, or the environment.

Each CAUTION notice is accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal
performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Thermo Scientific Surveyor Plus User Guide for LC Devices xvii

Preface

Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.

 To contact Technical Support

Phone 800-532-4752
Fax 561-688-8736
E-mail [email protected]
Knowledge base www.thermokb.com

Find software updates and utilities to download at mssupport.thermo.com.

 To contact Customer Service for ordering information

Phone 800-532-4752
Fax 561-688-8731
E-mail [email protected]
Web site www.thermo.com/ms

 To get local contact information for sales or service

Go to www.thermoscientific.com/wps/portal/ts/contactus.

 To copy manuals from the Internet

Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click

Customer Manuals in the left margin of the window.

 To suggest changes to documentation or to Help

• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.

• Send an e-mail message to the Technical Publications Editor at
[email protected].

xviii Surveyor Plus User Guide for LC Devices Thermo Scientific

 1

Introduction to the Surveyor Plus LC System

The Surveyor Plus high-performance liquid chromatography system (see Figure 1), which
integrates with the Thermo Scientific family of mass spectrometers, consists of an analytical
pump, an autosampler, an optional PDA detector or UV/Vis detector, and a solvent platform.
Figure 1. Surveyor Plus LC instrument
Solvent
platform

Detector

Autosampler

Analytical
pump

Contents
• Analytical Pump
• Autosampler
• Detector
• Solvent Platform
• Communication with the Data System Computer
• Turning Off the Computer’s Energy Saving Features
• Synchronization of the LC Devices
• Status LEDs

Thermo Scientific Surveyor Plus User Guide for LC Devices 1

1 Introduction to the Surveyor Plus LC System
Analytical Pump

Analytical Pump
Thermo Scientific, part of Thermo Fisher Scientific Inc., offers two analytical pumps in the
Surveyor Plus product line: the Surveyor MS Pump Plus, which provides optimum
performance in the lower flow rate ranges needed for mass spectrometry; and the Surveyor LC
Pump Plus, which provides optimum performance in the flow rate ranges needed for
chromatography.

Both analytical pumps contain a built-in solvent degassing system that consists of four
independent chambers maintained at a constant vacuum of approximately 27 in. Hg. Each
chamber contains an 18 in. length of 0.045 in. ID Teflon™ AF tubing. This translates to a
volume of less than 500 μL per channel, adding very little to the quantity of solvent required
to purge the lines when you replace an eluent.

These topics describe the features of the Surveyor analytical pumps:

• Surveyor MS Pump Plus
• Surveyor LC Pump Plus

Surveyor MS Pump Plus

The Surveyor MS Pump Plus is a dual-piston, quaternary, low-pressure mixing pump with a
built-in vacuum degasser and pulse dampener. The pumping system provides flow rates from
1 to 2000 μL/min, which is the range needed to perform LC and LC/MS applications. You
can run precise gradients from 200 to 2000 μL/min, while the extremely low gradient delay
volume of 65 μL ensures minimum system cycle times.

The pulse dampening assembly consists of a low volume T-connector that the mobile phase
passes through. Attached to the side leg of the T-connector is a 2 mL loop of stainless steel
tubing. The loop terminates with a priming valve (pulse dampener flush valve). When the
priming valve is open, you can flush or fill the dampening loop with an appropriate solvent
such as methanol or isopropanol. When the priming valve is closed, the loop is shut off from
the flow path and absorbs pump pulsations. Because the 2 mL loop is shut off from the flow
path, it adds no gradient delay volume to the LC system.

The priming solvent in the loop does not interfere with the purity of the mobile phase, and its
composition does not need to match the mobile phase.

The data system remotely controls the pump with an RS-232 communication link from the
data system computer. The only manual control is the power switch located on the front of
the pump in the lower-left corner below the door.

2 Surveyor Plus User Guide for LC Devices Thermo Scientific

 1 Introduction to the Surveyor Plus LC System
Analytical Pump

Surveyor LC Pump Plus

The Surveyor LC Pump Plus is a dual-piston, quaternary, low-pressure mixing pump with a
built-in vacuum degasser and pulse dampener. The pumping system provides flow rates from
0.001 to 9.999 mL/min, which is the range needed to perform high-performance liquid
chromatography. You can run precise gradients from 0.200 to 2.000 mL/min.

The Surveyor LC Pump Plus is a bench-top unit for inclusion in the Surveyor Plus high
performance liquid chromatograph (HPLC). The Xcalibur™ data system controls the pump
through an Ethernet communication link with the data system computer. The only manual
controls are the power switch located on the front of the pump in the lower-left corner below
the door and the drain valve.

The Surveyor LC Pump Plus has five major components: the vacuum degassing assembly, the
solvent proportioning assembly, the pump head assemblies, the purge manifold assembly, and
the pulse dampening assembly (see Figure 2). The pulse dampening assembly adds 400 μL of
gradient delay volume to the system. The Surveyor LC Pump Plus has status LEDs on the
front door and a low-voltage power supply.
Figure 2. Front view of the Surveyor LC Pump Plus
Solvent lines entering Pump head Line body containing
and exiting the assemblies filter frit
degassing assembly

IN OUT
A

B Left Right
C

N
LO

PE
SE

DRAIN
O

On/Off Solvent Pulse dampening Purge

switch proportioning assembly (behind the manifold
assembly front panel) assembly

Thermo Scientific Surveyor Plus User Guide for LC Devices 3

1 Introduction to the Surveyor Plus LC System
Analytical Pump

You can use the Purge command from the data system to draw solvent at a rate of 10 mL/min
through the solvent lines connected to the pump after you open the purge valve. To open the
purge valve, turn the knob on the front of the purge manifold assembly counterclockwise
(see Figure 3). When the valve is in the open position, look for the word DRAIN to appear
upside down on the knob.
Figure 3. Drain valve positions
Closed position Open position

DRAIN

SE
O
PE

LO
N

C
C

N
LO

PE
SE

DRAIN
O

Figure 4 shows the line body fitting removed from the top of the purge manifold assembly.
The line body fitting contains an inline filter frit that captures particulate matter shed by the
pump seals. This prevents particulate matter from contaminating the tubing that connects the
pump to the autosampler. As this filter frit becomes clogged, the system backpressure rises.
Replace this filter frit when the system backpressure rises above its typical operating limits.
Figure 4. Line body and filter frit

4 Surveyor Plus User Guide for LC Devices Thermo Scientific

 1 Introduction to the Surveyor Plus LC System
Autosampler

Autosampler
Thermo Fisher Scientific offers two autosampler models in the Surveyor Plus product line:
the full-featured Surveyor Autosampler Plus and the Surveyor Autosampler Plus Lite. The
full-featured autosampler includes a built-in column oven (5 to 95 °C) and a temperature
controlled tray/sample compartment (0 to 60 °C). Both models let you inject samples and
perform sample preparation tasks automatically.

Note To convert from °C to °F, use the following equation:

°F = (1.8 × °C) + 32

For more information about the autosampler, see these topics:

• Tray Compartment
• Vial and Well Notation
• Injection System
• Injection Modes
• Temperature Control

Tray Compartment
The tray compartment (see Figure 5) can hold up to five conventional sample trays or one
carrier that holds three microwell plates. The tray compartment also holds up to four 16 mL
capacity reservoir vials that you can use to hold solvent, reagent, or diluent. The reservoir vials
are located behind the wash station and are designated RV1, RV2, RV3, and RV4.
Figure 5. Tray compartment
XYZ arm
mechanism RV4
RV3
RV2
RV1
Wash station
Injection port

Thermo Scientific Surveyor Plus User Guide for LC Devices 5

1 Introduction to the Surveyor Plus LC System
Autosampler

The five conventional sample trays, from the left side to the right side of the tray
compartment, are designated A, B, C, D, and E. Each sample tray holds up to 40 standard
1.8 mL vials, for a total capacity of 200 samples. Overlays allow the sample trays to
accommodate different vial sizes. The microwell carrier can hold up to three low-density
96-well microplates or up to three high-density 384-well microplates. The microplates are
designated A, B, and C.

The tray compartment door contains a magnetic switch. The magnet is located in the door
and the switch is attached to the chassis. When you open the door, the switch signals the
autosampler that the door is open.

When you configure the autosampler (from the data system) to verify whether the tray
compartment door is open or closed, the XYZ arm automatically moves to the back of the
tray compartment when you open the door, allowing you to remove trays or replace vials.
Opening the tray compartment door while the autosampler is making an injection does not
interrupt the current run. The XYZ arm moves to the back of the compartment after the
current injection is complete. The programmed sequence of injections then halts. When you
close the tray compartment door, the sequence resumes.

Vial and Well Notation

You specify the vial or microplate well location where you want the autosampler to withdraw
sample in the sequence table or the Inject Sample direct command. You also specify the vial or
microplate well locations for sample preparation tasks.

These topics describe the notation for specifying vial and well locations:
• Vial Notation
• 96-Well Microplate Notation
• 384-Well Microplate Notation

Vial Notation
The notation for the location of vials is as follows:
Tray location in tray compartment:Vial location in tray

Where:
Tray location in tray compartment = A, B, C, D, or E
Vial location in tray = 1 through 40

A colon separates the tray location in the tray compartment from the vial location in the tray.

Figure 6 shows the tray locations.

6 Surveyor Plus User Guide for LC Devices Thermo Scientific

 1 Introduction to the Surveyor Plus LC System
Autosampler

Figure 6. Standard trays

20 40 E:40
19 39
18 38
17 37
16 36
15 35
14 34
13 33
12 32
11 31
10 30
9 29
8 28
7 27
6 26
5 25
4 24
3 23
2 22
A:1 1 21

Tray A Tray B Tray C Tray D Tray E

96-Well Microplate Notation

The notation for the location of 96-well microplates is as follows:
Plate:RowColumn

Where:
Plate = A, B, or C
Row = A through H
Column = 1 through 12

Thermo Scientific Surveyor Plus User Guide for LC Devices 7

1 Introduction to the Surveyor Plus LC System
Autosampler

Figure 7 shows the notation for 96-well microplates when you select the top left orientation.
Figure 7. Notation for 96-well plates—Top left orientation

Plate C
A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12
C:A1
B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12

C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12

D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12

E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12

F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12

G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12

H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12

Plate B A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12

B:A1
B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12

C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12

D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12

E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12

F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12

G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12

H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12

Plate A
A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12
A:A1
B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12

C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12

D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12

E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12

F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12

G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12

H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12

8 Surveyor Plus User Guide for LC Devices Thermo Scientific

 1 Introduction to the Surveyor Plus LC System
Autosampler

Figure 8 shows the notation for 96-well microplates when you select the bottom right
orientation.
Figure 8. Notation for 96-well plates—Bottom right orientation

H12 H11 H10 H9 H8 H7 H6 H5 H4 H3 H2 H1

G12 G11 G10 G9 G8 G7 G6 G5 G4 G3 G2 G1

F12 F11 F10 F9 F8 F7 F6 F5 F4 F3 F2 F1

E12 E11 E10 E9 E8 E7 E6 E5 E4 E3 E2 E1

D12 D11 D10 D9 D8 D7 D6 D5 D4 D3 D2 D1

C12 C11 C10 C9 C8 C7 C6 C5 C4 C3 C2 C1

B12 B11 B10 B9 B8 B7 B6 B5 B4 B3 B2 B1

Plate C
A12 A11 A10 A9 A8 A7 A6 A5 A4 A3 A2 A1 C:A1

H12 H11 H10 H9 H8 H7 H6 H5 H4 H3 H2 H1

G12 G11 G10 G9 G8 G7 G6 G5 G4 G3 G2 G1

F12 F11 F10 F9 F8 F7 F6 F5 F4 F3 F2 F1

E12 E11 E10 E9 E8 E7 E6 E5 E4 E3 E2 E1

D12 D11 D10 D9 D8 D7 D6 D5 D4 D3 D2 D1

C12 C11 C10 C9 C8 C7 C6 C5 C4 C3 C2 C1

B12 B11 B10 B9 B8 B7 B6 B5 B4 B3 B2 B1

Plate B
A12 A11 A10 A9 A8 A7 A6 A5 A4 A3 A2 A1
B:A1

H12 H11 H10 H9 H8 H7 H6 H5 H4 H3 H2 H1

G12 G11 G10 G9 G8 G7 G6 G5 G4 G3 G2 G1

F12 F11 F10 F9 F8 F7 F6 F5 F4 F3 F2 F1

E12 E11 E10 E9 E8 E7 E6 E5 E4 E3 E2 E1

D12 D11 D10 D9 D8 D7 D6 D5 D4 D3 D2 D1

C12 C11 C10 C9 C8 C7 C6 C5 C4 C3 C2 C1

B12 B11 B10 B9 B8 B7 B6 B5 B4 B3 B2 B1

A12 A11 A10 A9 A8 A7 A6 A5 A4 A3 A2 A1 Plate A

A:A1

Thermo Scientific Surveyor Plus User Guide for LC Devices 9

1 Introduction to the Surveyor Plus LC System
Autosampler

384-Well Microplate Notation

The notation for the location of 384-well microplates is as follows:
Plate:RowColumn

Where:
Plate = A, B, or C
Row = A through P
Column = 1 through 24

Figure 9 shows the notation for 384-well microplates.

Figure 9. Notation for 384-well microplates

Top Left Bottom Right

C:A 1
C:A1 A P

P A C:A 1
C:A1

1 24 24 1

B:A1
B:A1 A P

P A B:A1
B:A1

1 24 24 1

A:A 1
A:A1 A P

P A A:A 1
A:A1

1 24 24 1

10 Surveyor Plus User Guide for LC Devices Thermo Scientific

 1 Introduction to the Surveyor Plus LC System
Autosampler

Injection System
The main components of the injection system include the following:
• Syringe Drive Assembly and Syringe Valve
• Wash Bottle Reservoir and Tubing
• Interchangeable Syringe
• XYZ Arm Mechanism
• Needle Assembly and Needle Tubing Assembly
• Injection Port and Transfer Tubing Assembly
• Injection Valve and Sample Loop

Syringe Drive Assembly and Syringe Valve

The syringe drive assembly holds the autosampler syringe. There are three holes with
grommets on the back of the syringe drive assembly. You mount the syringe drive assembly to
the front of the autosampler by matching these holes to one vertical mounting pin and two
horizontal mounting pins located in front of the autosampler injection port. The rubber
grommets minimize the effects of vibration, but also cause the connection between the syringe
drive assembly and the body of the autosampler to feel slack (see Figure 10).

Thermo Scientific Surveyor Plus User Guide for LC Devices 11

1 Introduction to the Surveyor Plus LC System
Autosampler

Figure 10. Syringe drive assembly for the Surveyor Autosampler Plus, showing the front and the back of assembly

Two-way
syringe valve

10-pin
connector
Wash bottle
tubing
Needle
tubing

Syringe
fitting
Mounting hole (with grommet)
to vertical mounting stud

Mounting holes (with

grommets) to horizontal
mounting studs
Front view Back view

Vertical mounting stud

Horizontal mounting studs

12 Surveyor Plus User Guide for LC Devices Thermo Scientific

 1 Introduction to the Surveyor Plus LC System
Autosampler

The syringe valve is a two-position rotary valve. In the wash bottle position, the syringe draws
wash solvent into its syringe barrel as its plunger descends. In the needle position, the syringe
draws sample solution into the needle tubing as its plunger descends and pushes sample
solution out of the needle tubing as its plunger ascends. The syringe never draws sample
solution into its barrel.

Note The needle tubing holds approximately 560 μL of solvent. If you installed the
2500 μL standard syringe (which must be special ordered) and you plan to make large
volume injections, install the 1 mL needle tubing extension that comes with this syringe.

Wash Bottle Reservoir and Tubing

The wash bottle rests in the solvent platform on the top of the LC stack. It is connected to the
syringe valve by way of the wash bottle tube. Both of the direct commands, Flush (from
bottle) and Wash Needle (from bottle), draw solvent from the wash bottle. In addition, both
the partial loop injection and the no waste injection modes draw transfer solution from the
wash bottle. If the wash bottle runs dry, the wash bottle tubing and the syringe barrel fill with
air. If the syringe runs dry, the autosampler cannot draw sample into the needle tubing.

Figure 11 shows the syringe valve in the wash bottle position.

Figure 11. Drawing wash solvent from the wash bottle

Two-way
syringe valve
Needle tubing
assembly

Wash
tubing
Wash
bottle

Wash solvent

Thermo Scientific Surveyor Plus User Guide for LC Devices 13

1 Introduction to the Surveyor Plus LC System
Autosampler

Interchangeable Syringe
The standard configuration for the autosampler consists of a 250 μL dual-concentric syringe.
The dual-concentric syringe consists of a small, inner plunger, and a larger, outer plunger
(see Figure 12).
Figure 12. Dual-concentric syringe
Inner plunger

Outer plunger

The syringe uses its inner plunger to draw and deliver sample amounts equal to or less than its
maximum capacity, which is 265 μL for the 250 μL concentric syringe. The syringe uses its
outer plunger to draw and expel large volumes of solvent, for example, during a flush or wash
cycle.

Dual-concentric syringes are available in 100, 250, and 500 μL sizes. The volume of the outer
plunger region, 565 μL, is the same for all three dual-concentric syringes. The size of the inner
plunger and the injection mode determine the available injection volume range. In addition
to offering three sizes of concentric syringes, Thermo Scientific also offers a 2500 μL standard
(single plunger) syringe.

XYZ Arm Mechanism

The XYZ arm mechanism moves the needle along the x-y plane to the requested vial or well
location. After it positions the needle above the vial or well, the XYZ arm mechanism lowers
the needle along the z axis to the requested needle height.

Figure 13 shows the needle descending to a depth of 2 mm from the bottom of a standard
1.8 mL vial.

14 Surveyor Plus User Guide for LC Devices Thermo Scientific

 1 Introduction to the Surveyor Plus LC System
Autosampler

Figure 13. Autosampler needle positioned 2 mm from the bottom of a vial

Needle height
from bottom

Bottom of vial
2 mm
Wash solvent
Sample

After the autosampler withdraws the sample from the sample vial or well into the needle
tubing, the XYZ arm mechanism moves along the x-y plane, back to the home position,
which is above the injection port of autosampler, and then lowers the needle into the injection
port where it expels the sample. The sample travels through transfer tubing and into the
sample loop of the injection valve.

IMPORTANT Because the XYZ arm moves to the sample position to withdraw sample,
do not place objects taller than 1.8 inches into the tray compartment, as they will stall the
XYZ arm.

Do not move the XYZ arm manually. Instead, use the following commands and options
provided by the data system to control the position of the XYZ arm:
• To make the XYZ arm automatically move to the back of the tray compartment when you
open the tray door, select the Verify Door is Closed option, which is available when you
configure the autosampler device driver (see “Communication Page” on page 52).
• To move the XYZ arm to the back of the tray compartment, use the Position Arm to
Access Tray direct command (see “Removing and Installing Sample Trays” on page 199).
• To move the XYZ arm mechanism to its home position above the injection port, use the
Set Arm to Home Position direct command.
• To move the XYZ arm mechanism to the middle front of the tray compartment, allowing
easy access to the needle, use the Remove Needle direct command.

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1 Introduction to the Surveyor Plus LC System
Autosampler

Needle Assembly and Needle Tubing Assembly

The needle assembly consists of a blunt-tip needle, a latch nut, a flag, a compression spring,
and a 10-32 fitting that connects to the needle tube assembly. The needle fits into the needle
mount on the XYZ arm.

The needle tube assembly connects the solvent path between the needle and the syringe valve
and consists of low-pressure tubing, an internally threaded fitting that connects to the needle
assembly fitting, a sleeve, a black or red PVC cap, a needle tube guide that attaches to the
x-axis positioning frame, and an externally threaded fitting with a flangeless ferrule that
connects to the right side of the syringe valve.

IMPORTANT To prevent damage to the needle tubing, take care when you connect the
needle tubing guide to the back of the syringe drive assembly. Pinched tubing causes
performance problems.

Figure 14 shows the needle assembly and the needle tubing assembly.
Figure 14. Needle assembly and needle tubing assembly
Needle assembly

Latch nut

Compression spring
Flag Needle tubing assembly
10-32
fitting Externally threaded nut and
flangeless ferrule that connect to
the right side of the syringe valve

Blunt-tip
needle

PEEK fitting Sleeve Two-pronged Black or red

(that connects to the needle guide PVC cap
needle assembly)

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 1 Introduction to the Surveyor Plus LC System
Autosampler

Injection Port and Transfer Tubing Assembly

Figure 15 shows the autosampler injection port.
Figure 15. Autosampler injection port

Injection port

Figure 16 shows the 0.012 in. ID transfer tube that connects the autosampler injection port
to port 2 of the injection valve.

IMPORTANT The label attached to the transfer tube assembly specifies its internal
volume. You must enter this value when you specify the configuration settings for the
autosampler.

Figure 16. Injection port and transfer tube

Wash station
Injection port

Transfer tube assembly label

(specifying the dead volume)

Transfer
tube

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1 Introduction to the Surveyor Plus LC System
Autosampler

Injection Valve and Sample Loop

The injection valve is a two-position, six-port valve that introduces sample onto the column
by way of the sample loop.

The sample loop is a section of stainless steel tubing with end fittings. It is an interchangeable
part that is attached to ports 1 and 4 of the injection valve. The autosampler comes with a
25 μL sample loop.

There are two positions for the six-port injection valve: fill and inject.

In the fill position (see Figure 17), the sample loop is isolated from the mobile phase stream.
As the mobile phase bypasses the sample loop, the upward movement of the autosampler
syringe plunger pushes sample into the front of the sample loop, connected to port 1 of the
injection valve. Once the sample loop is filled, excess solution exits the injection valve through
port 3 to waste.
Figure 17. Injection valve in the fill position
Transfer tubing
2 1 To
column
6
3
To
4 5
waste
Mobile phase From
Wash solvent pump

In the inject position (see Figure 18), mobile phase enters the sample loop from the back,
backflushing the contents of the sample loop onto the column. Excess sample left in the
transfer tube is expelled directly to waste. To allow ample rinsing of the sample loop with
mobile phase, the injection valve remains in the inject position during the entire run.
Figure 18. Injection valve in the inject position
Transfer tubing
2 1 To
column
6
3
To
4 5
waste
Mobile phase From
Wash solvent pump

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 1 Introduction to the Surveyor Plus LC System
Autosampler

Injection Modes
The autosampler can operate in any of the following three modes:
• No Waste Injection Mode
• Partial Loop Injection Mode
• Full Loop Injection Mode

The optimum injection mode depends on the amount of sample that you have and the degree
of precision that your application requires.

No Waste Injection Mode

The no waste injection mode is a technique that withdraws only the exact amount of sample
requested from the sample vial. Of the three injection modes, the no waste injection mode
uses the least amount of sample, but it is also the least precise. Use this injection mode to
conserve sample.

Approximately 0.25 μL of the sample is lost as it travels from the injection port, through the
transfer tubing, and into the injection valve. Because of this loss, the minimum recommended
injection volume is 1.0 μL.

The quantity of lost sample depends on the syringe rate. Decreasing the syringe rate decreases
the sample loss. For best results, use a syringe rate no greater than 4 μL/s for the no waste
injection mode.

IMPORTANT For no waste injections, do the following:

• Use a sample loop that is at least 5 μL larger than the injection volume. Because the
accuracy of the nominal size is ±20%, use an estimate of 80% for the actual size. For
example, use 20 μL as an estimate for the actual volume of a 25 μL loop, and inject no
more than 15 μL with this loop size.
• Consider matching the chemistry of the sample matrix, the flush solution, and the
mobile phase. For no waste injections, the autosampler loads approximately 2 μL of
flush solvent and 3 μL of air into the sample loop, regardless of the requested injection
volume.
• Inject at least 1.0 μL of sample.

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1 Introduction to the Surveyor Plus LC System
Autosampler

Partial Loop Injection Mode

The partial loop injection mode is a technique that withdraws 22 μL of excess sample from
the vial in addition to the requested injection volume. Approximately one-half of the excess
volume is expelled to waste before the center of the sample bolus is metered into the front of
the sample loop. The second portion of excess sample is expelled to waste after the sample
bolus is backflushed onto the column.

Partial loop injections are useful when you have a limited volume of sample. Using the partial
loop injection mode, you can inject variable amounts of sample, ranging from a minimum of
0.1 μL to a working maximum of one-half the volume of your sample loop. This maximum
volume limitation is caused by the laminar flow of fluid within the stainless steel sample loop.

IMPORTANT To make precise partial loop injections, use a sample loop that is at least
twice the size of the injection volume. The accuracy of the nominal sample loop volume
is ±20%. Because the actual volume of the 25 μL sample loop (provided with the
autosampler) is anywhere from 20 to 30 μL, limit the maximum injection volume with
this loop to 10 μL. To inject more sample, use a larger sample loop.

Full Loop Injection Mode

The full loop injection mode is a technique that withdraws a sample volume from the vial
sufficient to overfill the sample loop by a minimum factor of two. Because the physical size of
the sample loop determines the actual injection volume, not the metering action of the
stepper motor, a full loop injection is very reproducible. However, because the intent of the
full loop injection mode is to completely fill the sample loop, you cannot inject variable
amounts of sample.

Full loop injection is useful when you want maximum precision and have unlimited sample.
To change the injection volume, you must change the sample loop size.

Note Full loop injections are limited to the size of the configured sample loop.

In the full loop injection mode, the autosampler withdraws a large excess of solution from the
sample vial according to the following equation:
Amtw = 3 × Vinj + Vdead + 7.5 μL

Where:
Amtw = sample volume withdrawn by the autosampler
Vinj = user-specified injection volume
Vdead = dead volume held by the transfer tubing, injection port, and rotor slot

This equation is valid until the syringe reaches its maximum capacity, when only the
maximum capacity of the syringe is withdrawn. The maximum capacity of the 250 μL
concentric syringe is 265 μL.

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 1 Introduction to the Surveyor Plus LC System
Detector

Temperature Control
The full-featured Surveyor Autosampler Plus has two built-in temperature control features:
• Tray Temperature Control
• Column Oven Control

Tray Temperature Control

The tray temperature control feature provides temperature control of the samples in the range
from 0 to 60 °C. A Peltier device maintains the tray temperature.

Column Oven Control

The built-in column oven controls the temperature of the air surrounding the
chromatographic column. Isothermal temperature control is achieved using a Peltier device.
The Peltier device is a solid-state, heat-transferring assembly used to heat or cool the column
oven. The range of temperature control is 5 to 95 °C.

CAUTION The column oven can reach temperatures as high as 95 °C (203 °F).
To prevent personal injury, before installing the LC column or connecting the pump to
the autosampler, make sure that the column oven compartment is at room temperature.

Between the analytical pump and the autosampler injection valve, the mobile phase is diverted
through a heat exchanger located behind the column oven. As it passes through the heat
exchanger, the mobile phase equilibrates to the temperature of the column oven before it
reaches the injection valve. The heat exchanger adds only 3 μL of gradient delay volume to the
LC system.

Detector
The Surveyor Plus product line includes two detectors that you can control from your
Thermo Scientific data system: a PDA detector and a UV/Vis detector. The PDA detector, in
combination with the 5 or 1 cm LightPipe flowcell, provides the highest level of sensitivity
available in photodiode array detection for HPLC. The UV/Vis detector can monitor two
wavelength channels. Both detectors have a dual-lamp optical bench that covers the
UV-visible spectrum from 190 to 800 nm.

For more information about the Surveyor Plus detectors, see these topics:
• PDA Detector
• UV/Vis Detector

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1 Introduction to the Surveyor Plus LC System
Detector

PDA Detector
The PDA detector is a full-featured, time-programmable, photodiode array detector that can
scan the full ultraviolet-visible range from 190 to 800 nm. The detector can acquire data at a
rate of up to 20 Hz with a 20 bit digital conversion.

The optimal location for the PDA detector is above the autosampler and below the solvent
platform. The data system computer controls the PDA detector through an Ethernet
communication link. The PDA detector consists of a dual-light source, an optical bench, a
photodiode array, a low voltage power supply, several printed circuit boards (PCBs), and
four status light-emitting diodes (LEDs).

The dual-light source includes a deuterium lamp for detection in the ultraviolet
wavelength range (190 to 360 nm) and a tungsten-halogen lamp for detection in the
visible wavelength range (360 to 800 nm). The light emitted by the two lamps overlaps in
the 300 to 500 nm range. A pair of attenuators that you can manually adjust controls
the intensity of light reaching the photodiode array.

The optical bench contains a beam combiner, focusing lens, filter wheel, flow cell, beam
shaper, folding mirror, and grating (see Figure 19). The beam combiner reflects the light
coming from the tungsten-halogen lamp so that it is parallel to and coincident with the light
from the deuterium lamp. The combined beam is then focused on the inlet window of the
flow cell through the filter wheel. The standard filter wheel has two positions. Use
position 1 (Open), which places a clear, quartz window in the optical path, for normal
operation. Use position 2 (Holmium Oxide), which places a sealed, quartz cuvette filled with
a holmium oxide/perchloric acid solution (NIST™ traceable) in the optical path, for
wavelength accuracy verification and calibration.
Figure 19. Optical bench of the PDA detector
Deuterium Beam combiner Flow cell
lamp Focusing lens Beam shaper
Filter wheel Folding mirror

1 × 512
photo diode
array

Fixed grating
Attenuators

Tungsten-halogen lamp

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 1 Introduction to the Surveyor Plus LC System
Solvent Platform

The PDA detector does not have independent controls, such as a keypad, to create data
acquisition methods. Instead, you create instrument methods for data acquisition with the
data system. The only manual controls for the PDA detector are the On/Off switch that
controls line power, the attenuators that control the light throughput to the diode array, and
the holmium oxide wheel that controls the position of the wavelength calibration solution.

UV/Vis Detector
The UV/Vis detector is a full-featured, time-programmable, variable-wavelength UV/Vis
(ultraviolet/visible) absorbance detector. It operates in either the single wavelength mode, the
dual wavelength UV wavelength mode, or the dual wavelength Visible mode. The wavelength
range in the single wavelength mode is 190 to 800 nm. In the dual wavelength UV mode, the
range is 190 to 450 nm and in the dual wavelength Visible mode, the range is 366 to 700 nm.

The wavelength time table is available in all three modes. The time table can contain up to
10 lines. If you enable the Zero On Wavelength Change feature, the baseline absorbance
returns to zero between each line in the time table, even if the wavelengths remain the same.
The baseline absorbance does not return to zero between the last two lines in the table.

To provide a complete spectrum of ultraviolet and visible light, the detector uses a
deuterium lamp for the UV range (190 to 365 nm) and a tungsten lamp for the visible range
(366 to 800 nm). The lamps are protected by a cover with a special safety interlock to reduce
the possibility of human exposure to harmful UV light.

To control the UV/Vis Detector, you must first add the detector to the software instrument
configuration (see “Adding Devices to the Instrument Configuration” on page 44).

After you add the UV/Vis detector to the instrument configuration, you can set up the data
acquisition parameters from the UV/Vis detector view of the Thermo Xcalibur Instrument
Setup window (see “UV-Vis Detector Instrument Method Parameters” on page 106).

You can turn the detector lamps on or off and zero the detector output from the Direct
Control dialog box (see “UV-Vis Detector Direct Controls” on page 183).

Solvent Platform
The solvent platform, located on the top of the LC stack, holds four 1 liter solvent reservoir
bottles and one 1 liter wash bottle. Four 1/8 in. OD × 1/16 in. ID, FEP solvent lines carry
solvent from the reservoir bottles down to the vacuum membrane degasser, which is built into
the analytical pump. One 1/8 in. OD × 1/16 in. ID, FEP solvent line carries solvent from the
wash bottle to the two-position syringe valve of the autosampler.

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1 Introduction to the Surveyor Plus LC System
Communication with the Data System Computer

Communication with the Data System Computer

The Surveyor Autosampler Plus, Surveyor LC Pump Plus, Surveyor PDA Plus Detector, and
the Surveyor UV/Vis Plus Detector use an Ethernet link to communicate with the data system
computer. To establish communication with these devices, you connect one end of an
Ethernet cable to the Ethernet port on the back panel of the device and the other end of the
cable to an Ethernet switch. You use a second Ethernet cable to connect the Ethernet switch to
the computer that has the data system installed. The accessory kits include a shielded,
Category 5, RJ-45, 7 ft length Ethernet cable with ferrite.

The Surveyor MS Pump Plus uses an RS-232 serial link to communicate with the data system
computer. The accessory kit for the Surveyor MS Pump Plus includes a USB cable.

In addition to connecting the communication cables, you must enter the appropriate stack
addresses for the Surveyor Autosampler Plus, Surveyor PDA Plus Detector, Surveyor UV/Vis
Plus Detector, and Surveyor LC Pump Plus when you configure the device drivers. The stack
address or stack number that you enter when you add one of these devices to the
configuration for your instrument must match the unit ID setting on the back panel of the
device. For more information about configuring the Surveyor Plus device drivers, see
Chapter 2, “Thermo Foundation Instrument Configuration.”

Turning Off the Computer’s Energy Saving Features

The Surveyor PDA Plus Detector, Surveyor UV/Vis Detector, Surveyor LC Pump Plus, and
the Surveyor Autosampler Plus communicate with the data system computer through an
Ethernet link. To ensure communication between the data system computer and the LC
system, turn off the data system computer’s screen saver and energy saving features.

 To turn off the screen saver and energy saving features for the Windows XP operating
system
1. From the Windows™ XP™ desktop, choose Start > Control Panel.

Tip If you selected the Classic Start Menu option for the Start menu properties,
choose Start > Settings > Control Panel.

2. Double-click Display.
The Display Properties dialog box appears.

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 1 Introduction to the Surveyor Plus LC System
Turning Off the Computer’s Energy Saving Features

3. Click the Screen Saver tab.

The Screen Saver page appears (see Figure 20).
Figure 20. Screen Saver page of the Display Properties dialog box (Windows XP)

4. In the Screen Saver list, select None.

5. Click Apply to accept this setting.
6. Click Power.
The Power Options Properties dialog box opens to the Power Schemes page (see
Figure 21).

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1 Introduction to the Surveyor Plus LC System
Turning Off the Computer’s Energy Saving Features

Figure 21. Power Options Properties

7. Modify the power scheme settings as follows:

• In the Turn Off Monitor list, select Never.
• In the System Standby list, select Never.
8. Modify the hibernate setting as follows:
a. Click the Hibernate tab.
The Hibernate page appears (see Figure 22).

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 1 Introduction to the Surveyor Plus LC System
Turning Off the Computer’s Energy Saving Features

Figure 22. Hibernate page

b. If the Enable Hibernation check box is selected, clear it.

c. Click Apply to accept the setting.
9. Click OK to close the Power Options Properties dialog box.
10. Click OK to close the Display Properties dialog box.
11. Close the Control Panel window.

 To turn off the screen saver an energy saving features for the Windows 7 operating
system
1. From the Windows 7 desktop, choose Start > Control Panel.
2. Choose Large Icons from the View By menu.

3. Click the Personalization icon .

The Personalization window appears (see Figure 23).

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1 Introduction to the Surveyor Plus LC System
Turning Off the Computer’s Energy Saving Features

Figure 23. Personalization window

4. Click the Screen Saver icon on the bottom-right side of the window.
The Screen Saver Settings dialog box appears (see Figure 24).

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 1 Introduction to the Surveyor Plus LC System
Turning Off the Computer’s Energy Saving Features

5. Change the screen saver setting as follows:

a. In the Screen Saver list, select None.
Figure 24. Screen Saver Settings dialog box (Windows 7 operating system)

b. Click Apply to accept this setting.

6. Change the power settings as follows:
a. Click Change Power Settings.
The Select a Power Plan page of the Power Options dialog box appears (see
Figure 25).

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1 Introduction to the Surveyor Plus LC System
Turning Off the Computer’s Energy Saving Features

Figure 25. Select a Power Plan page of the Power Options dialog box

b. Select the Balanced option.

c. Click Change Plan Settings for the Balanced option.
The Edit Plan Settings dialog box appears (see Figure 26).
Figure 26. Edit Plan Settings dialog box

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 1 Introduction to the Surveyor Plus LC System
Turning Off the Computer’s Energy Saving Features

d. Click Change Advanced Power Settings.

The Advanced Settings page of the Power Options dialog box appears (see Figure 27).
Figure 27. Advanced Settings page of the Power Options dialog box

e. Set the Turn Off Hard Disk After option to Never as follows:
i. Click the icon to the left of Hard Disk.
ii. Click the icon to the left of Turn Off Hard Disk After.
iii. If the setting is not set to Never, click the setting and select Never.
f. Set the Hibernate After option to Never as follows:
i. Click the icon to the left of Sleep.
ii. Click the icon to the left of Hibernate After.
iii. If the setting is not set to Never, click the setting and select Never.
g. Click Apply to accept these settings.
h. Click OK to close the Advanced Settings page.
7. Close the Control Panel window.

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1 Introduction to the Surveyor Plus LC System
Synchronization of the LC Devices

Synchronization of the LC Devices

A system interconnect cable (contact closure) provided in the Surveyor System Kit coordinates
the run control signals between the Surveyor Plus devices.

Figure 28 shows the cable assembly with seven green combicon connectors: two are labeled
PUMP; three are labeled DETECTOR; and two are unlabeled. You can identify the
connector for the autosampler by the small, A/S tag on its adjacent cable. You can identify the
M/S connector by its shape and by the small, M/S tag on its adjacent cable.
Figure 28. 7-connector system interconnect cable

DETECTOR
M/S To
detector
DETECTOR
To To
detector

DETECTOR
MS detector To
detector
To

PUMP
A/S
autosampler

To
To
PUMP

pump
pump

Using the 7-connector cable with the Surveyor MS Pump Plus requires an additional adapter
cable. Figure 29 shows the interconnect cable connections for a Surveyor LC system.

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 1 Introduction to the Surveyor Plus LC System
Synchronization of the LC Devices

Figure 29. Back panels of Surveyor devices, showing the 7-connector system interconnect cable

MS Detector

DETECTOR
M/S Detector

DETECTOR
Detector

DETECTOR
Detector
Autosampler Pump

PUMP
A/S

Pump
PUMP

Interconnect cable

Solvent platform Solvent platform

Detector Detector
(back panel) (back panel)

To To
MS detector Autosampler MS detector Autosampler
(back panel) (back panel)

Pump
connector

MS pump connection
MS PUMP
PUMP

Pump
connector of
MS pump Surveyor MS adapter cable LC pump
adapter cable Pump (back panel)
(back panel)
Surveyor MS Pump
connector

Figure 30 shows the cable assembly with five green combicon connectors. The assembly has
two pump connectors: one is labeled MS PUMP and one is labeled LC Pump. You can
identify the connectors for the autosampler, detector, and MS detector by the small tags on
their adjacent cables. To connect the MSQ Plus Mass Detector, you must modify the wiring
connections inside the MS detector connector.

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1 Introduction to the Surveyor Plus LC System
Synchronization of the LC Devices

Figure 30. 5-connector system interconnect cable (P/N F5049-010)

To
Detector

M/S F5049-010 DET

To To A/S
MS Detector Autosampler

LC PUMP
To

MS PUMP
LC Pump
To
MS Pump

Figure 31 shows the interconnect cable connections for a Surveyor LC system.

Figure 31. Back panels of the Surveyor devices, showing the 5-connector interconnect cable
MS
Detector M/S DET Detector
Autosampler A/S
Solvent platform
LC PUMP

LC Pump
MS PUMP

MS Pump

Detector
Interconnect cable (back panel)
To
MS detector
Autosampler
(back panel)

Surveyor MS
Pump Plus
(back panel)

Not drawn to scale Not used

LC PUMP

For more information about connecting the interconnect cable to the devices of your LC
system, refer to the Surveyor Plus LC System Getting Connected Guide.

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 1 Introduction to the Surveyor Plus LC System
Status LEDs

During a run, the system issues the following sequence of run control signals:
1. The data system computer issues a request to perform an injection.
2. When the autosampler becomes ready, it issues the A/S Ready signal.
The autosampler goes into the Ready state when all the configuration and instrument
method conditions are met, including the closing of the tray compartment door, and the
sample tray and column oven temperature zone readings showing they are within
tolerance of their setpoints.
3. When the pump pressure stabilizes, the pump issues the Pump Ready signal to the
autosampler.
The autosampler injection valve switches to the fill position, and then the autosampler
pushes sample into the sample loop.
4. The autosampler issues the Gradient Start signal to the pump. This signal commands the
pump to start its gradient program.
5. When its piston cam reaches the home position, the pump issues the Inject Hold release
signal to the autosampler.
6. The autosampler injection valve switches to the inject position, allowing the mobile phase
to backflush the contents of the sample loop onto the column. The autosampler then
issues a momentary Inject Out signal to the detector.
7. The detector starts acquiring data.

Status LEDs
Each of the Surveyor Plus LC devices has a panel of four status LEDs located on the front of
the left door. All of the devices have these three LEDs: Power, Comm, and Run. In addition,
the detector has a Lamps LED; the autosampler has a Temp LED; and the analytical pump
has a Degas LED.

These topics describe the meanings of the LED states:

• Surveyor MS Pump Plus LED States
• Surveyor LC Pump Plus LED States
• Autosampler LED States
• PDA Detector LED States
• UV-Vis Detector LED States

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1 Introduction to the Surveyor Plus LC System
Status LEDs

Surveyor MS Pump Plus LED States

Table 1 lists the states of the Surveyor MS Pump Plus LEDs.
Table 1. Pump status LEDs and their meaning
LED Status Meaning
Power Green The pump is on and receiving power.
Comm Amber The pump is not communicating with the data
system.
Green Communication to the data system has been
established.
Flashing green A pump program is downloading from the data
system computer.
Run Amber The power is switched on, but the pistons are idle,
producing no flow.
Flashing amber A firmware download is in progress or an error
condition has occurred.
Green The pump pistons are moving, but a pump program
is not running. This state can occur when the pump
is under direct control or a pump program has ended.
Flashing green The pump is running a pump program from a
downloaded method.
Degas Amber The degas unit is building vacuum.
Flashing amber A failure, such as a loss of vacuum, has occurred.
Green Sufficient vacuum has developed to perform
chromatography.

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 1 Introduction to the Surveyor Plus LC System
Status LEDs

Surveyor LC Pump Plus LED States

Table 2 list the LED states for the Surveyor LC Pump Plus.
Table 2. Surveyor LC Pump Plus status LEDs and meaning
LED Status Meaning
Power Green The pump is on and receiving power.
Comm Amber The pump is not communicating with the data
system computer.
Flashing amber The rotary switches on the back panel of the LC
pump are set to 00 for downloading firmware.
Green The pump is communicating with the data system
computer.
Run Amber The pump is not communicating with the data
system computer, the pump’s motor is stopped, the
pistons are homing, or the pump is stabilizing (except
during a run).
Flashing amber The pump is experiencing an error condition.
Green The pump is in the Ready state.
Flashing green The pump is performing a run or the pump is
stabilizing during a run.
Degas Amber The pump is powering up and the degas unit is
building vacuum.
Flashing amber The degas unit is experiencing a failure, such as a
loss of vacuum.
Green The degas unit has developed sufficient vacuum to
degas the mobile phase solvents when the pump
flow is set to a typical flow rate for chromatography.

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1 Introduction to the Surveyor Plus LC System
Status LEDs

Autosampler LED States

Table 3 lists the LED states for the autosampler.

Tip To ensure that the controlled temperature zones are in equilibrium at the set
temperature before the autosampler makes an injection, select the Wait for Temperature
Ready check box when you add the autosampler to the data system instrument
configuration.

When you select this check box, the autosampler waits until the controlled temperature
zones are in equilibrium at the set temperature before it makes an injection. While the
temperature zones are equilibrating to the set temperature, the Temp LED remains amber.

When you do not select this check box, the autosampler does not wait for the temperature
zones to equilibrate to the set temperature before making an injection and the Temp LED
remains green.

Table 3. Surveyor Autosampler status LEDs and their meaning

LED State Meaning
Power Green The autosampler is on and receiving power.
Comm Amber Communication with the data system has not been
established.
Green Communication with the data system has been
established.
Run Flashing Amber An error condition, such as an XYZ arm jam or
initialization startup error, has occurred.
Green The autosampler is in the Ready state.
Flashing Green An injection or timed event is in progress.
Temp Amber A temperature change within the column oven or
tray temperature zones is in progress.
Green The column oven and tray temperature zones are in
equilibrium at the set temperature.

–or–

The Wait for Temperature Ready check box on the

Communication page of the Instrument
Configuration application is not selected.

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 1 Introduction to the Surveyor Plus LC System
Status LEDs

PDA Detector LED States

Table 4 lists the LED states for the PDA detector.
Table 4. PDA detector LED states and their meaning
LED State Amber
Power Green The detector is turned on and receiving power.
Comm Amber There is no communication with the data system.
Flashing amber The rotary switches are set to 00 and firmware is being
downloaded to the CPU of the detector.
Green Communication to the data system computer has been
established.
Run Amber The PDA detector is not ready to start a run for one of
the following reasons:
• You have not downloaded a valid instrument
method since the last time you powered on the
detector.
• Both lamps are off, or one of the lamps is failing to
turn on.
• The lamp or wavelength calibration is not valid.
Flashing amber The PDA detector is in an error state while in the
Run mode.
Green The detector is ready for a run.
Flashing green A run is in progress and the detector is sending data to
the data system computer.
Lamps Amber The lamps are off or the D2 lamp is starting. It takes
approximately 10 seconds for the D2 lamp to turn on.
Green One or both lamps are turned on.

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1 Introduction to the Surveyor Plus LC System
Status LEDs

UV-Vis Detector LED States

Table 5 lists the LED states for the UV/Vis detector.
Table 5. UV/Vis detector LED states and their meaning
LED State Meaning
Power Green The detector is on.
Comm Green Communication to the data system computer has been
established.
Amber There is no communication with the data system.
Run Green The detector is ready for a run.
Flashing green A run is in progress and the detector is sending data to the
data system computer.
Flashing Amber An error has occurred during a run.
Lamps Green One or both lamps are turned on.
Amber The lamps are off.

40 Surveyor Plus User Guide for LC Devices Thermo Scientific

 2

Thermo Foundation Instrument Configuration

This chapter provides information about configuring the LC device drivers.

Contents
• Checking the Communication Hardware
• Opening the Thermo Foundation Instrument Configuration Application
• Adding Devices to the Instrument Configuration
• Specifying the Configuration Settings
• Closing the Foundation Application

 To set up the software instrument configuration for your LC system

1. Open the Thermo Foundation™ application.

2. Add the devices of your LC system to the instrument configuration.
3. Specify the configuration settings for each device.
4. Close the Foundation application.

Checking the Communication Hardware

The autosampler and detector communicate with your Thermo Scientific data system
through an Ethernet connection. Each device has an Ethernet port on its back panel. A
shielded, Category 5 Ethernet cable with ferrite connects each device to an Ethernet switch,
which in turn connects by way of an Ethernet cable to the data system computer. The unit ID
setting on the back panel of the autosampler and PDA detector must match the stack number
in the configuration.

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2 Thermo Foundation Instrument Configuration
Checking the Communication Hardware

Before you specify the configuration settings, check the unit ID setting on the back panels of
the autosampler, LC pump, UV/Vis detector, and PDA detector. The unit ID consists of two
rotary switches that are factory set to 01 (see Figure 32).
Figure 32. Unit ID with a stack address of 01

2 3 2 3
0 1

0 1
4

4
5 6

5 6
9

9
7 8 7 8

Set to 0 Set to 1

Unlike the other Surveyor Plus devices, the Surveyor MS Pump Plus communicates with the
data system through an RS-232 serial connection.

 To check the communication connections

1. Check the settings of the rotary switches on the back panels of the Surveyor Autosampler
Plus, the Surveyor UV/Vis Plus Detector or the Surveyor PDA Plus Detector, and the
Surveyor LC Pump Plus.
2. For the Surveyor MS Pump Plus, verify that the serial communication cable connecting
the MS pump to the data system computer is attached to COM port 1.

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 2 Thermo Foundation Instrument Configuration
Opening the Thermo Foundation Instrument Configuration Application

Opening the Thermo Foundation Instrument Configuration Application

 To open the Thermo Foundation Instrument Configuration application

From the Windows taskbar, choose Start > Programs > Thermo Foundation 1.0 >
Instrument Configuration.
The Thermo Foundation Instrument Configuration window appears (see Figure 33).
This window lists the installed device drivers.
Figure 33. Thermo Foundation Instrument Configuration window

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2 Thermo Foundation Instrument Configuration
Adding Devices to the Instrument Configuration

Adding Devices to the Instrument Configuration

To control a device from the data system, the device must be listed in the Configured Devices
pane of the Thermo Foundation Instrument Configuration window.

 To add the LC device drivers to the Thermo Foundation instrument configuration

In the Available Devices list, double-click the icons for your LC devices.
A copy of the icon appears in the Configured Devices list (see Figure 34).

Figure 34. Thermo Foundation Instrument Configuration window with devices added to the
Configured Devices list

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Specifying the Configuration Settings

After you add the devices to the Configured Devices list, specify the configuration settings for
each device as described in these topics:
• Surveyor Autosampler Plus Configuration Settings
• Surveyor MS Pump Plus Configuration Settings
• Surveyor LC Pump Plus Configuration Settings
• Surveyor PDA Plus Detector Configuration Settings
• Surveyor UV/Vis Plus Detector Configuration Settings

After specifying the configuration options for the instrument devices, you must close the
Instrument Configuration application before you can open the Thermo Scientific data
system.

Note The Accela UV/Vis Detector driver is provided with LC Devices 2.5.0 or later.

Surveyor Autosampler Plus Configuration Settings

Use the Surveyor Autosampler Configuration dialog box to specify the configuration settings
for the autosampler.

For information about specifying the configuration settings for the autosampler, see these
topics:
• Tray Page
• Communication Page
• Signal Polarity Page
• Firmware Page

 To open the Surveyor Autosampler Configuration dialog box

1. If it is not already open, open the Thermo Foundation Instrument Configuration

window (see “Opening the Thermo Foundation Instrument Configuration Application”
on page 43).
2. In the Configured Devices list, double-click the Surveyor AS icon.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

The Surveyor Autosampler Configuration dialog box appears with the Tray page
displayed (see Figure 35).
Figure 35. Tray page of the Surveyor Autosampler Configuration dialog box

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Tray Page
The autosampler accessory kit contains several tray types, including trays that hold 1.8 mL
vials, trays that hold 96-well microplates, and trays that hold 384-well microplates.

Use the Tray page (see Figure 36) to specify the tray type that you are using.

 To select the tray type and orientation

1. In the list of tray types, select the tray type.

Table 6 lists the available selections. For the three custom selections, you must calibrate
the well bottom distance before you use the trays.

Note The Autosampler Accessory Kit contains the vial trays and microplate carriers.
The current version of the accessory kit contains a standard tray, a short microwell
carrier, and a tall microwell carrier with a solid metal bottom.

Previous versions of the accessory kit contained a riser plate that you could use in
combination with the short microwell carrier to load standard depth 96-well or
384-well microplates into the autosampler tray compartment. Thermo Fisher
Scientific has replaced the short microwell carrier and riser plate option with a tall
microplate carrier that has a solid metal bottom for thermal conduction.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Table 6. Tray type selections

Tray type Requires
well bottom
distance
calibration
1 1.8 mL Vial, 5 trays, 40 vials each No
2 Custom Vial Setting Yes
3 96 Well Microplate + Tall Microwell Carrier No
4 96 Well Microplate + Tall, Solid Microwell Carrier No
–or–
96 Well Microplate + Short Microwell Carrier + Riser Plate
5 1 mL or 2 mL Deep Well Plate + Short Microwell Carrier No
6 96 Well Microplate + Short Microwell Carrier No
7 96 Well PCR Plate + Cooling Adapter + Short Microwell Carrier No
8 Custom 96 Well Setting Yes
9 384 Well Microplate + Tall Microwell Carrier No
10 384 Well Microplate + Tall, Solid Microwell Carrier No
–or–
384 Well Microplate + Short Microwell Carrier + Riser Plate
11 Custom 384 Well Setting Yes

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

2. For a microplate tray type, do the following:

a. In the A1 Well Position area, select either the Top Left or the Bottom Right option
(see Figure 36).
Figure 36. Tray page with a 96-well plate selection

b. In the Well Ordering area, click the button that represents your preference for the
order of sequence injections.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Autosampler Tray Page Parameters

Table 7 describes the configuration parameters on the Tray page.
Table 7. Tray page parameters (Sheet 1 of 2)
Parameter Description
Tray Type The Tray Type list displays pictures of the 11 sample tray configurations. When you choose
96-well plates or 384-well plates, two additional options appear: A1 Well Position and
Well Ordering.

The conventional autosampler tray holds 40 standard 1.8 mL vials. For other types of vials,
select the custom vial setting and the appropriate tray adapter.

The autosampler accommodates a variety of microwell plates. You can use the tall or short
microwell carriers to accurately position the various microwell plates at an appropriate
location in the autosampler tray compartment. The tall microwell carrier with a solid metal
bottom provides the same height as the short microwell carrier and riser plate combination.

The distance that the needle travels to reach the bottom of the vial is pre-calibrated for the
eight standard configurations. You must perform a Well Bottom Distance calibration
(see “Well Bottom Distance Calibration” on page 305) to use one of the three custom
configurations.

For information about the height limitations for the various tray selections, see Table 8.
Note Do not use the short microwell carrier to hold the 384-well, high density microtitre
plates. Do not use the tall microwell carrier to hold PCR plates.

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 2 Thermo Foundation Instrument Configuration
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Table 7. Tray page parameters (Sheet 2 of 2)

Parameter Description
A1 Well Position Use the options in the A1 Well Position area to select the orientation of the microplate when
(for the microplate it is mounted in the autosampler plate holder. You can mount the plate in the plate holder
trays) so that the A1 well is located at the top left or located at the bottom right of the plate.
Top Specifies that the A1 well is located at the top left of the microplate.
Left
A A
B
C
D
E
F
G
H P

1 2 3 4 5 6 7 8 9 10 11 12 1 24

Bottom Specifies that the A1 well is located at the bottom right of the microplate.
Right
H P
G
F
E
D
C
B
A A
12 11 10 9 8 7 6 5 4 3 2 1 24 1

Well Ordering Use the buttons in the Well Ordering area to select the sampling path that the autosampler
(for the microplate follows during a sequence run. The sampling path you select is independent of the A1 well
trays) position.
The path options are shown below:
Graphic Description
The autosampler samples wells from bottom to top and then from left to
right, as you view the plate from the top.

The autosampler samples wells from left to right and then from bottom to
top, as you view the plate from the top.

The autosampler samples wells from top to bottom and then from left to
right, as you view the plate from the top.

The autosampler samples wells from left to right and then from top to
bottom, as you view the plate from the top.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Placing objects taller than 1.87 in. into the autosampler tray compartment will stall the
autosampler arm. For custom vials, use the appropriate tray insert to ensure correct
positioning. In addition, to trigger the vial sensor, position the vials in the tray so that the top
of each vial reaches the minimum height of 1.55 in.

Do not use microtitre plates that exceed the heights listed in Table 8.
Table 8. Autosampler tray compartment height limitations
Tray type Maximum height
Conventional (standard 1.8 mL vials) N/A
Custom Vial Setting N/A
96 Well Microplate + Tall Microwell Carrier 0.77 in.
96 Well Microplate + Tall, Solid Microwell Carrier or 0.77 in.
96 Well Microplate + Short Microwell Carrier + Riser Plate
1 mL or 2 mL Deep Well Plate + Short Microwell Carrier 1.80 in.
96 Well Microplate + Short Microwell Carrier 1.80 in.
96 Well PCR Plate + Short Microwell Carrier 1.80 in.
Custom 96 Well Setting 1.80 in.
384 Well Microplate + Tall Microwell Carrier 0.77 in.
384 Well Microplate + Tall, Solid Microwell Carrier or 0.77 in.
384 Well Microplate + Short Microwell Carrier + Riser Plate
Custom 384 Well Setting 0.77 in.

Communication Page
Use the Communication page to specify these options:
• The autosampler’s stack address
• The syringe size and the sample loop size
• The dead volume of the transfer tubing that connects the autosampler injection port to
the injection valve
• Whether the controlled temperature zones must be at their set temperature, the tray
compartment door must be closed, or both before the autosampler makes an injection
• Whether the autosampler uses the bottom distance for the configured tray type or the
stored custom value, or determines the bottom distance of sample vials or wells for each
injection or at the start of a sequence
• Whether the maintenance log is enabled

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

 To specify the configuration settings on the Communication page

1. Open the Surveyor Autosampler Configuration dialog box (see “Surveyor Autosampler
Plus Configuration Settings” on page 45).
2. Click the Communication tab.
The Communication page appears (see Figure 37).
Figure 37. Communication page

When this option is selected, the

XYZ arm moves to the back of the
tray compartment when you open
the tray compartment door.

Type the value specified on the

label attached to the transfer tube
assembly.

3. In the Stack Address box, type the appropriate stack address or use the up and down
arrows to select the appropriate stack address.
The stack address must match the unit ID setting located on the back panel of the
autosampler. The rotary switches of the unit ID are factory set to 01 and the default Stack
Address is 1. The value of 00 is reserved for service functions.
4. Under Syringe, in the Type list, select the size of the syringe that is attached to the
autosampler.
The default is Concentric 250 μL, the syringe that ships with the autosampler.
5. (Optional) To prevent the autosampler from making an injection when the temperature
zones are not equilibrated at the set temperature, select the Wait for Temperature Ready
check box.
When the Wait for Temperature Ready check box is selected, the autosampler does not
trigger a run until the column oven temperature, the sample tray temperature, or both
have reached their setpoint values.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

6. (Optional) To prevent the autosampler from making an injection when the tray
compartment door is open, select the Verify Door Is Closed check box.
When the Verify Door Is Closed check box is selected, the autosampler cannot trigger a
run when the tray compartment door is open. If the tray door is opened during a
sequence run, the XYZ arm moves to the back of the tray compartment at the end of the
current run, and the Xcalibur sequence halts.
7. (Optional) To activate the maintenance log, select the Enable Maintenance Log check
box.
The maintenance log keeps an internal count of the total injections, total valve cycles,
total needle usage, and total syringe cycles. When any of the counters exceed the user set
scheduled maintenance time (SMT), the autosampler cannot trigger a run until you
perform the scheduled maintenance or you clear the check box.
8. In the Vial Bottom Sensing area, select the type of vial bottom sensing that is appropriate
for your application:
• To activate vial bottom sensing for every injection in a sequence, select the On
option.
• To activate vial bottom sensing for only the first injection in a sequence, select the
Auto option.
• To deactivate vial bottom sensing, select the Off option.
Each tray type has a stored value for the distance that the needle must travel to reach the
bottom of the vial or well. When you activate vial bottom sensing, the autosampler
performs a search routine to determine the actual location of the vial or well bottom. If
the search routine determines a new value for the bottom distance, it is stored until you
modify the tray type. If you do not want the needle to touch the bottom of a vial or well,
deactivate vial bottom sensing.
9. In the Dead Volume (μL) box, type the value specified on the label attached to the
transfer tube assembly.

Tip When you use the No Waste injection mode, for best results, calibrate the transfer
tube volume, and then type the empirically determined value in the Dead Volume
box. To calibrate the transfer tube volume, refer to the hardware manual for the
autosampler.

10. In the Sample Loop Volume (μL) box, type the nominal size of the sample loop attached
to the injection valve.
The autosampler ships with a 25 μL sample loop.

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Autosampler Communication Page Parameters

Table 9 describes the parameters on the Communication page.
Table 9. Communication page parameters (Sheet 1 of 2)
Parameter Description
Communication
Stack Address Specifies the stack address of the autosampler. The stack address must match the unit ID
setting. The unit ID setting is specified by two rotary switches on the back panel of the
autosampler. The rotary switches are set to 01 at the factory.
Syringe Specifies the syringe type. The selections are 100, 250, 500, and 2500 μL.
Wait for Temperature Selecting this check box specifies that the autosampler waits for the column oven
Ready temperature and the tray compartment temperature to reach their set temperatures before
going to the Ready state.

Select this check box if you want the heated zones to reach their setpoint before the
autosampler makes an injection.
Verify Door Is Closed Selecting this check box specifies that the autosampler waits for the door to be closed before
starting a run and that the XYZ arm moves to the back of the tray compartment when you
open the tray compartment door.

Select this check box if you want the autosampler to pause a sequence and send the XYZ
arm to the back of the tray compartment when you open the tray compartment door.
Enable Maintenance Selecting this check box activates the maintenance log.
Log
The maintenance log keeps an internal count of the total injections, total valve cycles, total
needle usage, and total syringe cycles. When any of the counters exceed the user-set
scheduled maintenance time (SMT), the autosampler cannot trigger a run until you
perform the scheduled maintenance or you clear the check box.

For information about setting up the scheduled maintenance time for the autosampler’s
hardware components, see “Autosampler Maintenance Information” on page 309.
Tip When you select the Enable maintenance log check box, check the maintenance
schedule and make sure that the settings are appropriate for your autosampler.
Vial Bottom Sensing Specifies whether the vial bottom sensing feature is turned on or off or is set to determine
the distance to the bottom of the first vial or well in a sequence of injections.

The selections are as follows:

• Off. Deactivates the vial bottom sensing feature.
• On. Activates the vial bottom sensing feature for every injection.
• Auto. Activates the vial bottom sensing feature for the first injection of a sequence.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Table 9. Communication page parameters (Sheet 2 of 2)

Parameter Description
Dead Volume (μL) Specifies the volume of the transfer tubing that connects the autosampler’s injection port to
the autosampler’s injection valve.

The transfer tubing has a label that specifies its dead volume.
Sample Loop Volume Specifies the nominal size of the sample loop that is connected to the injection valve. The
autosampler cannot detect the sample loop size; it uses the sample loop size that you type in
this box.

Signal Polarity Page

During a run, the autosampler receives a Pump Ready signal and an Injection Hold release
signal from the pump. When the autosampler switches its injection valve to the inject
position, it sends an Inject Out signal to the detector. Figure 38 shows the signal terminals on
the autosampler’s back panel.
Figure 38. Signal terminals on the autosampler’s back panel
From pump To detector

2 3 2 3
0 1

0 1
4

4
5 6

5 6
9

7 8 7 8

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 UNIT ID ENET
GND
+ 5V @ 150mA
PUMP STOP
GRAD START
PUMP READY
INJECT HOLD
INJECT OUT
A/S READY
GND
+ 5V @ 150mA
TF 4
TF 3
TF 2
TF 1
GND
GND

Use the Signal Polarity page of the Surveyor Autosampler Configuration dialog box to specify
the signal polarities for the input and output run signals. For the Surveyor LC Pump Plus and
the Surveyor MS Pump Plus, ensure that the Pump Ready Active High and the Injection
Hold Release Active High check boxes in the Input area are selected.

 To specify the signal polarities for the autosampler

1. Open the Surveyor Autosampler Configuration dialog box (see “Surveyor Autosampler
Plus Configuration Settings” on page 45).
2. Click the Signal Polarity tab.
The Signal Polarity page appears (see Figure 39).

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Figure 39. Signal Polarity page parameters

Ensure that these check boxes

are selected for
a Surveyor Plus LC system.

3. In the Input area, ensure that the Pump Ready Active High and Injection Hold Release
Active High check boxes are selected (see Figure 39). These check boxes are selected in
the default instrument method.
4. In the Output area, if your instrument consists entirely of Surveyor Plus devices, do not
select the check boxes.

Autosampler Signal Polarity Page Parameters

Table 10 describes the parameters on the Signal Polarity page.
Table 10. Signal Polarity page parameters (Sheet 1 of 3)
Parameter Description
Input

The Pump Ready Active High and the Injection Hold Release check boxes are selected in the default instrument
method.

Leave these check boxes selected for a Surveyor Plus pump.

Pump Ready Active Use this check box to specify the polarity of the input signal from the pump:
High
• If the signal from the pump is LO (Closed) and goes HI (Open) when the pump is
ready, select the Pump Ready Active High check box.
• If the signal from the pump is HI (Open) and goes LO (Closed) when the pump is
ready, clear the Pump Ready Active High check box.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Table 10. Signal Polarity page parameters (Sheet 2 of 3)

Parameter Description
Injection Hold Release Use this check box to specify the polarity of the input signal from the pump:
Active High
• If the signal from the pump is LO (Closed) and goes HI (Open) when the pump is
ready, select the Injection Hold Release Active High check box.
• If the signal from the pump is HI (Open) and goes LO (Closed) when the pump is
ready, clear the Injection Hold Release Active High check box.
Output

These check boxes are clear in the default instrument method. For a Thermo Scientific LC/MS system, leave these
check boxes clear.
Autosampler Ready Use this check box to set the polarity of the A/S Ready output signal:
Active High
• When this check box is selected, the signal from the autosampler is LO (Closed) and
goes HI (Open) when the autosampler is ready.
• When this check box is clear, the signal from the autosampler is HI (Open) and goes
LO (Closed) when the autosampler is ready.
Note The A/S Ready terminal sends a signal that indicates that the autosampler is in the
Ready state. The autosampler is ready when it meets the selected ready conditions. The
ready conditions you select include sample tray temperature, column oven temperature,
door is closed, maintenance log, and vial bottom sensing (see “Communication Page” on
page 52).
Injection Out Active Use this check box to set the polarity of the Inject Out output signal:
High
• When this check box is selected, the signal from the autosampler is LO (Closed) and
goes HI (Open) when the autosampler injects a sample.
• When this check box is clear, the signal from the autosampler is HI (Open) and goes
LO (Closed) when the autosampler injects a sample.
Note The Injection Out terminal sends a signal to the other LC modules or peripheral
devices when the autosampler injects a sample.
Gradient Start Active Use this check box to set the polarity of the Gradient Start output signal:
High
• When the check box is selected, the signal from the autosampler is LO (Closed) and
goes HI (Open) to trigger the start of the pump’s gradient program.
• When the check box is clear, the signal from the autosampler is HI (Open) and goes LO
(Closed) to trigger the start of the pump’s gradient program.
Note The Grad Start terminal sends a signal to the pump to start the gradient program.

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Table 10. Signal Polarity page parameters (Sheet 3 of 3)

Parameter Description
Pump Stop Active Use this check box to set the polarity of the Pump Stop output signal:
High
• When the check box is selected, the signal from the autosampler is LO (CLosed) and
goes HI (Open) when the pump is to stop.
• When the check box is clear, the signal from the autosampler is HI (Open) and goes LO
(Closed) when the pump is to stop.
Note The Pump Stop terminal sends a signal to the pump to stop. The Pump Stop output
signal is not active during the injection sequence. The computer must make an explicit
request to issue the Pump Stop signal.
Timed Events Active Use this check box to set the polarity of the Timed Events output signals:
High
• When the check box is selected, the signal from the autosampler is LO (Closed) and
goes HI (Open) when the timed events program is to start.
• When the check box is clear, the signal from the autosampler is HI (Open) and goes LO
(Closed) when the timed events program is to start.
Note The TF terminals send signals for events entered in the timed events table of the
instrument method. For information about setting up the timed events table for the
autosampler, see “Timed Events Page for the Autosampler” on page 93.

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2 Thermo Foundation Instrument Configuration
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Firmware Page
Use the Firmware page to check the firmware version of the autosampler.

 To check the firmware version of the autosampler

1. Open the Surveyor Autosampler Configuration dialog box (see “Surveyor Autosampler
Plus Configuration Settings” on page 45).
2. Click the Firmware tab.
The Firmware page appears (see Figure 40).
Figure 40. Firmware page

3. If you have upgraded your autosampler, upload the firmware version as follows:
a. Click Upload Firmware Version.
The firmware version of the autosampler appears next to Current Version.
b. Click OK to save the settings and close the dialog box.

If you have finished configuring all of your LC devices, go to “Closing the Foundation
Application” on page 66.

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Surveyor MS Pump Plus Configuration Settings

During normal operation, the Surveyor MS Pump Plus communicates with the data system
computer through an RS-232 link. Before you configure the pump device driver, connect the
pump to the data system computer. If your LC system contains two pumps, connect both
pumps to the data system computer.

 To specify the configuration settings for the Surveyor MS Pump Plus

1. Ensure that the pump is connected to the data system computer and powered on.
2. For a dual-pump system, ensure that pump 2 is powered off.
3. In the Configured Devices list, double-click the Surveyor MS Pump Plus icon.

The Surveyor MS Pump Plus dialog box appears (see Figure 41).
Figure 41. Surveyor MS Pump Plus dialog box

4. If two pumps are connected to the data system computer, make sure that the appropriate
pumps are selected in the Pump 1 and Pump 2 area.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

You can use two pumps of the same pump type to perform two-dimensional
chromatography or high-pressure gradient mixing.
5. Click OK to close the dialog box.

Surveyor MS Pump Configuration Parameters

Table 11 provides descriptions of the parameters in the Surveyor MS Pump Configuration
dialog box.
Table 11. Surveyor MS Pump Plus Configuration dialog box parameters
Parameter Description
Serial number Lists the serial number stored by the Surveyor MS Pump Plus.
Status Displays the pump’s status. The states are Not Connected or Connected.
Communication Port Displays the type of communication port on the data system computer where the pump is
connected.
Stroke Count Displays the total stroke counts for the pump’s pistons.
Pump Type Displays the pump type: Thermo Pump.
Configuration Displays Quaternary.
Firmware Version Displays the firmware version.
Use Leak Sensor When this check box is selected, the leak sensor is in use.

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 2 Thermo Foundation Instrument Configuration
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Surveyor LC Pump Plus Configuration Settings

The Surveyor LC Pump communicates with the data system by way of an Ethernet
connection. To make this connection, connect the Ethernet cable to the Ethernet port on the
back of the pump and to the Ethernet switch. The unit ID setting on the back panel of the
pump must match the stack address in the configuration.

 To specify the configuration options for the Surveyor LC Pump Plus

1. In the Configured Devices list, double-click the Surveyor LC Pump icon.

The Surveyor LC Pump dialog box appears (see Figure 42).

Figure 42. Surveyor LC Pump dialog box

2. Make the following entries and selections:

• From the Pressure Units list, select the unit of measurement that you want to use to
display the backpressure of your system.

Note 1 MPa = 10 bar = 145 psi

• In the Stack Number box, type an appropriate value.

The value must match the Unit ID setting on the back panel of the Surveyor
LC Pump.
• If you want sequence runs to pause following a degasser error, select the
Pause Sequence Following Degasser Error check box.
3. Click OK to exit the Surveyor LC Pump dialog box.

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2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Surveyor LC Pump Plus Configuration Parameters

Table 12 describes the configuration parameters for the Surveyor LC Pump Plus.
Table 12. Surveyor LC Pump Plus configuration parameters
Parameter Description
Configuration
Pressure Units Specifies the pressure units for the status display.

The selections are MPa, bar, and psi.

To convert psi to bar, multiply by 0.0689476. To convert bar to

psi, multiply by 14.5038.
Stack Number Specifies the unit ID value for the Surveyor LC Pump Plus. The
unit ID on the back panel of the pump consists of two rotary
switches. Each switch contains ten positions. The arrow on the left
switch points to the first digit of the unit ID. The arrow on the
right switch points to the second digit of the unit ID.

The rotary switches are set to 01 at the factory.

Error Handling
Pause Sequence Select this check box to pause the injection sequence when the
following Degasser pump detects a degassing error.
Error
Clear this check box if you do not want the injection sequence to
pause when the pump detects a degassing error.

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 2 Thermo Foundation Instrument Configuration
Specifying the Configuration Settings

Surveyor PDA Plus Detector Configuration Settings

The PDA detector communicates with the Xcalibur data system through an Ethernet
connection. To make this connection, connect the Ethernet cable to the Ethernet port on the
back of the detector and to the Ethernet switch. The unit ID setting on the back panel of the
detector must match the configured stack number.

 To specify the configuration options for the PDA detector

1. In the Configured Devices list, double-click the Surveyor PDA Plus icon.

The Surveyor PDA Plus Configuration dialog box appears (see Figure 43).
Figure 43. Surveyor PDA Plus Configuration dialog box

2. In the Stack Number box, type the appropriate number (unit ID).
3. Click OK to close the Surveyor PDA Plus Configuration dialog box.

When you have finished configuring the instrument devices, go to the next topic: Closing the
Foundation Application.

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2 Thermo Foundation Instrument Configuration
Closing the Foundation Application

Surveyor UV/Vis Plus Detector Configuration Settings

The UV/Vis Detector communicates with the data system computer through an Ethernet
connection.

 To specify the configuration settings for the UV/Vis detector

1. In the Configured Devices list, double-click the Surveyor UV/Vis icon.

The Surveyor UV/Vis Configuration dialog box appears (see Figure 44).
Figure 44. Surveyor UV/Vis Configuration dialog box

2. In the Stack Address box, type the appropriate number (unit ID). The Stack Address
setting must match the rotary switches on the back panel of the detector.
3. Click OK to close the Surveyor UV/Vis Configuration dialog box.
When you have finished configuring all of your LC devices, go to the next topic: Closing
the Foundation Application.

Closing the Foundation Application

Before you can open your Thermo Scientific data system, you must close the Foundation
application.

 To save the instrument configuration and close the Instrument Configuration window

Click Done at the bottom of the Thermo Foundation Instrument Configuration

window.
The Windows desktop appears.

Tip You must close the Instrument Configuration window before you open the
Xcalibur data system. The two applications cannot be open at the same time.

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 3

Instrument Method Setup

This chapter describes the instrument control parameters for the Surveyor Plus LC devices. It
does not describe the instrument control parameters for your Thermo Scientific mass
spectrometer. For information about setting up the data acquisition parameters for a Thermo
Scientific mass spectrometer, refer to the getting started guide or Help for the mass
spectrometer.

To automate control of the liquid chromatography devices, you must create an instrument
method, and then specify the instrument method to be used for each run in an acquisition
sequence from the Sequence Setup window.

Instrument methods contain the analysis wavelengths, the chromatographic conditions, and
the autosampler injection parameters, such as the injection mode, required for data
acquisition.

 To create an instrument method

1. Open the Instrument Setup window (Xcalibur data system) or equivalent window for
your Thermo Scientific mass spectrometry application.
2. Specify the instrument method settings for each device.
3. Save the instrument method.

Contents
• Opening the Instrument Setup Window
• Surveyor LC Pump Plus Instrument Method Parameters
• Surveyor MS Pump Plus Instrument Method Settings
• Autosampler Instrument Method Parameters
• PDA Detector Instrument Method Parameters
• Triggering an External Device with the PDA Detector
• UV-Vis Detector Instrument Method Parameters
• Saving the Instrument Method

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3 Instrument Method Setup
Opening the Instrument Setup Window

Opening the Instrument Setup Window

The Instrument Setup window of the Xcalibur data system is where you create instrument
methods and access the direct control commands for your instrument devices. If you are
controlling your LC/MS instrument from another Thermo Scientific mass spectrometry
application, open the equivalent window.

 To open the Instrument Setup window

1. Start the Xcalibur data system.

2. In the Thermo Xcalibur Roadmap window, click the Instrument Setup icon on the
Road Map or choose GoTo > Instrument Setup.
The Instrument Setup window appears (see Figure 45). The view bar on the left side of
the window contains an icon for each configured instrument device. Clicking the device
icon opens the view for that device.
Figure 45. Instrument Setup window

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 3 Instrument Method Setup
Surveyor LC Pump Plus Instrument Method Parameters

Surveyor LC Pump Plus Instrument Method Parameters

Use the Surveyor LC Pump view to set up the instrument method parameters for the pump.

To set up the instrument method parameters for the Surveyor LC Pump Plus, see these topics:
• Surveyor LC Pump Plus General Page
• Surveyor LC Pump Plus Gradient Program Page

Surveyor LC Pump Plus General Page

Use the General page for the Surveyor LC Pump Plus to identify the mobile phase solvents,
the LC column, and the operation pressure limits for the pump (see Figure 46).
Figure 46. General page for the Surveyor LC Pump Plus

 To specify the instrument method settings on the General page

1. In the Solvent Name boxes in the Solvents area, type the solvent names.
2. In the Description box in the Column area, type a description of the LC column.
3. In the Pressure Limits area, do the following:
a. In the Min Pressure box, type the minimum operating pressure.

Note Pressure drops can indicate the following problems:

• Mobile phase in the solvent reservoir bottles has run out.
• A leak has occurred in the flow line or lines.
• An excessive amount of air has entered the pump head assemblies.

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3 Instrument Method Setup
Surveyor LC Pump Plus Instrument Method Parameters

b. In the Max Pressure box, type the maximum operating pressure.

Note The maximum pressure setting is 43.10 MPa, 431.00 bar, or 6258.00 psi.
Reduce the maximum pressure setting for PEEK fittings to 28 MPa, 276 bar, or
4000 psi.

1 bar = 14.5 psi = 10 MPa

Surveyor LC Pump Plus General Page Parameters

Table 13 describes the parameters on the General page.
Table 13. General page parameters for the Surveyor LC Pump Plus
Parameter Description
Solvents
A Solvent Name Specifies the solvent contained in the solvent A reservoir bottle.
B Solvent Name Specifies the solvent contained in the solvent B reservoir bottle.
C Solvent Name Specifies the solvent contained in the solvent C reservoir bottle.
D Solvent Name Specifies the solvent contained in the solvent D reservoir bottle.
Column
Description User-specified description for the LC column.
Pressure Limits
Min Pressure Specifies the minimum operating pressure for the pump. If the
system pressure falls below this limit, the data system turns off the
solvent flow from the pump.
Pressure units Minimum Maximum
MPa 0.00 43.10
bar 0.00 431.00
psi 0.00 6258.00
Max Pressure Specifies the maximum operating pressure for the pump. If the
system pressure rises above this limit, the data system turns off the
solvent flow from the pump.

The maximum pressure setting must be greater than the

minimum pressure setting.
Pressure units Minimum Maximum
MPa 1.00 43.10
bar 10.00 431.00
psi 143.00 6258.00

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 3 Instrument Method Setup
Surveyor LC Pump Plus Instrument Method Parameters

Surveyor LC Pump Plus Gradient Program Page

Use the Gradient Program page (see Figure 47) to specify the solvent composition and flow
rate for your chromatographic method.
Figure 47. Example of an isocratic pump program for the Surveyor LC Pump Plus

Placeholder line

 To specify the solvent conditions for the Surveyor LC Pump Plus

1. Click the Gradient Program tab.

The Gradient Program page appears (see Figure 47).
2. Type the initial flow rate and the initial solvent composition for your pump program in
the first time line of the time program table, and then press ENTER.
If you are not creating a gradient program, skip the next step.

Note If you set the limit for the maximum pressure to less than 21 MPa, the
allowable flow rate range is 0.000 to 9.999 mL/min. If you set the maximum pressure
limit to 21 MPa (215 bar, 3129 psi) or higher, the maximum allowable flow rate is
5.000 mL/min.

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3 Instrument Method Setup
Surveyor LC Pump Plus Instrument Method Parameters

The first time line in the time program table is set to 0.00 minutes and is uneditable. The
second time line in the program is a placeholder line and has no effect on the pumping
conditions.
For example, the pump program shown in Figure 47 produces a proportioned mobile
phase consisting of 80% methanol and 20% water (v/v). The proportions of the solvents
remain constant throughout the run. The mobile phase flow rate remains constant
at 1 mL/min throughout the run.
3. To create a gradient pump method, enter at least two steps in the Gradient Program table.
For each additional line in the program, type these values:
• A time value in the Time column
• A flow rate in the Flow column
• The solvent percentages for the mobile phase in the solvent columns
4. Press ENTER.
The last line in the gradient table, which has an * in place of a line number, is a
placeholder and has no effect on the pump conditions.
Table 14 lists the gradient conditions used to create the gradient profile shown in
Figure 48.
Table 14. Gradient program
Time (min) Solvent composition
0.00 to 5.00 Held constant at 90:10 water/methanol
5.00 to 25.00 Linear ramp from 10% to 90% methanol
25.00 to 25.01 Stepped down to initial solvent composition of
90:10 water/methanol
25.01 to 40.00 Column is equilibrated at the initial solvent composition of
90:10 water/methanol

At 25.01 minutes, the program returns to its initial solvent composition. To equilibrate
the column prior to the next run, the solvent composition is held at the initial solvent
composition for a period of 15 minutes.

Note When you are performing a sequence of gradient runs, add an equilibration
step at the end of the Gradient Program.

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 3 Instrument Method Setup
Surveyor LC Pump Plus Instrument Method Parameters

Figure 48. Example of a gradient program for the Surveyor LC Pump Plus

Placeholder line

Surveyor LC Pump Gradient Program Page Parameters

Table 15 describes the parameters on the Gradient Program page.
Table 15. Gradient Program page parameters for the Surveyor LC Pump Plus (Sheet 1 of 2)
Parameter Description
Graph
Displays the percent composition of solvents A, B, C and D as a function of time.
Table

Specifies the gradient steps. The table can contain up to 80 rows. The solvent composition boxes are interactive. After
you type a value in column A and press ENTER or click another box, the value in column B changes to maintain a
total of 100%, and so on. The solvent composition changes linearly between time points.
Time (min) Specifies the time duration for each gradient step. The initial time is always 0 minutes.

Range: 0 to 655.35 minutes

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3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

Table 15. Gradient Program page parameters for the Surveyor LC Pump Plus (Sheet 2 of 2)
Parameter Description
Flow (mL/min) Specifies the flow rate.

Range: 0.000 to 9.999 mL/min

%A Specifies the percent composition of solvent A for each time point.
%B Specifies the percent composition of solvent B for each time point.
%C Specifies the percent composition of solvent C for each time point.
%D Specifies the percent composition of solvent D for each time point.

Surveyor MS Pump Plus Instrument Method Settings

Use the Surveyor MS Pump Plus view in the Instrument Setup window to specify the
chromatographic conditions for your instrument method.

To open the Surveyor MS Pump Plus view, click the Surveyor MS Pump Plus icon in the
view bar of the Instrument Setup window.

To set up the chromatographic conditions, see these topics:

• Specifying the Chromatographic Conditions for a Single-Pump System
• Programming the Pumps in a Dual-Pump System

Specifying the Chromatographic Conditions for a Single-Pump System

To specify the chromatographic conditions for a single-pump system, follow these procedures
in order:
1. Setting Up the Pump General Parameters
2. Setting Up the Gradient Program

Tip After you specify the solvents that make up the mobile phase, you can switch back
and forth between the Pump General and Gradient Program pages.

Setting Up the Pump General Parameters

Use the Pump General page to specify the solvents that the pump uses to create the mobile
phase and operating conditions for the pump (see Figure 49).

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 3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

Figure 49. General page for the Surveyor MS Pump Plus

When you connect two pumps to the data system computer, you must specify the general
parameters for both pumps. The autosampler triggers the gradient program for Pump 1 at the
start of a run. Pump 1 triggers the gradient program for Pump 2 at a user-specified time
during the run (see “Programming the Pumps in a Dual-Pump System” on page 84).

Note You can use a dual-pump system to perform two-dimensional chromatography or to

create a high-pressure gradient.

The Instrument Method report attached to the raw file contains the values that you select or
enter on this page. You can access this report in the Qual Browser view by choosing
View > Reports > Instrument Method.

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3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

 To specify the parameters on the Pump General page

1. Open the view for your pump.

For information about opening the device views from the Xcalibur 2.1.x data system, see
“Opening the Instrument Setup Window” on page 68.
The pump view includes a Pump 1 area for a single-pump system or a Pump 1 area and a
Pump 2 area for a dual-pump system.
2. On the Pump General page, specify the parameters as follows:
a. In the Name box, use the default label (Pump 1 for a single-pump system) or type a
label.
The label can be up to 16 alphanumeric characters. The data system uses this label
for the pump view on the Status page of the Information view.
b. In the Comment box, type additional information about the chromatographic
method (for example, the specifications for the liquid chromatography column).
c. Identify the solvents that make up the mobile phase.
All of the solvent check boxes are selected by default. Clearing a solvent check box
makes the solvent unavailable on the Gradient Program page.
In the boxes to the right of the solvent check boxes, type the names of the solvents
that make up the mobile phase.
• In the Operating Mode list, the only selection for the Surveyor MS Pump Plus is Low
Pressure.
d. In the Start Settings list, select how the system is triggered to start a run: Surveyor AS
Autosampler Injection Logic or Manual.
To trigger a run when the autosampler makes an injection, select Surveyor AS
Autosampler Injection Logic.
e. In the Method Finalizing list, select the ending conditions for the run.
• For a gradient method, do one of the following:
– Select First Line Conditions to return the mobile phase conditions to the
first line of the gradient program following the last time line in the gradient
program table.
– Select Last Line Conditions so that the mobile phase conditions remain at
those of the last time line in the gradient program.
• For a shutdown method that turns off the solvent flow at the end of a run, select
Stop after the End.

Note The Idle Settings list is available for a dual-pump system in the Pump 2
area of the Pump General page.

f. In the Min Pressure (bar) box, type or select the minimum operating pressure for the
pump.

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 3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

An appropriate minimum pressure setting prevents the pump from operating when
the solvent reservoirs have run dry or the system plumbing has developed a leak.
Running the pump without solvent quickly ruins the piston seals. Select a value that
is well below the typical operating pressure for your application. In the event that the
pressure falls below this limit for more than one minute, the pump automatically
stops and sends an error message to the computer.
The range is 0 to 400 bar (5800 psi) with a default value of 0 bar.
g. In the Max Pressure (bar) box, type or select the maximum operating pressure for the
pump.
An appropriate maximum pressure setting prevents the pump from operating with a
restriction on the outlet side of the pump. Excess pressure can damage the HPLC
column and any other component between the restriction and the pump. Select a
value that is well above the typical operating pressure for your application, but also
below the pressure that can damage your system. If the pressure rises above this limit,
the pump automatically stops and sends an error message to the computer.
The range is 0 to 400 bar (5800 psi) with a default value of 400 bar.
h. In the Pressure Stability (bar) box, type or select an appropriate pressure stability
value from 1 to 100.
The MS pump sends a Ready signal when the system pressure reaches this limit. A
lower value requires greater pressure stability before the pump becomes ready. A
higher value is more forgiving of pressure pulsations.
i. In the Pressure Units list, select the pressure units for the pressure readback.
Note 1 bar = 14.5 psi

Thermo Pump General Page Parameters

Table 16 describes the parameters on the General page.
Table 16. Thermo pump method parameters (Sheet 1 of 3)
Parameter Description
Name Identifies the pump on the pump view of the Status page of the Info view.

The text string can consist of up to 16 alphanumeric characters.

Comment User text that provides additional information. The text string can consist of up to
255 alphanumeric characters.
Solvent A, B, C, and D When these check boxes are selected, the associated solvent column on the Gradient
check boxes and Program page is available. Select the check boxes corresponding to the solvent bottles to be
adjacent boxes used to create the mobile phase. Type a description of the solvent in the adjacent box.

Clearing the check box associated with a solvent (A, B, C, or D) makes the solvent column
unavailable on the Gradient Program page.

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3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

Table 16. Thermo pump method parameters (Sheet 2 of 3)

Parameter Description
Operating Mode Specifies the operating mode for the pump. The selection is (0~7000 PSI).
Start settings Specifies the device that triggers the start of a run and the run synchronization signals
between the pump and the autosampler.

The selections are as follows:

Surveyor AS injection At the start of a run, the Surveyor Autosampler Plus waits for the
logic pump to issue the Pump Ready and the Release Injection signal
before making an injection. The pump then waits for the Start
gradient signal from the autosampler before starting the pump
program.

When you use this injection logic, set up the Surveyor

Autosampler Plus as the start instrument that triggers the run.
Manual At the start of a run, the pump program starts immediately.

When you use this injection logic, set up the pump as the start
instrument.
Min Pressure Specifies the minimum operating pressure of the pump. If the system pressure falls below
this level for more than one minute, the data system triggers turns off the mobile phase flow.

Default: 0 bar
Max pressure Specifies the maximum operating pressure of the pump. If the system backpressure rises
above this level for more than one minute, the data system triggers the pump to turn off the
mobile phase flow.

Default: 400 bar

Pressure Stability Specifies the stability condition required for the pump to go into a Ready state. A lower
value requires greater pressure stability before the pump state goes to Ready. A higher value
is more forgiving of pressure pulsations.

Default: 10

The range depends on the pressure units selection.

Units Range
psi 1 to 1450
MPa 1 to 10
bar 1 to 100

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Surveyor MS Pump Plus Instrument Method Settings

Table 16. Thermo pump method parameters (Sheet 3 of 3)

Parameter Description
Pressure Units Specifies the units for the pressure readout.

Selections: PSI and MPa

1.00 MPa = 10.0 bar = 145 psi

Idle Settings (Pump 2 Specifies the conditions for Pump 2 while it is waiting to be triggered by Pump 1.
of a dual-pump system)
Default: Standby

Selections: Standby, First Line Conditions, and Last Line Conditions

In the Standby mode, the pump remains in the Idle state.

Setting Up the Gradient Program

The pump contains a built-in solvent proportioning assembly that is capable of proportioning
up to four solvents to create binary, tertiary, and quaternary mobile phases. This capability
reduces the need to make premixed mobile phases. You can run the pump in either the
isocratic mode or the gradient mode. In the isocratic mode, you maintain the same
proportions of solvent throughout the run.

Use the Gradient Program page to specify the solvent composition and flow rate for your
chromatographic method.

The Gradient Program page contains a gradient table with time lines for the solvent
composition and flow rate, and an interactive view that displays a graphical profile of the
solvent gradient or flow rate gradient.

Each row in the gradient table defines the solvent composition and flow rate for a specific
time point. The solvent composition columns (A%, B%, C%, and D%) work interactively
with each other, maintaining a total solvent composition of 100%.

Between time points, the solvent composition changes linearly, whereas the flow rate changes
as a discontinuous step-function.

The gradient table can contain 2 to 398 time lines.

IMPORTANT The gradient table must contain at least two time lines. For an isocratic
gradient program, the two time lines specify the same solvent composition and flow rate.

 To set up the gradient program for the Surveyor MS Pump Plus

1. Open the view for your pump.

2. Specify the general pump parameters (see “Specifying the Chromatographic Conditions
for a Single-Pump System” on page 74).

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3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

3. Click the Gradient Program tab.

The Gradient Program page appears (see Figure 50). The columns that represent the
solvents selected on the Pump General page are available for editing.
Figure 50. Gradient Program page

4. For time = 0.00, do the following:

a. Type the initial solvent composition in the A%, B%, C%, and D% columns. For
each solvent, after you type the percent composition, press ENTER or click another
box in the gradient program table.
The first row in the gradient program table is set to 0.00 min and is uneditable. As
you change the percent composition for each solvent, the data system maintains a
total solvent composition of 100%.
b. Type the initial flow rate in the μL/min column, and then press ENTER or click
another box in the gradient program table.
The minimum flow rate setting depends on the start setting for the gradient program
as follows:
• When you select Surveyor AS Injection Logic or Manual and the Home Before
Run check box, the minimum flow rate is 10.0 μL/min.
• When you select Manual and leave the Home Before Run check box cleared, the
minimum flow rate is 0.0 μL/min.
The maximum flow rate setting is 2000 μL/min for the Surveyor MS Pump Plus.

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 3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

5. For an isocratic separation method, do the following on the Gradient Program page for
the Surveyor MS Pump Plus:
a. Double-click the Time column in the second row of the gradient program table, and
then type a time value in this cell.
The time range is 0.01 to 655.00 minutes.
If the time value for the second time point is longer than the data acquisition time for
the PDA detector or the MS detector, the data system waits for the gradient program
to finish before proceeding to the next row in the acquisition sequence.
b. Type the same values for the solvent composition and the flow rate that you specified
for the initial time point. Press ENTER to accept the values.

IMPORTANT You must specify the flow rate and solvent composition for at
least two time lines.

c. Verify the gradient program in the Solvent Gradient view (see Figure 51).
Figure 51. Isocratic gradient program

Solvent Gradient view The program must contain at

least two time lines.

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Surveyor MS Pump Plus Instrument Method Settings

6. For a gradient separation method, do the following:

a. For each row in the program, type the solvent composition and the flow rate, and
then press ENTER.
The pump program can contain from 2 to 398 rows (time lines). The last row in the
gradient program is a placeholder and has no effect on the pump conditions. The last
row does not have a time entry in the Time column.
The flow rate range is the same as for an isocratic run (see step 4b on page 80). To
produce a stable gradient, enter a flow rate of at least 25 μL/min.
b. To return the solvent conditions to those specified in the first line of the gradient
program, select First Line Conditions in the Method Finalizing list. First Line
Conditions is the default selection.
Figure 52 shows the gradient program entries for the gradient program in Table 17.
After 30 minutes the gradient program returns to the first line conditions for the
remainder of the run. To equilibrate the LC column at the first line conditions for
10 minutes, you must set the run time for the PDA detector or MS detector to
40 minutes.

Tip If you do not want the detector to acquire data during the column
equilibration period, you can add an equilibration period to the end of the
gradient program and make the gradient program time for the pump longer than
the data acquisition time for the detector.

Figure 52. Example of a pump gradient program

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 3 Instrument Method Setup
Surveyor MS Pump Plus Instrument Method Settings

Table 17. Gradient program

Time (min) Solvent composition
0.00 to 5.00 Held constant at 90% solvent A /10% solvent B
5.00 to 25.00 Linear ramp from 10% solvent B to 90% solvent B
25.00 to 30.00 Held constant at 10% solvent B /90% solvent B
30.00 to 40.00 Column is equilibrated at the initial solvent composition
of 90% solvent A /10% solvent B

Thermo Pump Gradient Program Page Parameters

Table 18 describes the parameters on the Gradient Program page.
Table 18. Thermo pump method parameters
Parameter Description
Gradient table
Each row in the gradient table defines the solvent composition and flow rate for a specific time point. Between time
points, the solvent composition changes linearly, whereas the flow rate changes as a discontinuous step-function. The
pump program can contain up to 398 time lines.
Time The time parameter (min box) specifies at what point in the run the associated solvent
composition and flow rate become effective. The first time line remains set to 0 min.
A%, B%, C%, and The solvent composition parameters (A%, B%, C%, and D% columns) work interactively
D% with each other and specify the mobile phase composition at the time point specified in the
associated Min box. The mobile phase composition changes linearly between two
consecutive time points.

Default: 100% A
μL/min The μL/min box specifies the flow rate of the mobile phase at the time specified in the
associated Time box.

Default: 10 μL/min
P2 (Dual-pump For a dual-pump system, the time line position of the ball in the P2 column specifies the
system) time when Pump 1 triggers Pump 2.
Graph view
Type of View Select Solvent Gradient to view the solvent gradient profile created by the pump program.
Select Flow Gradient to view the flow rate changes created by the pump program.
The Gradient Profile area graphically displays the values entered in the pump program. The
y axis represents percent composition or flow rate and the x axis represents time in minutes.
Each solvent is color-coded for better visualization of the programmed gradient.

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Programming the Pumps in a Dual-Pump System

 To program the pumps in a dual-pump system

1. On the Pump General page, do the following:

a. Follow the instructions in “Setting Up the Pump General Parameters” on page 74.
b. In the Pump 2 area, select the Idle settings for the pump that you configured as the
sample pump (Pump 2) as follows:
In the Idle Settings list, select the solvent conditions for Pump 2 before it starts its
gradient program:
• If you want Pump 2 to remain idle until Pump 1 sends the start signal, select
Standby.
• If you want Pump 2 to pump solvent at the solvent composition and flow rate
specified in the first line of its gradient program until Pump 1 sends the start
signal, select First Line.
• If you want Pump 2 to pump solvent at the solvent composition and flow rate
specified in the last line of its gradient program until Pump 1 sends the start
signal, select Last Line.
c. Specify the remaining parameters for Pump 2.
2. On the Gradient Program page (see Figure 53), do the following:
a. To specify the gradient programs for both pumps, follow the instructions in “Setting
Up the Gradient Program” on page 79.
b. In the Pump 1 area, in the P2 column, select the time line that corresponds to the
time that you want the start pump to trigger the sample pump.
To select the trigger time for Pump 2, click the appropriate row in the P2 column.
The button appears in the P2 column.
Figure 53. Gradient page for a dual-pump system
At 1.00 minute into the run, Pump 1 triggers the start of the
Pump 2 gradient program.

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 3 Instrument Method Setup
Autosampler Instrument Method Parameters

Autosampler Instrument Method Parameters

Use these three pages of the Surveyor AS view to specify the injection settings, the
temperatures of the controlled temperature zones, the solvents contained in the wash bottle
and the autosampler’s 16 mL reservoir bottles, and any external events triggered by the
autosampler.
• Surveyor AS Method Page
• Reservoir Content Page
• Timed Events Page for the Autosampler

For information about the Sample Preparation page, see Chapter 4, “Sample Preparation
Routines.”

Surveyor AS Method Page

Use the Surveyor AS Method page to set the injection and the temperature control parameters
for the autosampler (see Figure 54).
Figure 54. Surveyor AS Method page

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Autosampler Instrument Method Parameters

 To specify the injection and temperature control settings for your instrument method

1. Select the injection mode:

• If you want to vary the volume of your sample injections, select the Partial Loop
option.
• If you want a high degree in injection-to-injection precision, select the Full Loop
option. When you select Full loop, the Injection Volume (μL) box becomes
unavailable.
• If you have a limited amount of sample, select the No Waste option. When you select
No Waste, the Loop Loading Speed (μL/s) box becomes available.

Note For more information about the injection modes, see “Injection Modes” on
page 19.

2. For the No Waste injection mode, type or select a loop loading speed in the Loop Loading
Speed box.
For most applications, keep the loop loading speed at its default value.
3. For the Partial Loop and No Waste injection modes, type or select an injection volume in
the Injection Volume box.
The injection volume range depends on the syringe size (see “Injection Volume Range”
on page 91).
4. In the Needle Height from Bottom (mm) box, type or select the height from the bottom
of the vial or well that the needle of the autosampler descends to before withdrawing
sample from the vial/well location.
The default value is 2 mm and the range is 0.1 to 18 mm. Entering a lower value causes
the needle to descend closer to the bottom of the vial or well. The standard 1.8 mL vials
supplied with the autosampler have a depth of approximately 20 mm.
Figure 13 on page 15 shows the needle descending to a depth of 2 mm from the bottom
of a standard 1.8 mL vial.
5. In the Syringe Speed (μL/s) box, keep the syringe speed at its default value (8 μL/s for the
250 μL concentric syringe) for most applications.
If you see the sample in the needle tubing break up as the autosampler withdraws sample
from a vial or well location into the needle tubing, adjust the syringe speed.
6. In the Flush Volume (μL) box, type or select a volume from 0 to 6000 μL or keep the
value at its default of 400 μL.
7. In the Flush/Wash Source list, select a flush/wash solution.
For most applications, select Bottle (wash bottle). If you select one of the reservoir vial
locations as your flush/wash source, make sure that you load the autosampler with a
reservoir vial.

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For information about the location of the 16 mL reservoir vials, see “Tray Compartment”
on page 5. For information about specifying the contents of the reservoir vials and the
wash bottle, see “Reservoir Content Page” on page 92.
8. In the Wash Volume (μL) box, keep the wash volume at its default value of 0 μL.
To wash the exterior of the needle after each injection, type a value from 1 to 6000 μL in
the Wash Volume box.
9. In the Flush Speed (μL/s) box, set a flush speed appropriate for the flush solvent:
• If you are using a flush solvent of low viscosity such as methanol, keep the flush speed
at its default (100 μL/s for the 250 μL concentric syringe)
• If you are using water or a methanol/water mixture as the flush solvent, reduce the
flush speed.

Tip If you hear a grinding noise from the autosampler as it performs a flush, lower the
flush speed.

10. In the Post-Injection Valve Switch Time (min) box, keep the time value at its default of
0 minutes for most applications. This leaves the sample loop in the inject position during
the entire run, allowing ample rinsing of the sample loop between injections.
11. In the Tray Temperature Control area, to control the temperature of the tray
compartment, select the Enable Tray Temperature Control check box. Then type an
appropriate temperature from 0 to 60 °C in the Temperature box.
12. In the Column Oven Control area, to control the temperature of the LC column, select
the Enable Column Oven Control check box. Then type an appropriate temperature
from 5 to 95 °C in the Temperature box. Controlling the temperature of the LC column
increases the reproducibility of the chromatographic retention times.

Autosampler Method Page Parameters

Table 19 describes the parameters on the Surveyor AS Method page.

The autosampler ships with a 250 μL concentric plunger syringe, but you can replace this
syringe with a 100 or 500 μL concentric plunger syringe or a 2500 μL single plunger syringe.

The injection volume range and the syringe speeds depend on the syringe size as described in
these topics:
• Injection Volume Range
• Syringe and Loop Loading Speeds for Injections

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Table 19. Autosampler Method page parameters (Sheet 1 of 3)

Parameter Description
Injection Volume (μL) Specifies the sample volume that the autosampler loads into the sample loop.

The default value and the range depend on the syringe size (see “Injection Volume Range”
on page 91).
Needle Height from Specifies the height from the bottom of the vial or well where the needle withdraws liquid
Bottom (mm) (see Figure 13 on page 15).

Range: 0.1 to 18.0 mm

Default: 2 mm
Syringe Speed (μL/s) Specifies the rate at which the syringe withdraws liquid from a tray vial or a plate well.

The default value and the range depend on the syringe size (see “Syringe and Loop Loading
Speeds for Injections” on page 91).
Flush Volume (μL) Specifies the volume of liquid that the autosampler flushes through the inside of the needle,
the injection port, and the transfer tube. During a flush cycle, the injection valve is in the
inject position to prevent the flush solvent from entering the sample loop.

To reduce carryover, increase the flush volume. When the specified flush volume exceeds the
syringe capacity, the autosampler takes multiple draws from the reservoir or bottle.

Range: 0.0 to 6000.0 μL

Default: 400 μL
Flush/Wash source Specifies the flush/wash source.

Selections: bottle, RV1, RV2, RV3, or RV4

Default: bottle (wash bottle)
Wash Volume (μL) Specifies the volume of liquid used to wash the internal and external surfaces of the needle.

During a wash cycle, the autosampler lowers the needle into the wash port. When the
specified wash volume exceeds the syringe capacity, the autosampler takes multiple draws
from the reservoir vial or wash bottle.

Range: 0.0 to 6000.0 μL

Default: 0 μL

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Table 19. Autosampler Method page parameters (Sheet 2 of 3)

Parameter Description
Flush Speed (μL/s) Specifies the rate at which the syringe draws flush solvent into its chamber and expels flush
solvent through the needle during a flush cycle.
Syringe type Default Range
Concentric dual-plunger 1.65 to 661.38 μL/s 100.0 μL/s
Standard single-plunger 8.27 to 330.85 μL/s 82.71 μL/s
IMPORTANT A flush speed of 250 μL/s for the 250 μL concentric syringe is the
maximum flush speed for a solvent of low viscosity such as 100% methanol. If you are
using a solvent of higher viscosity, reduce the flush speed accordingly. For example,
because water has approximately twice the viscosity as methanol, if you are using water as
your flush solvent, lower the flush speed to 100 μL/s. At high flush speeds, viscous
solvents can cause the autosampler to make a grinding sound.
Post-Injection Valve At the default post-injection valve switch time of 0 minutes, the injection valve remains in
Switch Time (min) the inject position during the run.

A time value greater than 0.1 minutes specifies the time when the injection valve switches
from the inject position to the load position at the end of an injection cycle.

To reduce the gradient delay volume for low-flow gradient applications, consider switching
the injection valve from the inject position to the load position during the run by typing a
nonzero value in this box. Allow enough time for the mobile phase to backflush the sample
out of the sample loop.

Default: 0 minutes
Range: 0 to 999.0 minutes
Loop Loading Speed Specifies the rate at which the autosampler meters the sample into the sample loop for no
(μL/s) waste injections. During a no waste injection, the autosampler meters the sample through
the transfer tubing to the injection valve at the specified syringe speed. The injection valve
then switches to the load position, and the autosampler meters the sample into the sample
loop at the specified loop loading speed.

This parameter is only available in the No Waste injection mode.

The default value and range depend on the syringe size (see “Syringe and Loop Loading
Speeds for Injections” on page 91).
Injection Mode
Partial Loop Select this option if you want to inject variable volumes.
IMPORTANT To make precise partial loop injections, limit the maximum injection
volume to less than half the nominal sample loop size. Because the accuracy of the
nominal volume of the sample loop is ± 20% (which means that the actual volume of the
standard 25 μL sample loop is between 20 and 30 μL), for best results, limit the maximum
injection volume to 10 μL for the standard 25 μL sample loop.

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Table 19. Autosampler Method page parameters (Sheet 3 of 3)

Parameter Description
Full Loop Select this option when you need a high degree of accuracy. The Injection Volume box is
unavailable with this selection.
No Waste Select this option when you have a limited amount of sample.
IMPORTANT For no waste injections, follow these suggestions to optimize
injection-to-injection reproducibility and minimize baseline disturbances:
• Use a sample loop that is at least 5 μL larger than the injection volume. Because the
accuracy of the nominal size is ± 20%, use an estimate of 80% for the actual size.
• Consider matching the chemistry of the sample matrix, the flush solution, and the
mobile phase.
• Inject at least 1.0 μL of sample.
Tray Temperature Control
Enable Tray Temp Select this check box to enable temperature control for the tray compartment.
Control
In the default instrument method, this check box is clear; temperature control for the tray
compartment is not enabled.

To maintain a stable temperature, set the temperature to a value that is a least 10 °C above
or below the ambient room temperature. As a safety feature, a thermostat turns off the
power to the sample tray if the temperature reaches 65 °C.
Temperature (° C) Specifies the tray temperature.

Default: 30 °C
Range: 0 to 60 °C
Column Oven Control
Enable Tray Temp Select this check box to enable temperature control for the column oven.
Control
In the default instrument method, this check box is clear; temperature control for the
column compartment is not enabled.
Temperature (° C) Specifies the column oven temperature.

To maintain a stable temperature, set the temperature to a value that is a least 10 °C above
or below the ambient room temperature. As a safety feature, a thermostat turns off the
power to the column oven if the temperature reaches 110 °C.

Default: 30 °C
Range: 5 to 95 °C

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Injection Volume Range

The injection volume for full loop injections is automatically set to the value in the Sample
Loop Volume box on the Communication page of the Surveyor Autosampler dialog box (see
“Communication Page” on page 52).

For partial loop and no waste injections, the minimum injection volume is 0.1 μL. The
maximum injection volume depends on the syringe size (see Table 20).

For optimal performance, follow these guidelines:

• For no waste injections, do not inject less than 1.0 μL and limit the maximum injection
volume to 80% of the nominal loop size minus an additional 5 μL.
• For partial loop injections, limit the maximum injection volume to 40% of the nominal
loop size. For the standard 25 μL sample loop, limit the maximum injection volume to
10 μL.
Table 20. Maximum injection volume
Syringe size (μL) Maximum injection volume (μL)
100 20
250 125
500 300
2500 1250

Syringe and Loop Loading Speeds for Injections

During an injection sequence, the inner plunger of the concentric syringe descends, pulling
liquid from a sample vial or well into the needle tubing. After the autosampler withdraws
sample, the XYZ arm moves the needle to the injection port. The inner plunger of the
concentric syringe ascends, pushing liquid through the transfer tubing and into the sample
loop. A stepper motor controls the speed of the plunger.

You can specify how fast, in microliters per second, the syringe withdraws liquid from a tray
vial or plate well, and then expels liquid into the autosampler injection port. The default
syringe speed and the syringe speed range depend on the syringe size (see Table 21).

The appropriate syringe speed depends on the sample. For viscous samples, use a syringe
speed lower than the default value to avoid stalling the syringe. For samples of low viscosity or
surface tension, use a lower syringe speed to prevent the sample bolus from breaking apart
during the transport process.

Tip Select the syringe size on the Communication page of the Surveyor Autosampler
Configuration dialog box. The autosampler ships with a 250 μL concentric syringe.

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Table 21. Syringe speeds for injections

Syringe size Minimum speed Maximum speed Default speed
(μL) (μL/s) (μL/s) (μL/s)
100 0.3 13.2 3.00
250 0.8 33.0 8.0
500 1.6 66.1 8.0
2500 8.2 330.8 25.0

For no waste injections, you can use a higher syringe speed to push the sample from the
autosampler injection port to the injection valve and a lower loop loading speed to meter the
sample into the sample loop. The range for the loop loading speed depends on the syringe size
(see Table 22).
Table 22. Loop loading speeds
Syringe size Minimum speed Maximum speed Default speed
(μL) (μL/s) (μL/s) (μL/s)
100 0.01 13.20 3.00
250 0.04 33.00 8.00
500 0.08 66.11 8.00
2500 0.41 330.80 25.00

Reservoir Content Page

Use the Reservoir Content page (see Figure 56) to enter descriptions for the contents of the
four 16 mL reservoir vials located on the right side of the tray compartment and the wash
solvent bottle located in the solvent platform at the top of the LC system stack. You can type
up to 80 characters in each box.

Figure 55 shows the relative size of the 1 liter wash bottle and the 16 mL reservoir vials.
Figure 55. Reservoir vials and wash solvent bottle

Wash bottle

Reservoir vials

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 To specify the solvents in the wash bottle and reservoir vials

1. Click the Reservoir Content tab.

The Reservoir Content page appears (see Figure 56).
Figure 56. Reservoir Content page for the autosampler

2. Identify the solvents contained in the 16 mL reservoir vials and the 1 L wash bottle by
typing their names in their respective boxes.

Timed Events Page for the Autosampler

You can use the TF terminals (see Figure 57) on the back panel of the autosampler to control
peripheral devices that the data system does not control.

The TF terminal output signal is LO (Closed) by default. To change the polarity of the TF
output signal to HI (Open), select the Timed Events Active High check box on the Signal
Polarity page of the Surveyor Autosampler Configuration dialog box (see “Signal Polarity
Page” on page 56).
Figure 57. Time function event terminals on the back panel of the autosampler

TF terminals

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Use the Timed Events page (see Figure 58) to specify the timed events for the time function
terminals (TF1 to TF4).
Figure 58. Timed Events page for the autosampler

 To control external devices (not controlled by your Thermo Scientific MS application)

1. Click the Timed Events tab.

The Timed Events page appears (see Figure 58).
2. Specify the appropriate timed events in the table.
3. Make the appropriate hardwire connections between the TF terminals on the back panel
of the autosampler and the external device.

Autosampler Timed Events Page Parameters

Table 23 describes the columns in the timed events table for the autosampler.
Table 23. Autosampler timed events table
Parameter Description
Table of timed events Use this table to set up timed events.
Time Specifies the time (in minutes) when the autosampler
TF terminal (TF1 to TF4) signals an event. Time 0.00 is
defined as the time when the autosampler issues an INJECT
OUT signal.

The autosampler issues the specified Timed Event signals after

issuing the Inject Out signal.

Default: 0
Range: 0 to 9999.0 minutes
TF1, TF2, TF3, and TF4 Specifies whether the event is on or off at the specified time.

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PDA Detector Instrument Method Parameters

Use the Surveyor PDA Plus Method page to specify the data acquisition settings for the
detector and to trigger external devices from the detector.

 To program the PDA detector to acquire absorbance data

1. In the view bar, click the Surveyor PDA Plus icon.
The view for the Surveyor PDA Plus Detector appears with the Surveyor PDA Plus
Method page displayed (see Figure 59).
Figure 59. Surveyor PDA Plus Method page with the default settings

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2. In the Run Length (min) box, type a run time from 0 to 600 minutes.
3. In the Filter Rise Time (sec) list, select a rise time from 0 to 10.0 seconds.
Rise time is inversely proportional to the amount of baseline noise. If your chromatogram
contains closely eluting peaks, minimize baseline noise while retaining maximum
resolution by selecting a rise time that is approximately one-tenth of the narrowest peak’s
width at half-height (FWHM). Increasing the rise time above this level increases peak
tailing, which can reduce the resolution of closely eluting peaks.
Figure 60 shows the effect of rise time on peak tailing.
Figure 60. Effect of rise time on peak tailing

0.1 s rise time

2.0 s rise time

5.0 s rise time

mAU

10.0 s rise time

Minutes

4. In the Units area, select the Wavelength/Absorbance option.

Note For information about using the Diode/Intensity option to perform

diagnostics, see “Creating a Display Method” on page 313. Methods that record light
intensities for the PDA detector have the .spda file extension.

5. To collect a wavelength scan, select the Collect Spectra Data check box, and then make
the following entries and selections:
a. In the Start Wavelength (nm) box, type a starting wavelength from 190 to 799 nm.
b. In the End Wavelength (nm) box, type an ending wavelength from 191 to 800 nm.
The ending wavelength must be greater than the starting wavelength.

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c. In the Wavelength Step (nm) box, type a value for the wavelength interval.
The default value is 1 nm. The maximum step size depends on the wavelength range
defined by the starting and ending wavelengths. The range is 1 to 610 nm for a scan
from 190 to 800 nm. If you are collecting spectral data for a spectral library, use a
wavelength step of 1 nm.
d. In the Sample Rate (Hz) list, select a sample rate.
For optimal integration of the chromatographic peaks, select a sample rate that
acquires a minimum of 20 points across the baseline width of the narrowest peak of
interest. For example, if the baseline width of the narrowest peak is 20 seconds, select
a sample rate of 1 Hz or higher.
Increasing the sampling rate increases the data file size.
e. In the Filter Bandwidth (nm) box, type a bandwidth.
Depending on the wavelength range defined by the starting and ending wavelengths,
the range is the subset of odd integers from 1 to 49 nm. The maximum scan range for
a particular bandwidth is limited as follows:
• Start Wavelength (minimum) = 190 nm + (bandwidth – 1)/ 2
• End Wavelength (maximum) = 800 nm – (bandwidth – 1)/ 2
Increasing the bandwidth decreases the spectral resolution (see Figure 61).
Figure 61. Spectra of toluene, effect of bandwidth on spectral resolution

1 nm bandwidth

11 nm bandwidth

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6. To collect discrete channel data, select one of the options in the Channels area, and then
make the following entries:
a. In the Sample Rate list, select a sampling rate (in data points per second). Higher data
rates for discrete channels do not add significantly to the data file size.
b. For each discrete channel (A, B, and C), type a wavelength from 190 to 800 nm in
the Wavelength (nm) box and a filter bandwidth in the Filter Bandwidth (nm) box.
Depending on the discrete wavelength, the acceptable bandwidth range is 1 to 49 nm
in odd-number increments with 1 nm meaning no filtering. Bandwidth values
outside the range of the detector are not allowed. For example, for the discrete
wavelength of 200 nm, the maximum bandwidth setting is 21 nm. At a bandwidth
setting of 21 nm, the reported absorbance value for 200 nm is a weighted average
from 190 to 210 nm. A value greater than 21 nm would be outside the lower range
limit of the detector, which is 190 nm.

For information about the Method page parameters, see these topics:
• PDA Detector Instrument Method Parameters
• Display Method Parameters
• Timed Events Table for the PDA Detector

For information about adding timed events to trigger external devices, see “Triggering an
External Device with the PDA Detector” on page 104.

PDA Detector Instrument Method Parameters

Table 24 describes the parameters for an instrument method. These parameters are available
when you select the Wavelength/Absorbance option in the Units area.
Table 24. PDA detector Method page parameters for an instrument method (Sheet 1 of 3)
Parameter Description
Run
Run Length Specifies the time in minutes that the PDA detector acquires data.

Default: 10.00 minutes

Range: 0.00 to 600.00 minutes

At the end of the run time, the PDA detector goes to the Ready for Download state.
Filter Rise Time Specifies the detector’s response time to the signal in seconds.

The selections are 0.00, 0.10, 0.20, 0.50, 1.00, 2.00, 5.00, and 10.00 seconds.

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Table 24. PDA detector Method page parameters for an instrument method (Sheet 2 of 3)
Parameter Description
Units
Wavelength/ Displays absorbance spectra with the wavelength in nanometers on the x axis and the
Absorbance absorbance in milli-absorbance units (mAU) on the x axis.

Default: Wavelength/Absorbance.

Select the Wavelength/Absorbance option for instrument methods.

Spectra (with Wavelength/Absorbance option)
Collect Spectral Data To collect scans having a specific wavelength range (nm), bandwidth (nm), scan rate (Hz),
and step (nm), select this check box.
Start Wavelength (nm) Specifies the first wavelength in nanometers of the scan range.

Default: 200 nm
Range: 190 to 799 nm
End Wavelength (nm) Specifies the last wavelength in nanometers of the scan range.

Default: 600 nm
Range: 191 to 800 nm

The end wavelength must be greater than the start wavelength.

Wavelength Step Specifies the wavelength interval between data points across the wavelength range.

Default: 1 nm

The maximum step size is the full width of the scan.

The highest spectral resolution is 1 nm and the lowest resolution is the full width of the
scan. When you specify a spectral scan from 200 to 300 nm at a step of 10 nm, the PDA
detector sends 11 scan wavelengths to the data system computer.
Sample Rate Specifies the number of data points per second that the PDA detector sends to the data
system for each scan wavelength.

For optimal integration of the chromatographic peaks, acquire 20 points across the baseline
width of the peak.

For the Surveyor PDA Detector Plus, the sample rates are 0.5, 1.0, 2.0, 4.0, 5.0, 10.0, and
20 Hz.

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Table 24. PDA detector Method page parameters for an instrument method (Sheet 3 of 3)
Parameter Description
Filter Bandwidth Specifies the bandwidth for the scan wavelengths.

Bandwidth values are limited to the subset of odd integers from 1 to 49. In addition, the
maximum scan range for a particular bandwidth is limited as follows:
Lower range = 190 nm + (bandwidth – 1) / 2
Upper range = 800 nm – (bandwidth – 1) / 2

The maximum scan range for a bandwidth of 49 nm is 214 to 776 nm.

Note Wider bandwidths decrease both spectral noise and the resolution of the spectra. In
general, the detector bandwidth should not exceed 10 percent of the bandwidth at
half-height of the narrowest spectral feature of interest.
Channels (with Wavelength/ Absorbance Units)
No Channels Specifies that no discrete channel measurements are to be acquired. When you select this
option, the parameters in the Channels area are unavailable.
One Channel Specifies the acquisition of one discrete channel. The data for Channel A is displayed in the
bottom view of the Display page in black.
Two Channels Specifies the acquisition of two discrete channels. The data for Channel B is displayed in the
bottom view of the Display page in red.
Three Channels Specifies the acquisition of three discrete channels. The data for Channel C is displayed in
the bottom view of the Display page in green.
Sample Rate Specifies the sample rate in Hz for all of the discrete channels selected (see sample rate in the
Spectra area).
[Ch. A, B, C] Specifies the discrete channel wavelength to be acquired.
Wavelength
Channel A default: 214
Channel B default: 254
Channel C default: 280

Range: 190 to 800 nm

[Ch. A, B, C] Specifies the bandwidth for the corresponding discrete channel. Bandwidth values are
Filter Bandwidth limited to the subset of odd integers from 1 to 49.

Default: 9 nm

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Display Method Parameters

Table 25 describes the parameters for a display method. These parameters are available when
you select the Diode/Intensity option in the Units area.
Table 25. PDA Method page parameters for a display method (Sheet 1 of 2)
Parameter Description
Run
Run Length Not applicable
Filter Rise Time Not applicable
Units
Units: Diode/Intensity Specifies the display units for the spectrum plots.

When you select the Diode/Intensity option, you can view the light intensity detected by
the photo diodes of the diode array. The x axis corresponds to the photo diode number
(2 to 511).

There are 512 diodes in the diode array. Diodes 0 and 1 are not used. Diode 2 corresponds
to wavelength 190 nm and diode 511 corresponds to 800 nm. This gives a spacing of
611 nm/510 diodes = 1.2 nm/diode. The PDA detector interpolates the data to give
integer values.
Spectra (with Diode/Intensity option)
Collect Spectral Data Select this check box to scan a range of diodes.
Start Diode Specifies the first diode in the scan range.
(diode num)
Default: 2
Range: 2 to 510, in increments of 1

Diode 2 corresponds to 190 nm.

End Diode Specifies the last diode in the scan range.
(diode num)
Default: 511
Range: 3 to 511, in increments of 1

Diode 511 corresponds to 800 nm.

Diode Step Specifies the interval between data points across the range of diode numbers.

The selections are 1, 2, 4, 5, or 10 diodes.

Sample Rate Not applicable

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Table 25. PDA Method page parameters for a display method (Sheet 2 of 2)
Parameter Description
Channels (with Intensity Units)
No Channels Specifies that no discrete channel measurements are to be acquired. When you select this
option, the parameters in the Channels area are unavailable.
One Channel Specifies the acquisition of one discrete channel. The data for Channel A is displayed in the
bottom view of the Display page in black.
Two Channels Specifies the acquisition of two discrete channels. The data for Channel B is displayed in the
bottom view of the Display page in red.
Three Channels Specifies the acquisition of three discrete channels. The data for Channel C is displayed in
the bottom view of the Display page in green.
Sample Rate Not applicable
[Ch. A, B, C] Specifies the diode that you want the detector to monitor.
Diode Number
Channel A default: 40
Channel B default: 55
Channel C default: 450

Range: 2 to 511, in increments of 1

Timed Events Table for the PDA Detector

Table 26 describes the timed events area at the bottom of the Surveyor PDA Plus Method
page.

Use the Timed Events area to program actuation of a back panel contact closure as a function
of either time or the absorbance level from one of the discrete wavelength channels. You can
use this feature to trigger an external device, such as a fraction collector, and to zero the
absorbance level during an acquisition run.

For information about connecting an external device to the PDA detector, refer to the
Surveyor PDA Plus Detector Hardware Manual.
Table 26. Timed events table on the Surveyor PDA Plus Method page (Sheet 1 of 2)
Parameter Description
Timed Events

Use this area to add, modify, and remove timed events. You can specify the time when the event occurs, the event
type, the channel, the absorbance level (mAU), and the delay settings. Click New to open the Timed Events dialog
box.
Timed Events table This table lists all the events in chronological order. You can add, modify, and remove events
by double-clicking the event setting you want to modify, or by using the New, Delete, and
Delete All buttons.

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Table 26. Timed events table on the Surveyor PDA Plus Method page (Sheet 2 of 2)
Parameter Description
Time Specifies the time in minutes when the detector triggers the event. The maximum time is
the data acquisition time specified in the Run Length box (see Figure 59 on page 95).

Default: 0.00 minutes

Type Specifies an event type: Event Off, Event On, Zero Data, or Level Trigger.

Use a Level Trigger event to specify the absorbance threshold level for triggering an event.
When you select a Level type event, you must specify the channel of the event, the
absorbance level that is to trigger the event, and the delay time that the event is to occur
after the absorbance level trigger event.

Use a Zero event to zero the absorbance from the detector.

Channel Note This list is available if you select Level Trigger in the [Event] Type list.
Specifies the discrete wavelength channel (Channel A, Channel B, or Channel C) that the
PDA detector monitors to activate the external event.
Level Note This box is available if you select Level Trigger in the [Event] Type list.
Specifies the absorbance level that triggers the external event.

Range: –2000 to 4000 milli-absorbance units (mAU)

Delay Note This box is available if you select Level Trigger in the [Event] Type list.
Specifies the delay time in seconds that is to occur between the activation of the event (by
the preset absorbance level being exceeded) and the actual change of the event output state
(at the back panel terminals of the PDA detector). This delay compensates for the time
interval between, for example, when a compound leaves the detector and when it reaches a
fraction collector.

Default: 0 seconds
Range: 0 to 65 535, in increments of 1
Buttons
New Click this button to open the Timed Event dialog box where you can add external events to
the external events table.
Delete Click this button to remove an external event from the external events table. Select the
external event that you want to remove, and then click Delete.
Delete All Click this button to remove all external events from the external events table. To remove all
events, click Delete All.

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3 Instrument Method Setup
Triggering an External Device with the PDA Detector

Triggering an External Device with the PDA Detector

The PDA detector can trigger an external device during a chromatographic run. For example,
you can program the PDA detector to trigger a fraction collector as an analyte begins to elute
from the LC column.

Note You can also zero the absorbance level for a discrete channel during an acquisition
run by adding a zero event to the Timed Events table.

 To add a timed event to the instrument method

1. In the Timed Events area of the Surveyor PDA Plus Method page (see Figure 62), click
New.
Figure 62. Timed Events area of the Method page

The Timed Event dialog box appears (see Figure 63).

Figure 63. Timed Event dialog box

2. In the Type list, select an event type.

The selections are Event Off, Event On, Zero Data, or Level Trigger.

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Triggering an External Device with the PDA Detector

3. In the Time (min) box, type the length of time after the chromatographic run starts that
the event is to occur.
The range is 0.00 to the run length time for the detector. The Event Off, Event On, and
Zero Data event types occur at this time. Because the Level Trigger event type occurs after
this time is exceeded, do not enter a time value that exceeds the expected time (for
example, the expected retention time of the analyte that you want a fraction collector to
collect) of the triggering event.
The Channel list, Level box, and Delay box are available for the Level Trigger event type.
For more information about the Level trigger type, see the next procedure.
4. To trigger an external device when the absorbance for a discrete channel reaches a specific
level, do the following:
a. In the Type list, select Level Trigger.
b. In the Channel list, select the discrete wavelength channel to be used to trigger the
event.
The available selections are A, B, or C.
c. In the Level (mAU) box, type a value for the absorbance value that triggers the event.
The default value is 0.00 mAU and the range is –2000 to 4000.00 mAU.
d. In the Delay (sec) box, type a time in seconds.
The delay time compensates for the time interval between, for example, when a
compound leaves the detector and when it reaches a fraction collector. The default
value is 0 and the range is the set of integers from 0 to 65 535.
5. To zero the absorbance level for all the wavelength channels that the detector is
monitoring at a particular time in the run, do the following:
a. In the Type list, select Zero Data.
b. In the Time box, type the time that you want the absorbance level to be zeroed.
6. Click OK to accept the new event and close the Timed Event dialog box.

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3 Instrument Method Setup
UV-Vis Detector Instrument Method Parameters

UV-Vis Detector Instrument Method Parameters

In the UV/Vis detector view, use the Method page to set up the instrument method
parameters for the UV/Vis detector (see Figure 64).
Figure 64. Instrument Setup view for the UV/Vis detector

 To open the UV/Vis Detector view

Click the Surveyor UV/Vis icon on the view bar.

 To set up the instrument method parameters for the UV/Vis detector

1. In the Rise Time (sec) list, select a rise time from 0 to 10.0 seconds.
Rise time is the response time of the detector, in seconds, to the signal. Increasing the rise
time decreases the baseline noise; however, setting the rise time to a value greater than
one-tenth the width of the chromatographic peak at half-height results in peak
broadening. The one-second default value is appropriate for most LC applications.
Figure 65 shows the effect of rise time on peak tailing.

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 3 Instrument Method Setup
UV-Vis Detector Instrument Method Parameters

Figure 65. Effect of rise time on band broadening

0.1 s rise time

2.0 s rise time

5.0 s rise time

mAU

Minutes

2. In the Data Rate (Hz) list, select a data rate from 4 to 20 points per second.
The optimal data rate depends on the expected baseline width of your chromatographic
peaks. For optimal integration, acquire a minimum of 20 data points across the baseline
width of the narrowest peak. For example, if the narrowest chromatographic peak has a
baseline width of 10 seconds, select a data rate of 2 Hz or higher.
3. To zero the baseline at a specific time point, select the Enable Autozero check box and
type a time in the Autozero Time (min) box.
The detector resets its output voltage to zero at this time point.
4. In the Program Type area, select one of the following options:
• To collect one chromatogram during a run, select the Single Wavelength
190 to 800 nm option. You can program time wavelength changes in the program
table.
• To collect two chromatograms in the UV range during a run, select the Dual
Wavelength UV 190 to 450 nm option. You can program time wavelength changes
in the program table.
• To collect two chromatograms in the visible range during a run, select the Dual
Wavelength Vis 366 to 700 nm option. You can program time wavelength changes
in the program table.
5. To zero the baseline when a programmed wavelength change occurs, select the Zero on
Wavelength Change check box.

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3 Instrument Method Setup
UV-Vis Detector Instrument Method Parameters

The detector does not zero the baseline on the first or last rows of a wavelength program.
If the wavelength program contains three or more rows, the detector zeroes the baseline
on the second row and all successive rows until it reaches the last row. The detector zeroes
its output signal even if the same wavelength is listed in the second through second to last
rows of the table.

UV-Vis Detector Instrument Method Parameters

Table 27 describes the parameters on the Method page for the UV/Vis detector.
Table 27. UV/Vis detector method parameters (Sheet 1 of 2)
Parameter Description
Rise Time Specifies the filtering in the time domain.

Default: 2.0 seconds

Selections: 0.0, 0.01, 0.1, 0.2, 0.5, 1.0, 2.0, 3.0, 4.0, and 5.0 seconds
Data Rate Specifies the number of points per second acquired per wavelength.

Default: 10 Hz

Selections: 20, 10, 6.67, 5, and 4 Hz

Enable Autozero
Enable Autozero When this check box is selected, the detector zeros the absorbance data at the specified time.
Autozero Time (min) Specifies the time when the detector zeros the absorbance data.

Default: 0 minutes
Range: 0 minutes to the run length
Program Type
Single Wavelength Specifies that the detector is to acquire data on one wavelength channel. The acquisition
UV/Vis 190–800 nm wavelength is time programmable.
Dual Wavelength UV Specifies that the detector is to acquire data on two wavelength channels in the UV range.
190–365 nm The acquisition wavelengths are time programmable.
Dual Wavelength Vis Specifies that the detector is to acquire data on two wavelength channels in the visible range.
366–700 nm The acquisition wavelengths are time programmable.
Other options
Zero on Wavelength When this check box is selected, the detector zeros the absorbance data at the times specified
Change in the Time column for rows 2 through the last time line.
Programmable wavelength table
Time Specifies the time when the detector is to start monitoring the wavelength or wavelengths
listed in the Wavelength 1 and Wavelength 2 columns.

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Saving the Instrument Method

Table 27. UV/Vis detector method parameters (Sheet 2 of 2)

Parameter Description
Wavelength 1 Specifies the wavelength that the detector is to start monitoring at the time specified in the
Time column.

To view the chromatogram for this wavelength in Qual Browser, select Wavelength 1 in the
Range list for the Chromatogram window.
Wavelength 2 Specifies the wavelength that the detector is to start monitoring at the time specified in the
Time column.

To view the chromatogram for this wavelength in Qual Browser, select Wavelength 2 in the
Range list for the Chromatogram window.

Saving the Instrument Method

The following procedure applies only to the Xcalibur data system. For other
Thermo Scientific mass spectrometry applications, refer to the Help.

 To save the instrument method

1. Choose File > Save As.

The Save As dialog box appears (see Figure 66).
Figure 66. Save As dialog box, showing the file extension for an instrument method

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3 Instrument Method Setup
Saving the Instrument Method

2. Browse to the following folder:

drive:\Xcalibur\methods
3. In the File Name box, type a file name.
4. Click Save.
The File Summary Information dialog box appears (see Figure 67).
Figure 67. File Summary Information dialog box

5. In the Description box, type a description of the method file.

6. Click OK.
If the Authorization Manager – Comment check box is selected, the File Save – Audit
Trail dialog box appears (see Figure 68).

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 3 Instrument Method Setup
Saving the Instrument Method

Figure 68. File Save – Audit Trail dialog box

7. In the Comment box, type a comment concerning the changes you made to the
instrument method.
8. Click Continue to close the File Save – Audit Trail dialog box and save the instrument
method.

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 4

Sample Preparation Routines

Sample preparation routines are part of the instrument method. Use the Sample Preparation
page to create a multitask routine, containing up to 512 tasks. A task consists of a sample
preparation operation and its associated parameters.

The ability to add 512 tasks to a sample preparation routine gives you considerable flexibility;
however, the arrangement of the tasks in the task list must follow a logical order. For example,
you cannot add a task that deposits liquid before you add a task that draws liquid. In addition,
if you are using the 250 μL dual-concentric syringe that ships with the autosampler, you must
follow an additional set of rules that maintain the proper positioning of the inner and outer
plungers of the syringe.

Contents
• Opening the Sample Preparation Page
• Sample Preparation Rules
• Building the Sample Preparation Routine
• Sample Locations for the Sample Preparation Tasks
• Draw, Eject, and Transfer Volumes for Sample Preparation Tasks
• Syringe Speed Range for Sample Preparation Tasks
• Sample Preparation Routine Example

Opening the Sample Preparation Page

The Sample Preparation page is part of the instrument method.

 To open the Sample Preparation page

1. Open the autosampler view from your data system.

2. Click the Sample Preparation tab.
The Sample Preparation page appears (see Figure 69). For a new method, in the Prep
Operations list, the Deposit Liquid in Sample task is highlighted, and its parameters are
listed below the Add To Task List button.

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4 Sample Preparation Routines
Opening the Sample Preparation Page

Figure 69. Sample Preparation page of the Surveyor Autosampler view

Deposit liquid in sample task parameters Empty task list

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 4 Sample Preparation Routines
Sample Preparation Rules

Sample Preparation Rules

The maximum volume that the autosampler can deposit, draw, or transfer during a sample
preparation task depends on the syringe type, the task requested, and the previous step in the
sample preparation method.

Table 28 categorizes the sample preparation tasks into three groups based on whether the task
uses the inner bore only, the outer bore only, or either bore of the dual-plunger concentric
syringe. For information about the dual-plunger concentric syringe, see “Interchangeable
Syringe” on page 14.
Table 28. Sample preparation tasks arranged in groups according to bore usage
Inner bore only Outer bore only Inner or outer bore
Draw from Sample Mix at Sample Draw from Reservoir
Transfer from Mix at Reservoir Deposit Liquid in Sample
Sample to Sample
Transfer from Wash Needle Deposit Sample in Reservoir
Sample to Reservoir
Flush to Waste Transfer from Reservoir to Sample
Transfer from Reservoir to Reservoir

For the 250 μL concentric syringe, these rules restrict the arrangement of the tasks in the
sample preparation list:
• For tasks performed with the inner bore of the dual-concentric syringe, the maximum
volume (sample + air bubble) that the autosampler can draw, deposit, or transfer is
limited to the nominal size of the syringe, 250 μL.
• For tasks performed with either bore, if the sum of the requested volume
(liquid + air bubble) plus any volume left in the needle tubing from a previous step is
less than the nominal syringe size, the dual-plunger concentric syringe uses the small
bore. If this volume is greater than the nominal syringe size, the syringe uses the outer
bore.
• For tasks performed with the outer bore of the dual-plunger concentric syringe, the
maximum volume (sample + air bubble) that you can draw, deposit, or transfer is limited
to 500 μL, except for the Wash Needle and Flush to Waste tasks.
• Crossover between bores is not allowed. This means that you cannot add a task that uses
the outer syringe bore immediately following a task that uses the inner syringe bore.
To switch from the inner bore to the outer bore of the syringe, you must insert a
Flush to Waste step or a Wash Needle step. These tasks home the position of the syringe
plungers.

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4 Sample Preparation Routines
Building the Sample Preparation Routine

Building the Sample Preparation Routine

Sample preparation routines are part of the instrument method (see “Autosampler Instrument
Method Parameters” on page 85). A sample preparation routine consists of a list of tasks
performed in order by the autosampler before it makes an injection.

 To build a sample preparation routine

1. Do one of the following:

• To modify an existing sample preparation routine, go to step 2.
–or–
• To create a new sample preparation routine, go to step 3.
2. Import the sample preparation routine from a stored instrument method as follows:
a. Click Import.
The Open files dialog box appears.
b. Browse through your Methods folder and select the appropriate instrument method.
Then click Open.
Only the sample preparation task list contained in the stored instrument method is
imported into the current instrument method.
3. For each task that you want to add to the sample preparation routine, do the following:
a. In the Prep Operations list, select a task.
Table 29 lists the thirteen tasks that you can use to create a sample preparation
routine. When you select a task, the parameters available for the task appear below
the Add to Task List button.

Tip The syringe position and nominal volume limit the task order and transfer
volume:
• If the previous task used the small bore of the syringe, you must add a
Flush to Waste or a Wash Needle task before you can add a task that requires
the use of the large bore of the syringe. These tasks home the concentric
syringe plungers.
• If the previous task used the small bore of the syringe, the transfer volume of
the current task is limited to the nominal syringe size or less. See “Sample
Preparation Rules” on page 115 for more information.

b. Make the appropriate selections and entries for each task parameter.
c. Click Add To Task List.
The task appears in the task list in the Method area.

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 4 Sample Preparation Routines
Building the Sample Preparation Routine

4. Edit the task list as needed:

• To remove the last task in the list, click Remove Task.
• To remove a specific task, select the task, and then click Remove Task.
• To clear the entire task list, click Clear All Tasks.

Tip To save an instrument method, the sample preparation routine must conform
to the rules described in “Sample Preparation Rules” on page 115.

Sample Preparation Parameters

Table 29. Sample Preparation page (Sheet 1 of 5)
Parameter Description
Prep Operations

Use this area to select and add tasks to the task list in the Method area.

You can add up to 512 tasks to a sample preparation routine; however, the arrangement of the tasks in the task list
must follow a logical order or you will not be able to save the instrument method. For example, a draw task must
precede a deposit task. In addition, if you are using the 250 μL concentric syringe that comes with the autosampler,
you must follow an additional set of rules that allow for the proper positioning of the inner and outer plungers of the
syringe. (See “Sample Preparation Rules” on page 115).

If you are using the 2500 μL, single plunger syringe, to transfer volumes larger than 500 μL, add an optional tubing
extension assembly to the needle tubing.
Task List Description
Deposit Liquid in Deposits liquid in a sample vial or well.
Sample Parameter Reference, range, or selections
Sample Location “Sample Locations for the Sample Preparation Tasks” on page 122
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125
Needle Height Default: 2 mm
Range: 0 to 18 mm
Deposit Liquid in Deposit liquids in a reservoir vial.
Reservoir Parameter Reference, range, or selections
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Destination RV1, RV2, RV3, or RV4
Reservoir
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125

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4 Sample Preparation Routines
Building the Sample Preparation Routine

Table 29. Sample Preparation page (Sheet 2 of 5)

Parameter Description
Draw from Reservoir Draws liquid from a reservoir vial or the wash bottle.
Parameter Reference, range, or selections
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Source Reservoir RV1, RV2, RV3, RV4, or Bottle
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125
Air Bubble Range: 0 to 10 μL
Draw from Sample Draws liquid from a vial or well.
Parameter Reference, range, or selections
Sample Location “Sample Locations for the Sample Preparation Tasks” on page 122
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125
Needle Height Default: 2 mm
Range: 0 to 18 mm
Air Bubble Range: 0 to 10 μL
Flush to Waste Flushes the needle tubing and homes the syringe.

When the concentric syringe plungers are in the home position and the needle tubing is
flushed, the autosampler can next perform any of the sample preparation tasks, with the
exception of the deposit tasks.
Parameter Reference, range, or selections
Volume Range: 100 to 6000 μL
Reservoir bottle, RV1, RV2, RV3, or RV4
Syringe Speed 1.65 to 661.38 μL/s for the concentric syringes
0.83 to 330.85 μL/s for the 2500 μL standard syringe

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 4 Sample Preparation Routines
Building the Sample Preparation Routine

Table 29. Sample Preparation page (Sheet 3 of 5)

Parameter Description
Mix at Sample Mixes the contents of a vial or well.

To mix a sample, the autosampler draws a specified volume of the sample into the needle
tubing at a specified speed, and then ejects the sample back into the same location at a
specified speed.
Parameter Reference, range, or selections
Sample Location “Sample Locations for the Sample Preparation Tasks” on page 122
Volume The maximum volume is 490 μL for the concentric syringes and
1490 μL for the standard 2500 μL syringe.
Draw Speed The draw or delivery speed range is from 1.65 to 661.38 μL/s for the
Delivery Speed concentric syringes, and from 0.83 to 330.85 μL/s for the standard
2500 μL syringe.
Cycles Range: 1 to 10
Needle Height Default: 2 mm
Range: 0 to 18 mm
Mix at Reservoir Mixes the contents of a reservoir vial.
Parameter Reference, range, or selections
Volume The maximum volume is 490 μL for the concentric syringes and
1490 μL for the standard 2500 μL syringe.
Destination RV1, RV2, RV3, or RV4
Reservoir
Draw Speed The draw or delivery speed range is from 1.65 to 661.38 μL/s for the
concentric syringes, and from 0.83 to 330.85 μL/s for the standard
Delivery Speed
2500 μL syringe.
Cycles Range: 1 to 10
Needle Height Default: 2 mm
Range: 0 to 18 mm
Transfer from Reservoir Transfers liquid from one reservoir to another.
to Reservoir Parameter Reference, range, or selections
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Source Reservoir bottle, RV1, RV2, RV3, or RV4
Destination RV1, RV2, RV3, or RV4
Reservoir
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125

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4 Sample Preparation Routines
Building the Sample Preparation Routine

Table 29. Sample Preparation page (Sheet 4 of 5)

Parameter Description
Transfer from Reservoir Transfers liquid from a reservoir vial or the wash bottle to a vial or well.
to Sample Parameter Reference, range, or selections
Sample Location “Sample Locations for the Sample Preparation Tasks” on page 122
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125
Needle Height Default: 2 mm
Range: 0 to 18 mm
Source Reservoir bottle, RV1, RV2, RV3, or RV4
Transfer from Sample Transfers liquid from a vial or well to a reservoir vial.
to Reservoir Parameter Reference, range, or selections
Sample Location “Sample Locations for the Sample Preparation Tasks” on page 122
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Destination RV1, RV2, RV3, or RV4
Reservoir
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125
Needle Height Default: 2 mm
Range: 0 to 18 mm
Air Bubble 0 to 10 μL
Transfer from Sample Transfers liquid from one vial or well to another vial or well.
to Sample Parameter Reference, range, or selections
Source Sample “Sample Locations for the Sample Preparation Tasks” on page 122
Destination “Sample Locations for the Sample Preparation Tasks” on page 122
Sample
Volume “Draw, Eject, and Transfer Volumes for Sample Preparation Tasks” on
page 123
Syringe Speed “Syringe Speed for Tasks that Can Use Either Plunger” on page 125
Source Vial Needle Default: 2 mm
Height Range: 0 to 18 mm
Air Bubble 0 to 10 μL
Destination Vial Default: 2 mm
Needle Height Range: 0 to 18 mm

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 4 Sample Preparation Routines
Building the Sample Preparation Routine

Table 29. Sample Preparation page (Sheet 5 of 5)

Parameter Description
Wait Time Pauses the sample preparation routine for a period of time, for example, for a reaction to
occur.

Range: 0 to 1000 minutes

Wash Needle Washes the exterior of the needle with the solvent in a reservoir vial or the wash bottle.
Parameter Reference, range, or selections
Volume Range: 100 to 6000 μL
Reservoir bottle, RV1, RV2, RV3, or RV4
Button
Add To Task List Use the Add To Task List button to add a task to the sample preparation routine.
Method

Use the Method area to display the parameters of a task, remove a task, clear all tasks in the task list, or import the
sample preparation routine from a stored instrument method.

The Method area consists of the (sample preparation) task list, the Remove Task button, the Clear All Tasks button,
and the File Name (read only) box and Import (method) button.
File Name box Displays the name of the selected instrument method that contains the sample preparation
routine that you want to import into the current instrument method.
Buttons
Remove Task Use this button to remove a task from the task list in the Method area.
Clear All Tasks Use this button to clear all tasks from the task list in the Method area.
Import Use this button to open the Open dialog box where you can select an instrument method
with the sample preparation routine that you want to add to the current instrument
method.

After you select an instrument method and click Import, the File Name (read only) box
displays the file name of the instrument method you want to import.

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4 Sample Preparation Routines
Sample Locations for the Sample Preparation Tasks

Sample Locations for the Sample Preparation Tasks

For the sample preparation tasks, you can select an absolute or a relative location.

For the Relative Location option, the selections are Current, Current + 1, Current + 2, and
Current + 3. Current is the sample location in the current sequence row. Current + 1 is the
next adjacent vial or well location in the tray, and so on. For example, if the vial location in
the current sequence row is B:1, Current is B:1, then Current + 1 is B:2, and so on.

For the Absolute Location option, you specify an absolute vial or well location. The vial or
well locations depend on the tray configuration (see Table 30).

Tip Remember to place a vial at the selected location.

Table 30. Vial and well positions

Tray configuration Vial or well positions
Standard 1.8 mL vials A:1 to E:20
96 Well Plate A:A1 to C:H12
384 Well Plate A:A1 to C:P24

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 4 Sample Preparation Routines
Draw, Eject, and Transfer Volumes for Sample Preparation Tasks

Draw, Eject, and Transfer Volumes for Sample Preparation Tasks

The maximum volume that the autosampler can deposit, draw, or transfer during a sample
preparation task depends on the syringe type, the task requested, and the previous step in the
sample preparation method:
• For tasks performed with the inner plunger of the concentric syringe, the maximum
volume (liquid + air bubble) that the autosampler can draw, deposit, or transfer is limited
to the nominal size of the syringe.
• For tasks performed with the outer plunger of the concentric syringe, the maximum
volume (liquid + air bubble) that the autosampler can draw, deposit, or transfer is limited
to 500 μL, except for the Wash Needle and Flush to Waste tasks, which are limited to a
range of 100 to 6000 μL, and the Mixing tasks, which are limited to a maximum of
490 μL.

Table 31 lists the maximum volumes by task.

Table 31. Draw, eject, and transfer volumes for sample preparation tasks (Sheet 1 of 2)
Maximum volume (μL) Maximum volume (μL)
Task
with the inner plunger with the outer plunger
Draw from Sample Nominal size of the concentric syringe minus the current N/A
contents (liquid + air bubble) of the needle tubing
Transfer from Sample Nominal size of the concentric syringe minus the current N/A
to Sample contents (liquid + air bubble) of the needle tubing
Transfer from Sample Nominal size of the concentric syringe minus the current N/A
to Reservoir contents (liquid + air bubble) of the needle tubing
Mix at Sample N/A 490
Mix at Reservoir N/A 490
Tip If the ToolTip specifies a range of 0.0 to 0.0, the contents of the needle tubing already
equals 500 μL or the previous task used the inner plunger of the syringe. If the previous
task used the inner plunger, insert a Flush to Waste or a Needle Wash task to home the
syringe.

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4 Sample Preparation Routines
Syringe Speed Range for Sample Preparation Tasks

Table 31. Draw, eject, and transfer volumes for sample preparation tasks (Sheet 2 of 2)
Maximum volume (μL) Maximum volume (μL)
Task
with the inner plunger with the outer plunger
Wash Needle N/A 6000
Flush to Waste N/A 6000
Draw from Reservoir Nominal size of the concentric syringe minus the current 500 μL minus the current
contents (liquid + air bubble) of the needle tubing contents of the needle tubing
Deposit Liquid in Total contents (liquid + air bubble) of the needle tubing Total contents
Sample from previous steps (liquid + air bubble) of the
needle tubing from previous
steps
Deposit Sample in Total contents (liquid + air bubble) of the needle tubing Total contents
Reservoir from previous steps (liquid + air bubble) of the
needle tubing from previous
steps
Transfer from Nominal size of the concentric syringe minus the current 500 μL
Reservoir to Sample contents (liquid + air bubble) of the needle tubing
Transfer from Nominal size of the concentric syringe minus the current 500 μL
Reservoir to Reservoir contents (liquid + air bubble) of the needle tubing

Syringe Speed Range for Sample Preparation Tasks

The syringe speed range for sample preparation tasks depends on whether the task can use
either syringe plunger or only the inner plunger.

If you enter a speed that is invalid for the volume you are transferring, an error message
appears.

For information about the syringe speed range for the sample preparation tasks, see these
topics:
• Syringe Speed for Tasks that Can Use Either Plunger
• Syringe Speed for Tasks that Use the Inner Plunger

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 4 Sample Preparation Routines
Syringe Speed Range for Sample Preparation Tasks

Syringe Speed for Tasks that Can Use Either Plunger

The syringe speed range is determined by the type of syringe and the volume requested. For a
concentric syringe, the autosampler can use either the outer or inner plunger to draw liquid
into or expel liquid from the needle tubing.

For the tasks listed in Table 32, the autosampler uses the following:
• The outer plunger if the volume of liquid + air being transported is greater than the
nominal syringe size
• The inner plunger if the volume of liquid + air being transported is less than or equal to
the nominal syringe size
Table 32. Tasks that can use either syringe plunger
Task
Draw from Reservoir
Deposit Liquid in Sample
Deposit Sample in Reservoir
Transfer from Reservoir to Sample
Transfer from Reservoir to Reservoir

Table 33 lists the speed range for the sample preparation tasks that can use either plunger of
the concentric syringe.

Note The ToolTips for the speed parameters list a range of allowable speeds. The
minimum speed listed is valid for only the inner plunger, and the maximum speed listed is
valid for only the outer plunger of the configured syringe.

If you enter a volume that triggers the use of the outer plunger and a speed that is valid for
only the inner plunger, an error message appears when you attempt to add the task to the
sample preparation list.

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4 Sample Preparation Routines
Syringe Speed Range for Sample Preparation Tasks

Table 33. Syringe speed ranges for tasks that can use either syringe plunger
Syringe size Volume Minimum speed Maximum speed Default speed
(μL) (liquid + air) (μL/s) (μL/s) (μL/s)
100 ≤ 100 0.33 13.25 3.0
100 >100 1.65 661.38 250
250 ≤ 250 0.83 33.09 8.0
250 >250 1.65 661.38 250
500 ≤ 500 1.65 66.10 8.0
500 >500 1.65 661.38 250
2500 0 to 1500 0.83 331 25.0
(standard)

Syringe Speed for Tasks that Use the Inner Plunger

The autosampler uses the inner plunger of the concentric syringe to perform the following
tasks:
• Draw From Sample
• Transfer From Sample To Sample
• Transfer From Sample To Reservoir

The syringe size determines the default syringe speed and the syringe speed range
(see Table 34).

Use a syringe speed lower than the default for viscous samples. Also, use a syringe speed lower
than the default for samples of very low viscosity or surface tension to prevent the sample
bolus from breaking apart during the transport process.

Note You select the size of the syringe by using the Syringe Type list on the
Communication page of the Surveyor AS Configuration dialog box.

Table 34. Syringe speeds for tasks that use the inner plunger of the concentric syringe
Syringe size Minimum speed Maximum speed Default speed
(μL) (μL/s) (μL/s) (μL/s)
100 0.33 13.25 3
250 0.33 33.10 8
500 1.65 66.11 8

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Sample Preparation Routine Example

Sample Preparation Routine Example

The following procedure describes how to create a sample preparation routine to dilute
samples tenfold.

 To add a sample preparation routine that dilutes samples tenfold

1. From the Surveyor AS view, click the Sample Preparation tab.

The Sample Preparation page appears.
2. Open the .meth file that you want to modify.
In step 3 through step 6, you add the sample preparation tasks to the task list.
3. Add a task that transfers an aliquot of sample solution from the original sample location
to another sample location:
a. In the Prep Operations list, select Transfer from Sample to Sample. The task
parameters appear below the Add To Task List button.
b. Keep all the default parameter settings for the Transfer from Sample to Sample task,
except those that are shown below (see Figure 70).

Parameter Setting Autosampler action

Source Sample
Location Relative Location Withdraws sample from the
current vial location listed in the
Location Current
sequence table.
Destination Sample
Location Relative Location Deposits sample in the
current + 1 vial location listed in
Location Current + 1
the sequence table.
Volume 50 Transfers 50 μL of sample.

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Sample Preparation Routine Example

Figure 70. Settings for the Transfer from Sample to Sample task

Default settings

c. Click Add To Task List to add the task to the sample preparation routine.
When the autosampler performs this task, it withdraws 50 μL of sample from the
current vial location in the sequence table and deposits it in the current + 1 vial
location.
4. Add a task that transfers diluent (with the inner syringe plunger) from a reservoir vial to
the sample location:
a. In the Prep Operations list, select Transfer from Reservoir to Sample. The
parameters for the task appear below the Add To Task List button.

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Sample Preparation Routine Example

b. Keep all the default parameter settings for the Transfer from Reservoir to Sample task,
except those that are shown below (see Figure 71).

Tip When accuracy is important, keep the transfer volume below the nominal
syringe size, so that the autosampler uses the inner syringe plunger. Solvent
transfers made with the inner plunger are more accurate than solvent transfers
made with the outer plunger because the stepper motor for the inner plunger
takes smaller steps and provides finer control than the stepper motor for the outer
plunger.

Parameter Setting Autosampler action

Source reservoir RV1 Draws solvent from
reservoir vial 1.
Destination Sample
Location Relative Location Deposits solvent in the
current + 1 vial location listed in
Location Current + 1
the sequence table.
Volume 225 Transfers 225 μL of solvent.

Figure 71. Settings for the Transfer from Reservoir to Sample task

Default settings

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Sample Preparation Routine Example

c. To add this task to the sample preparation routine twice, click Add To Task List
twice.
When the autosampler performs this task, it uses the inner syringe plunger to
withdraw 225 μL of diluent from the reservoir vial 1 and deposit the diluent in the
current + 1 vial location. Performing this task twice transfers a total of 450 μL of
diluent to the current + 1 vial location.
5. Add a task that homes the position of the concentric syringe plungers as follows:

Note The syringe cannot switch between bores without first homing the position of
the two syringe plungers. The Transfer from Reservoir to Sample task that you added
in step 4 uses the inner syringe bore. The Mix at Sample task that you add in step 6
uses the outer syringe bore. The Wash Needle task that you add in this step homes the
position of the two syringe plungers.
a. In the Prep Operations list, select Wash Needle. The task parameters appear below
the Add To Task List button.
b. Keep all the default parameter settings for the Wash Needle task (see Figure 72).
Figure 72. Default parameter settings for the Wash Needle task

Default settings

c. Click Add To Task List to add this task to the sample preparation routine.

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6. Add a task that mixes the solution in the new sample location:
a. In the Prep Operations list, select Mix at Sample. The task parameters appear below
the Add To Task List button.
b. Keep all the default parameter settings for the Mix at Sample task, except those listed
below (see Figure 73).

Parameter Setting Autosampler action

Sample Location
Location Relative Location Aspirates and expunges 250 μL
Location Current + 1 sample from the current + 1 vial
location listed in the sequence
Volume 250 table 10 times.
Cycles 10

c. Click Add To Task List to add this task to the sample preparation routine.
When the autosampler performs this task, it aspirates and expunges 250 μL of the
sample solution in the current + 1 vial location 10 times.
Figure 73. Settings for the Mix at Sample task

Default settings

Default setting

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Sample Preparation Routine Example

7. Review the task list by expanding the tasks in the Method list (see Figure 74).
Figure 74. Method area with an expanded task list

8. Save the instrument method (see “Saving the Instrument Method” on page 109).
To perform this sample routine, you must insert empty vials into your sample tray.
For example, to dilute five samples, place the samples in vial locations A1, A3, A5, A7,
and A9. Place empty vials in vial locations A2, A4, A6, A8, and A10. Fill reservoir vial 1
with an appropriate diluent that matches the sample matrix.
If you do not want to inject the diluted samples, create a five-line sequence that lists the
vial locations of the original samples (A1, A3, A5, A7, and A9). The original samples are
not injected.
If you want to inject the diluted samples, create a ten-line sequence that lists all the vial
locations (A1 to A10). Ensure that you use the method that contains the sample
preparation routine on the odd rows only (Rows 1, 3. 5. 7. and 9).

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 5

Daily Operation
During the initial installation of the Surveyor Plus LC system, a Thermo Fisher Scientific field
service engineer sets up the solvent lines, primes the pulse dampener of the Surveyor MS
Pump Plus, and calibrates the PDA detector.

Note The pulse dampener of the Surveyor LC Pump Plus does not require priming.

To prepare the system for daily operation, check the status of the devices, warm up the
detector’s lamps, and remove air from the solvent lines.

To maintain optimal performance of the system, calibrate the PDA detector on a monthly
basis or whenever you move the detector, and check the light throughput to the diode array
whenever you move the detector, observe an increase in detector noise, or replace the flowcell
or lamps (see “Verifying the Performance of the PDA Detector” on page 313).

Prime the pulse dampener of the Surveyor MS Pump Plus on a monthly basis or when you
notice an increase in pump pulsation.

Contents
• Turning On the Power to Each LC Device
• Initiating Communication with the Data System
• Checking the Status of the LC Devices
• Turning Devices On, Off, or into Standby from the Info View
• Filling the Solvent Reservoir Lines with Fresh Solvent
• Priming the Pulse Dampener of the Surveyor MS Pump Plus
• Accessing the Direct Controls

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Turning On the Power to Each LC Device

Turning On the Power to Each LC Device

 To turn on the power to the LC devices

1. Depress the power switch on each device.

2. Observe the status LEDs for each device.
Shortly after you turn on the power, all the LEDs except the Comm LEDs turn green. In
addition, the autosampler syringe goes through its initialization process.
3. Verify that the Power LEDs, the Lamp LED, and the Degas LED turn green:
• If any of the Power LEDs remain amber, make sure that the power line to the affected
device or devices is connected.
• If the Degas LED on the pump is flashing amber, the degas unit has failed to produce
a vacuum. Call your local Thermo Fisher Scientific representative for repairs.
• If the Lamp LED remains amber, both of the lamps are turned off. If the lamps
are off, turn them on when you check the detector’s status from the data system.

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Initiating Communication with the Data System

Initiating Communication with the Data System

You control the LC devices from your Thermo Scientific mass spectrometry application. The
only manual control for the autosampler and UV/Vis detector are their ON/OFF power
switches. The PDA detector has two additional manual controls: the filter wheel and the
attenuators. The filter wheel controls the position of the holmium oxide calibration solution.
The attenuators control the light throughput to the diode array. The pump has a purge valve.

The following procedure describes how to verify instrument communications from the
Thermo Xcalibur data system.

 To open the data system and verify instrument communications

1. From your computer desktop, choose Start > Programs > Thermo Xcalibur > Xcalibur.
The Thermo Xcalibur Roadmap window appears (see Figure 75).
Figure 75. Thermo Xcalibur Homepage window with the Roadmap and Info view displayed
Information view Roadmap

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Shortly after you open the data system, the Comm LEDs on the front panels of the LC
devices turn green if the devices are powered on and connected to the data system
computer.
2. If the Comm LEDs remain amber, do the following:
• Verify that the Ethernet communication cables for the Surveyor PDA Plus Detector
or Surveyor UV/Vis Plus Detector, Surveyor Autosampler Plus, and Surveyor LC
Pump Plus are connected to the Ethernet switch and that the Ethernet switch is
connected to the data system computer. Verify that the RS-232 cable for the Surveyor
MS Pump Plus is connected to the data system computer.
• Verify that the stack addresses in the configuration for the Surveyor Autosampler
Plus, Surveyor PDA Plus Detector or Surveyor UV/Vis Plus Detector, and Surveyor
LC Pump Plus are correct.
For information about configuring your instrument devices, see Chapter 2, “Thermo
Foundation Instrument Configuration.”

Checking the Status of the LC Devices

After you turn on the power to the LC devices and open the Xcalibur data system, check the
status of each device.

Tip You can also view the system pressure on the pump page of the Inlet Direct Control
dialog box in the Tune window for your Thermo Scientific mass spectrometer.

To check the status of the LC devices, follow these procedures:

1. Opening the Status Page of the Information View
2. Viewing the Status of Each Device

Opening the Status Page of the Information View

You can monitor the status of the LC devices from the Information view of the Xcalibur data
system. This view is normally displayed on the left side of the Home Page window. If this view
is not displayed, the view has been closed. From the Home Page window, choose View > Info
View to open the Information view.

 To display the Status page of the Information view

1. In the Home Page window, open the Information view by doing one of the following:
• Choose View > Info View.
–or–
• Click the Information view icon ( ) in the toolbar.

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2. Click the Status tab.

The Status page appears (see Figure 76).
Figure 76. Status page of the Information View

If you have just recycled the power and have not yet downloaded a method, you see the
following status readouts on the Status page:
• Initializing is displayed while the data system attempts to connect to an instrument
module.
• Lamp Warm-up is displayed for the detector while the deuterium lamp is igniting.
• Ready to Download is displayed after the data system establishes communication
with an instrument device and after each run has ended.

Viewing the Status of Each Device

The Surveyor Plus LC system contains an autosampler and an analytical pump. In addition,
your system might contain an optional detector.

Check the status of each device by clicking its name in the device tree list. The status
information for a specific device is displayed in the lower portion of the Status page.

These topics describe the status views for the LC devices:

• Autosampler Status View
• Surveyor MS Pump Plus
• Surveyor LC Pump Plus
• Surveyor PDA Plus Detector Status View
• Surveyor UV/Vis Plus Detector Status View

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Autosampler Status View

The Status view for the autosampler (see Figure 77) contains four pages:
• AS Status Page
• Oven Page
• Tray Page
• Error Log (Autosampler) Page
Figure 77. Status page showing the AS Status page for the Surveyor Autosampler

See Table 35.

Table 35 describes the states that might appear below the Surveyor AS listing.

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Table 35. Autosampler states

State Meaning
Initializing The data system is attempting to establish communication with the autosampler.
Ready to Download The autosampler is ready to start a run.
Ready to Run This state appears momentarily when the data system is downloading an instrument
method for an LC/MS system.
Running The autosampler is making an injection. If the instrument method contains a time function
for the autosampler, this state is displayed until the time function has expired.
Direct Control The direct control or calibration windows are open.
Busy The autosampler is performing a direct control operation.
Error An error condition other than the loss of communication has occurred.
Off The data system has attempted to connect to the autosampler and failed five times.

AS Status Page
Table 36 describes the readbacks on the AS Status page of the autosampler status view.
Table 36. Status readbacks for the autosampler (Sheet 1 of 3)
Readback Description
Target injection
Vial Position Displays the current vial or microplate well position. For information about the vial and
well notation, see “Vial and Well Notation” on page 6.
Injection Volume Displays the injection volume for the current injection.

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Table 36. Status readbacks for the autosampler (Sheet 2 of 3)

Readback Description
Other
AS State Displays the following run conditions:
Waiting for The autosampler is waiting for the data system to download an
Download instrument method.
Waiting for Door The Verify Door Is Closed check box is selected (see “Communication
Close Page” on page 52) and the tray compartment door is open.
Waiting for The Wait for Temperature Ready check box is selected (see
Temperature “Communication Page” on page 52) and the tray compartment
temperature, column oven temperature, or both have not yet reached
the set temperature. This state remains until the temperature
controlled areas are equilibrated to the set temperature.
Injecting The autosampler is making an injection.
Waiting for Pump The autosampler has loaded the sample loop and is waiting for the
Inject Hold Release signal from the pump.
Ready The autosampler is ready to make an injection.
Error An error condition other than the loss of communication has
occurred. For example, if you enable the maintenance log and you
attempt to start a run when one or more of the maintenance counters
has exceeded its limit, an error condition occurs.
Door State Displays one of the following:
Open The Verify Door Is Closed check box on the Communication page of
the Surveyor Autosampler Configuration dialog box in the Instrument
Communication window is selected and the tray compartment door is
open.

For information about selecting the Verify Door Is Closed check box,
see “Communication Page” on page 52.
Closed The Door State displays Closed for these conditions:
• The Verify Door Is Closed Check box is selected and the tray
compartment door is closed.
• The Verify Door Is Closed check box is clear and the door is open
or closed.

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Table 36. Status readbacks for the autosampler (Sheet 3 of 3)

Readback Description
Maintenance Due Displays Yes or No.
No The Enable Maintenance Log check box is clear, none of the
maintenance counters has exceeded its limit, or both.
Yes The Enable Maintenance Log check box is selected and one or more of
the maintenance counters has exceeded its limit.

The autosampler cannot start a run until you zero the counter or clear
the Enable Maintenance Log check box.

For information about setting up the maintenance counters, see

“Autosampler Maintenance Information” on page 309. For
information about clearing the Enable Maintenance Log check box,
see “Communication Page” on page 52.
Firmware Version Displays the firmware version of the autosampler.

Oven Page
Figure 78 shows the Oven page of the status view for the autosampler.
Figure 78. Oven page

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Table 37 describes the readbacks on the Oven page of the autosampler status view.
Table 37. Oven page readbacks
Readback Description
Control On Displays Yes or No.

You can turn off the oven temperature control by doing one of the following:
• Using the Turn Off Oven Temperature command (see “Controlling the Tray and
Oven Compartment Temperatures” on page 199)
• Running an instrument method that has the Enable Column Oven Control check
box cleared
Current Temperature (C) Displays the temperature monitored by the autosampler’s internal temperature sensor.
Set Temperature (C) Displays the user-specified temperature.

You can change the set temperature by doing one of the following:
• Using the Set Oven Temperature command (see “Controlling the Tray and Oven
Compartment Temperatures” on page 199)
• Running an instrument method that has a temperature setting for the column oven
Ready Status Displays one of the following:
Ready The oven compartment temperature has reached the set temperature, you
did not select the Wait for Temperature Ready check box when you
specified the configuration settings for the autosampler, or both.

For information about the Wait for Temperature Ready check box, see
“Communication Page” on page 52.
Not Ready The oven compartment temperature has not reached the set temperature.

Tray Page
Figure 79 shows the Tray page of the autosampler status view.
Figure 79. Tray page

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Table 38 describes the readbacks on the Tray page of the autosampler status view.
Table 38. Tray page parameters
Readback Description
Control On Display Yes or No.

You can turn off the tray temperature control by doing one of the following:
• Using the Turn Off Tray Temperature command (see “Controlling the Tray and Oven
Compartment Temperatures” on page 199)
• Running an instrument method that has the Enable Column Oven Control check
box cleared
Current Temperature (C) Displays the temperature monitored by the autosampler’s internal temperature sensor.
Set Temperature (C) Displays the user-specified temperature.

You can change the set temperature by doing one of the following:
• Using the Set Tray Temperature command (see “Controlling the Tray and Oven
Compartment Temperatures” on page 199)
• Running an instrument method that has a temperature setting for the column oven
Ready Status Displays one of the following:
Ready The oven compartment temperature has reached the set temperature,
you did not select the Wait for Temperature Ready check box when
you specified the configuration settings for the autosampler, or both.

For information about the Wait for Temperature Ready check box,
see “Communication Page” on page 52.
Not Ready The oven compartment temperature has not reached the set
temperature.

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Error Log (Autosampler) Page

Figure 80 shows the Error Log page for the autosampler.
Figure 80. Error Log page

Table 39 describes the parameters on the Error Log page.

Table 39. Error Log page parameters
Parameter Description
Index Lists the order of the error events, in increments of 1. The index
number for the first error event that occurs after you clear the log
is 1.
Application code Refer to your autosampler hardware manual for information
about the application codes.
Buttons
Refresh Loads the error log messages stored by the autosampler.
Clear Clears the error log.

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Surveyor MS Pump Plus

For information about the status of the pump and the degassing unit, see these topics:
• General Page of the Pump Status View
• Extended Page of the Pump Status View
• Degasser Page of the Pump Status View

General Page of the Pump Status View

Figure 81 shows the General page of the pump status view.
Figure 81. General page pump status view

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Table 40 describes the status readbacks on the General page of the pump status view.
Table 40. General page of the pump status view (Sheet 1 of 2)
Readback Description
Status Displays the pump status as follows:
Ready The pump is ready for a run.
Running Isocratic The solvent flow is on, but the pump is not running a gradient
program.
Homing The pump pistons are moving toward the home position.
Running Gradient The pump is running the solvent conditions specified in the
gradient program of an instrument method. The gradient
program can contain isocratic or gradient solvent conditions.
Low Pressure Error The system pressure has fallen below the minimum pressure
setting for more than one minute.

If you are controlling the pump from the Direct Control dialog
box, the status returns to Ready after the pump stops pumping.
The error is posted to the pump’s event log.
High Pressure Error The system pressure has risen above the maximum pressure
setting.
Note When a pressure error occurs, one of the following occurs:
• If you are controlling the pump from the Direct Control dialog box, the status
returns to Ready after the pump stops pumping. The error is posted to the
pump’s event log.
• If you are controlling the pump from the Sequence Setup window, the
Acquisition Server dialog box appears.
Run Time Displays the elapsed time since the last instrument method downloaded, you turned the
device on from the Status page of the Information view, or you started the pump from the
Direct Control dialog box.
Flow Rate Displays the user-specified flow rate. For an instrument method, the flow rate changes
linearly between time lines.
Pressure Displays the pressure monitored by the pump.
Pressure SD Displays the standard deviation of the pressure monitored by the pump.
Start Gradient A check appears in this box when the pump receives the Start gradient signal from the
autosampler.
Pump Ready A check appears in this box when the pressure monitored by the pump reaches the stability
level specified in the instrument method.

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Table 40. General page of the pump status view (Sheet 2 of 2)

Readback Description
Release Injection A check appears in this box when the pump sends the Release Injection signal to the
autosampler.
Start 2nd Pump A check appears in this box when Pump 1 triggers Pump 2 to start its pump program.

Extended Page of the Pump Status View

Figure 82 shows the Extended page of the pump status view.
Figure 82. Extended page of the pump status view

Table 41 describes the status readbacks on the Extended page of the pump status view.
Table 41. General page of the pump status view
Readback Description
Flow Rate Displays the user-specified flow rate. Flow rate changes are linear between time lines in the
gradient program.
Tip You can change the percent composition of solvents A, B, C, and D by running an
instrument method or by downloading new solvent conditions from the (Inlet) Direct
Control dialog box.
Pressure Displays the pressure monitored by the pump.
Pressure SD Displays the standard deviation of the pressure monitored by the pump.
Solvent A, B, C, or D Displays the user-specified percent composition of solvent A, B, C, or D.
Stroke Count Displays the stroke count for the pump pistons.

When the stroke count exceeds 1 000 000, the number is displayed in red.

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Degasser Page of the Pump Status View

Figure 83 shows the Degasser page of the pump status view.
Figure 83. Degasser page of the pump status view

Table 42 describes the status readbacks on the Degasser page of the pump status view.
Table 42. General page of the pump status view
Readback Description
Degasser Status The states of the degasser are as follows:
Ready The vacuum level has reached a sufficient level to degas
the mobile phase solvents.
Not Connected The pump is not communicating with the data system
computer.
Error An error condition has occurred.
Vacuum Level Displays the vacuum level of the solvent degassing chambers.
Motor Speed Displays the motor speed of the vacuum degasser.

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Surveyor LC Pump Plus

Figure 84 shows the Status view for the Surveyor LC Pump Plus. You can view the system
pressure from this view.
Figure 84. Surveyor LC Pump Plus Status view

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Table 43 describes the readbacks on the pump status view.

Table 43. Surveyor LC Pump Plus status readbacks
Readback Description
Status Displays the following pump states:
READY The pump is ready to take a command.
Not Connected The pump is not communicating with the data system
computer.
Off The pump pistons are stopped.
Running Isocratic The pump flow is on.
Running Gradient The pump is running a gradient program.
Degasser Displays the following degasser states: READY or Not Connected.
Run Time Displays the run time.
Time Remaining Displays the remaining time for the run.
Flow Displays the user-specified flow rate.
Pressure Displays the pressure monitored by the pump.
A Displays the user-specified percent composition for solvent A.
B Displays the user-specified percent composition for solvent B.
C Displays the user-specified percent composition for solvent C.
D Displays the user-specified percent composition for solvent D.

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Surveyor PDA Plus Detector Status View

Figure 85 shows the Status view for the Surveyor PDA Plus Detector. You can view the status
of the lamps and the wavelength and dark current calibrations from this view.
Figure 85. Surveyor PDA Plus Detector Status view

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Table 44 describes the readbacks for the PDA detector.

Surveyor UV/Vis Plus Detector Status View

Table 44. PDA detector status readbacks
Readback Description
Connection status Displays whether the PDA detector is communicating with the data system computer.

The connection states are Connected or Not Connected.

Ready or Not Ready to Ready to Start Run The detector is ready to start a run or is currently
Start Run acquiring data.
Not Ready to Start Run The deuterium lamp is warming up.
Wavelength The wavelength calibration is valid or invalid.
Calibration
Dark Current The dark current calibration is valid or invalid.
Calibration
Method is Valid N/A
Filter Wheel Position The filter wheel has two positions:
Position 1 (Run) Light passes through the flowcell onto the diode array.
Position 2 (Closed) Light passes through the holmium oxide filter onto the
diode array.
Deuterium Lamp The deuterium lamp states are as follows:
The deuterium lamp is off.

The deuterium lamp is starting up, which requires about

1.5 min.

The deuterium lamp is on.

Tungsten Lamp The tungsten lamp states are as follows:

The tungsten lamp is on.

The tungsten lamp is off.

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Figure 86 shows the Status view for the Surveyor UV/Vis Plus Detector. You can view the
absorbance level of the chromatographic baseline from this view.
Figure 86. Surveyor UV/Vis Plus Detector Status view

Table 45 describes the status readbacks for the Surveyor UV/Vis Plus Detector.
Table 45. UV/Vis detector status readbacks
Readback Description
State Displays the following states: Ready for Run and Off.
Run Time Displays the elapsed run time.
Data Type Displays the program type specified in the current instrument method: Dual UV (D2),
Dual Visible (W), or Single Wavelength.
Lambda 1 (nm) Displays the current wavelength setting for the Wavelength 1 channel.
Lambda 2 (nm) Displays the current wavelength setting for the Wavelength 2 channel.
Absorbance 1 (AU) Displays the current absorbance level for the Wavelength l channel.
Absorbance 1 (AU) Displays the current absorbance level for the Wavelength 2 channel.

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Turning Devices On, Off, or into Standby from the Info View

Turning Devices On, Off, or into Standby from the Info View
You can turn on certain activities for a device from its device listing in the Info View. To use
this feature, the device must be powered on and communicating with the data system.

 To turn on a device from the Info View

Right-click the device listing on the Status page and choose Turn Device On.
Depending on the device, the following actions occur:
• When you turn on the pump, it begins pumping solvents from the last set of
downloaded parameters.
• When you turn on the detector, its lamps turn on.
• When you turn on the autosampler, it adjusts its controlled temperature zones to the
last set of downloaded parameters.

 To place a device in Standby mode

Right-click the device listing on the Status page and choose Turn Device into Standby.
Depending on the device, the following actions occur:
• When you place the pump in Standby mode, it stops pumping.
• When you place the detector in Standby mode, nothing happens.
• When you place the autosampler in Standby mode, nothing happens.

 To turn a device off

Right-click the device listing on the Status page and choose Turn Device Off.
Depending on the device, the following actions occur:
• When you turn off the pump, it stops pumping.
• When you turn off the detector, the lamps turn off.
• When you turn off the autosampler, nothing happens.

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Filling the Solvent Reservoir Lines with Fresh Solvent

Filling the Solvent Reservoir Lines with Fresh Solvent

After filling the solvent bottles, connecting the solvent lines to the degasser, and configuring
the pump to communicate with the data system, prepare the pump for operation by removing
the air from the solvent lines that connect the solvent reservoir bottles to the pump’s degassing
unit.

For information about using the direct controls to start the solvent flow from the Surveyor
MS Pump Plus, see “Pump Direct Controls” on page 185.

 To quickly draw fresh solvent into the solvent reservoir lines

1. For any solvent line that you want to pull solvent through, disconnect the tubing that is
connected to the corresponding degasser outlet port.
2. Connect a Luer-Lok™ fitting to the degasser outlet port.
3. Connect a 10 mL syringe to the Luer-Lok fitting, and pull solvent through the line.
4. Remove the Luer-Lok fitting from the outlet port.
5. Reconnect the solvent line to the degasser outlet port.

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Priming the Pulse Dampener of the Surveyor MS Pump Plus

Priming the Pulse Dampener of the Surveyor MS Pump Plus

Before you can operate the Surveyor MS Pump Plus, you must prime its built-in pulse
dampener. Priming the pulse dampener involves filling the dampening coil (see Figure 87)
with a solvent, such as methanol or isopropanol. After the coil is filled with solvent, it
effectively dampens pressure pulsations from the rest of your system.

Closing the pulse dampener flush valve after you fill the coil shuts the dampening coil off
from the mobile phase stream. Because a permeable membrane separates the mobile phase
stream from the dampening coil, the solvent in the coil slowly diffuses into the mobile phase
stream. When the pump is in continuous or frequent use, prime the pulse dampener on a
monthly basis.

Note Do not fill the pulse dampener with an aggressive acid or a buffered solution. The
recommended filling solvents are methanol, acetonitrile, or isopropyl alcohol. If you
accidentally fill the pulse dampener with an acidic or buffered solvent, flush the loop with
a miscible solvent, and then refill it with methanol, acetonitrile, or isopropyl alcohol.

Figure 87. Pulse dampening assembly of the Surveyor MS Pump Plus

Dual valve Diffusion barrier

cartridge cartridge

Manual bleeder valve 2 mL dampening loop

(for priming)

 To prime the pulse dampener of the Surveyor MS Pump Plus

1. Fill a solvent bottle with particulate-free, HPLC-grade methanol.

2. Connect an HPLC column or a flow restrictor to the LDA outlet.
3. Insert the tip of the 10 mL syringe into the tubing connected to the manual bleeder valve
(see Figure 88).

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Figure 88. Manual bleeder valve with attached tubing

Outlet of pulse dampener

Manual bleeder valve with

attached tubing

4. Open the valve by turning it counterclockwise.

5. To open the direct controls for the Surveyor MS Pump Plus, do one of the following:
• From the Surveyor MS Pump Plus view, choose Surveyor MS Pump Plus >
Direct Control. The Direct Control dialog box appears.

Note For information about using the Direct Control dialog box for the Surveyor
MS Pump Plus, see “Pump Direct Controls” on page 185.

–or–
• From the tune window for your Thermo Scientific mass spectrometer, choose
Setup > Inlet Direct Control. The Inlet Direct Control dialog box that contains
tabbed pages for each configured LC device appears. Click the Surveyor MS Pump
Plus tab.

Note For information about using the Inlet Direct Control dialog box, see
Chapter 12, “Making a Single Injection from the Tune Window.”

6. Start pumping 100% methanol at a flow rate of 1000 μL/min.

7. Fill the loop completely to expel any air that might be trapped in the dampener loop.
8. Set the flow rate to one that is appropriate for your system.
9. Close the manual bleeder valve (see Figure 87 on page 156) by turning the valve
clockwise. Always keep the pulse dampener valve closed during normal operation.

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Accessing the Direct Controls

Accessing the Direct Controls

You can access the direct controls for each instrument from the Instrument Setup window.
You can use the direct controls to start and stop the solvent flow from the LC pump, move the
autosampler’s XYZ arm, turn the detector’s lamps on and off, flush the autosampler’s syringe,
and so on.

For information about using the direct controls to prepare your LC system for daily operation,
see the Chapter 6, “Direct Controls.”

 To access the direct controls

1. Depending on the data system, do one of the following:

• If you are controlling your instrument from the Xcalibur data system, do the
following:

a. If it is not already open, open the Roadmap view by clicking the

Roadmap button in the toolbar.
b. Click the Instrument Setup button on the toolbar or the larger
Instrument Setup icon in the Roadmap View.

The Instrument Setup window opens to the first module displayed in

the view bar (see Figure 89). The view bar is a vertical bar on the left
side of the Instrument Setup window. It contains an icon for each
configured device. When you click a device icon, a green triangle
appears in the lower-right corner of the icon, and the device view
appears.

• If you are controlling your instrument from a Thermo Scientific data system other
than Xcalibur, open the instrument control area.
The instrument control area opens to the first module displayed in the view bar on
the left side of the window.

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Figure 89. Instrument Setup window open to the Surveyor AS Method page of the Surveyor AS view

2. To open the view for the device of interest, click its corresponding icon in the view bar.
The view for the specific device appears.
3. Access the direct controls for each device from the menu bar of the device view as follows:

Device Menu Reference

Surveyor LC Pump Plus Choose > Surveyor LC Pump > “Surveyor LC Pump Plus Direct
Direct Control > Operation. Controls” on page 185
Surveyor MS Pump Plus Choose Surveyor MS Pump > “Surveyor MS Pump Plus Direct
Direct Control. Controls” on page 190
Surveyor PDA Plus Detector Choose Surveyor PDA Plus > “PDA Detector Direct Controls” on
Direct Control. Then click the page 162
Configuration tab.
Surveyor UV/Vis Plus Detector Choose Surveyor UV/Vis > “UV-Vis Detector Direct Controls” on
Direct Control. page 183
Surveyor Autosampler Plus Choose Surveyor AS > Direct Control. “Autosampler Direct Controls” on
page 192

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Direct Controls
You can control some device features without downloading an instrument method. For
example, you can turn the lamps on or off, set the solvent conditions for the pump, start and
stop the solvent flow from the pump, and control the autosampler’s temperature zones and its
XYZ arm by using the direct controls provided by the data system.

For information about accessing the direct controls for each device, see “Accessing the Direct
Controls” on page 158.

Contents
• PDA Detector Direct Controls
• UV-Vis Detector Direct Controls
• Pump Direct Controls
• Autosampler Direct Controls

Note For instructions on loading samples into the autosampler, see “Loading the
Autosampler” on page 210.

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PDA Detector Direct Controls

The Direct Control dialog box for the PDA detector contains the following pages: Display,
Configuration, Information, and Calibration.

 To open the Direct Control dialog box for the PDA detector

1. Open the PDA detector view.

2. From the menu bar, choose Surveyor PDA Plus > Direct Control (see Figure 90).
Figure 90. Surveyor PDA Plus menu

The Surveyor PDA Plus Direct Control dialog box opens to the Display page
(see Figure 91).
Figure 91. Surveyor PDA Plus Control dialog box tabs

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Table 46 lists the direct control procedures by the page where they are performed.
Table 46. Direct control procedures
Page Procedure
Display Page “Checking the Chromatographic Baseline” on page 168
“Verifying the Performance of the PDA Detector” on page 313
Configuration Page “Turning the Lamps On or Off ” on page 163
“Resetting the Lamp Usage Hours” on page 164
“Changing the Polarity of the Analog Outputs” on page 164
“Testing the Analog Outputs” on page 165
“Setting the Lamp Startup Time” on page 166
Information Page “Viewing, Exporting, and Clearing the Error Log for the PDA Detector” on page 171
“Checking the Firmware Version of the PDA Detector” on page 171

For information about using the Calibration page to determine the wavelength accuracy of
the detector and the dark current produced by the diode array, see “Calibrating the PDA
Detector” on page 319.

Turning the Lamps On or Off

Use the Configuration page of the Surveyor PDA Plus Direct Control dialog box to turn each
lamp on or off.

 To turn the lamps on or off

1. Open the Configuration page of the Surveyor PDA Plus Direct Control dialog box
(see “Configuration Page” on page 171).
2. Click Turn On for the associated lamp.
When you turn on the deuterium lamp, its Status readback reads Starting during the
30-second ignition period, and then it changes to On. If there is a problem with either
lamp, its Status readback reads Failed.

Note The intensity of the deuterium lamp falls off very slightly over a period of time
after the lamp is turned on. Plan to wait at least one hour for the lamp to stabilize
after a cold start before collecting data in the spectral range of the deuterium lamp.

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Resetting the Lamp Usage Hours

Use the Configuration page of the Surveyor PDA Direct Control dialog box to reset the lamp
usage hours.

 To reset the lamp usage hours (lifetime hours elapsed)

1. Open the Configuration page of the Surveyor PDA Direct Control dialog box
(see “Configuration Page” on page 171).
2. Click Reset Lifetime for the associated lamp.
The stored total run time for the associated lamp resets to zero, and the Last Lifetime
Reset readback is updated to the current date and time.

Tip Avoid indiscriminately clicking the Reset buttons. Click Reset only after you
replace the associated lamp with a new one.

Changing the Polarity of the Analog Outputs

Use the Configuration page of the Surveyor PDA Direct Control dialog box to change the
polarity of the analog outputs.

There are two output signal terminals on the back panel of the PDA detector: Event and
Ready (see Figure 92).
Figure 92. Event and Ready terminals on the back panel of the PDA detector
Ready terminal

Event terminal

2 3 2 3
0 1

0 1
4

4
5 6

5 6
9

7 8 7 8

 To change the polarity of the analog outputs

1. Open the Configuration page of the Surveyor PDA Direct Control dialog box
(see “Configuration Page” on page 171).
If the output polarity is Active Low, the Set Active High button is available. If the output
polarity is Active High, the Set Active Low button is available.

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2. Under Analog Outputs (see Figure 93), do one of the following:

• Click Set Active High to change the output polarity from Active Low to Active
High.
–or–
• Click Set Active Low to change the output polarity from Active High to Active Low.
Figure 93. Analog Outputs area on the Configuration page

Testing the Analog Outputs

Use the Configuration page of the Surveyor PDA Plus Direct Control dialog box to change
the polarity of the analog outputs.

 To test the analog outputs

1. Open the Configuration page of the Surveyor PDA Plus Direct Control dialog box
(see “Configuration Page” on page 171).
2. Under Analog Outputs (see Figure 93), do the following:
• Click Turn On or Turn Off to trigger the external device.
• Click Zero DACs to calibrate external instruments, such as an SS420X analog to
digital converter.
When you click Zero DACs, the DACs outputs are set to zero for about 20 seconds.
You can extend this calibration time by clicking the button again.

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Setting the Lamp Startup Time

Use the Lamp Startup Time dialog box to set the startup time for the lamps.

If you do not change the lamp startup time, the data system automatically turns the lamps on
at 4:55 PM on weekdays.

 To open the Lamp Startup Time dialog box

1. Open the Configuration page of the Surveyor PDA Plus Direct Control dialog box
(see “Configuration Page” on page 171).
2. In the Programmed Lamp Startup area, click Change (see Figure 94).
Figure 94. Programmed Lamp Startup area of the Configuration page

The Lamp Startup Time dialog box appears (see Figure 95).
Figure 95. Lamp Startup Time dialog box

 To set the startup time for the lamps

1. In the Xcalibur Should Start the Lamps At box, click the hours or minutes text to
highlight it.

Tip To change both the hours and the minutes, change one time field, and then click
OK to accept the setting and close the dialog box. Then open the dialog box a second
time and change the other time field.

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2. To change the numeric values, do one of the following:

• Use the up or down arrow to the left of the time entry to scroll to the time value that
you want.
–or–
• Press the UP or DOWN key on your computer keyboard to scroll to the time value
that you want.
–or–
• Type the numeric value that you want.
3. To change AM to PM or the reverse, highlight the current setting, and then type AM
or PM.
4. To change the day of the week or to turn off the lamp startup feature, in the On These
Days list, select Never, Weekdays, or Everyday.
5. Click OK to apply the new lamp startup time.

Lamp Startup Time Parameters

Table 47 describes the parameters in the Lamp Startup Time dialog box.
Table 47. Lamp Startup Time dialog box parameters
Parameter Description
Xcalibur Should Start the Lamps At Specifies the time that the Xcalibur data system
automatically turns the lamps on.

Default: 4:55 PM
On These Days Specifies the days that the Xcalibur data system
automatically turns the lamps on. The selections are
Never, Weekdays, and Every Day.

Default: Weekdays
Buttons
OK Applies the settings and closes the dialog box.
Cancel Cancels the applied time value or date.

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Checking the Chromatographic Baseline

Use the Display page of the Direct Control dialog box to check the chromatographic baseline
(see “Display Page” on page 176).

 To check the stability of the chromatographic baseline before starting a sequence run

1. Open the Instrument Setup window of the Xcalibur data system.

2. In the view bar, click the icon for the LC pump, and then open the Direct Control dialog
box for the LC pump.
3. Start the solvent flow from the LC pump. Use the chromatographic conditions specified
on first line pump program in the instrument method.
For information about starting the solvent flow from the LC pump, refer to the Help for
the pump.
4. In the view bar of the Instrument Setup window, click the icon for your PDA detector.
The PDA detector view of the Instrument Setup window appears with the Method page
displayed.
5. From the menu bar, choose Surveyor PDA Plus > Direct Control.
The Direct Control dialog box appears.
6. Click the Display tab.
The Display page appears (see Figure 96).
Figure 96. Control area buttons on the Display page

7. In the Control area, click Load Method.

The Open Display Method dialog box appears (see Figure 97).

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Figure 97. Open Display Method dialog box

8. Select the instrument method that you plan to use in your acquisition sequence.
9. Click Open to download the method to the PDA detector and close the dialog box.
10. In the Control area, click Start Data.
The graphical display begins to update. The spectral scan appears in the top pane and the
chromatographic data for the discrete channel wavelengths appears in the bottom pane.
When you click Start Data, the Start Data button changes to the SNAPSHOT button
and the Zero Data button is available (see Figure 98).
Figure 98. Display page with data displaying for an instrument method
Instrument method with
a .meth file extension

Spectral data

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11. To zero the absorbance level, click Zero Data.

The Current method readback displays Zeroed Data Display (see Figure 99).
Figure 99. Effect of clicking the Zero Data button

12. To stop data acquisition, click Stop Data.

If the noise level is too high, check the light throughput to the diode array.

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Viewing, Exporting, and Clearing the Error Log for the PDA Detector
You can access an error log for the PDA detector from the Xcalibur data system.

 To view the error log

1. Open the Information page of the Surveyor PDA Direct Control dialog box (see
“Information Page” on page 181).
2. Click Request Log.

 To export the log to a Microsoft Excel Spreadsheet

Click Export Log.

 To clear the error log

Click Clear Log.

Checking the Firmware Version of the PDA Detector

 To check the firmware version of the PDA detector

Open the Information page of the Direct Control dialog box for the PDA detector
(see “Information Page” on page 181).
The firmware version of the PDA detector is displayed in the lower-right portion of the
Information page.

Configuration Page
Use the Configuration page of the Surveyor PDA Plus Direct Control dialog box to perform
these procedures:
• Turning the Lamps On or Off
• Resetting the Lamp Usage Hours
• Changing the Polarity of the Analog Outputs
• Testing the Analog Outputs
• Setting the Lamp Startup Time

 To open the Configuration page of the Direct Control dialog box

1. Open the Surveyor PDA Direct Control dialog box (see “PDA Detector Direct Controls”
on page 162).
2. Click the Configuration tab.
The Configuration page appears (see Figure 100).

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Figure 100. Configuration page

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Configuration Page Parameters

Table 48 describes the parameters on the Configuration page.
Table 48. Configuration page of the Direct Control dialog box for the PDA detector (Sheet 1 of 4)
Parameter Description
Lamp Maintenance

Use the controls in this area to turn the lamps on and off and to reset the lamp lifetime hours after you replace a lamp.
Deuterium Lamp
Status readback Indicates the status of the deuterium lamp.
Graphic Text Meaning
Off The deuterium lamp is off.

Starting The deuterium lamp is starting up,

which requires about 1.5 min.
On The deuterium lamp is on. When the
status is On, the Turn Off button is
available. When the status is Off, the
Turn On button is available.
Last Lifetime Reset Displays the date and time that the deuterium lamp was last reset.
readback
Lifetime Hours Elapsed Displays the cumulative time in hours that the deuterium lamp has been in the On state
since you clicked the Reset Lifetime button.
Turn On/Off button Turns on the deuterium lamp if its current status is Off.

Turns off the deuterium lamp if its current status is On.

Reset Lifetime button Resets the date and time monitored by the Last Reset readback and the Lifetime readback.
Note Click Reset Lifetime whenever you replace the deuterium lamp. This resets the Last
Reset readback to the current date and time and restarts the Lifetime readback at zero.

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Table 48. Configuration page of the Direct Control dialog box for the PDA detector (Sheet 2 of 4)
Parameter Description
Tungsten Lamp
Status readback Indicates the status of the tungsten lamp, as follows:
Graphic Test Meaning
On The tungsten lamp is on.

Off The tungsten lamp is off.

When the status is On, the Turn Off

button is available. When the status
is Off, the Turn On button is
available.
Last Lifetime Reset Displays the date and time that the tungsten lamp was last reset.
readback
Lifetime Hours Elapsed Displays the cumulative time in hours that the tungsten lamp has been in the On state since
you clicked the Reset Lifetime button.
Turn On/Off button Turns on the tungsten lamp if its current status is Off.

Turns off the tungsten lamp if its current status is On.

Reset Lifetime button Resets the date and time monitored by the Last Reset readback and the Lifetime readback.
Note Click Reset Lifetime whenever you replace the tungsten lamp. This resets the Last
Reset readback to the current date and time and restarts the Lifetime readback at zero.
Analog Outputs

Use the controls in this area to configure and test the Event and Ready outputs.

Determine if the external device is triggered by contact closure or a TTL (transistor - transistor - logic) signal. If the
external device requires a TTL signal, determine the polarity of the signal: active high or active low.
Note For TTL connections:
• Logic level zero (0) is less than +0.8 Vdc (reading from Ground).
• Logic level one (5) is approximately +5 Vdc (+2.4 Vdc minimum from Ground).
Possible configurations of the Event and Ready outputs include the following:
Output state Output polarity Vdc
Off Active High +5

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Table 48. Configuration page of the Direct Control dialog box for the PDA detector (Sheet 3 of 4)
Parameter Description
Ready Output
Turn On and Turn Off Indicates whether the Ready output state is On or Off. If the Ready output state is On, the
buttons Turn Off button is available. If the Ready output state is Off, the Turn On button is
available.
Ready Output Indicates whether the Ready output polarity is Active High or Active Low. If the Ready
readback output polarity is Active Low, the Set Active High button is available. If the Ready output
polarity is Active High, the Set Active Low button is available.
Set Active Low or Set Set the polarity of the Ready Output signal.
Active High buttons
Note The output polarity must match the polarity (either Active High or Active Low) of the instrument connected
to the Ready output connection on the back panel of the PDA detector. The signal terminal is the high connection
and the ground (GND) terminal is the low connection. The autosampler requires active low remote inputs.
Event Output

Use the controls in this area to specify the parameters for output events.

If the external device is triggered by a contact closure, connect the PDA EVENT terminal (pin 8) to the positive pin
on the external device input, and connect one of the PDA GND terminals (either of pins 1 or 7) to the external
device negative pin.

If the external device is triggered using a TTL signal, connect the PDA +5V output (pin 2) to the positive Input
terminal of the external device, and connect the PDA EVENT output (pin 8) to the negative Input terminal of the
external device.
Turn On and Turn Off Indicates whether the Event output state is On or Off. If the Event output state is On, the
buttons Turn Off button is available. If the Event output state is Off, the Turn On button is
available.
Event Output readback Indicates whether the Event output polarity is Active High or Active Low. If the Event
output polarity is Active Low, the Set Active High button is available. If the Event output
polarity is Active High, the Set Active Low button is available.
Set Active Low or Set Set the polarity of the Event Output signal.
Active High buttons
Note The output polarity must match the polarity (either Active High or Active Low) of the instrument connected
to the Event output connection on the back panel of the PDA detector. The signal terminal is the high connection
and the GND Terminal is the low connection.
Short DACs Output
Zero DACs button To calibrate external instruments, such as an SS420X analog to digital converter, use the
controls in this area to short the DACs outputs to zero for about 20 seconds.

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Table 48. Configuration page of the Direct Control dialog box for the PDA detector (Sheet 4 of 4)
Parameter Description
Programmed Lamp Startup
Programmed Lamp Displays the current lamp startup program and provides controls to create a lamp startup
Startup program that automatically turns on the lamps for operation at a specified time and day
(never, weekdays, every day).
Change Opens the Lamp Startup Time dialog box where you can specify a lamp startup time
(see “Setting the Lamp Startup Time” on page 166).

Display Page
Use the Display page to perform these procedures:
• “Checking the Chromatographic Baseline” on page 168
• “Adjusting the Light Throughput to the Diode Array” on page 315

 To open the Display page

1. Open the Surveyor PDA Direct Control dialog box (see “PDA Detector Direct Controls”
on page 162).
2. Click the Display tab.
The Display page appears (see Figure 101).

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Figure 101. Display page

Display Page Parameters

Table 49 describes the parameters on the Display page.
Table 49. Display page parameters (Sheet 1 of 4)
Parameter Description
Control
Control The buttons in this area provide control of the display method (.spda).
Load Method Loads the display method or the data acquisition parameters of an instrument method to
the detector.
Start Data Initiates the graphical display of the intensity data or the wavelength data.

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Table 49. Display page parameters (Sheet 2 of 4)

Parameter Description
Snapshot Saves a comma-separated values file named PDASnapshot.csv to the following folder on
the data system computer:
drive:\Xcalibur\data

A date and time stamp are appended to the file name. The format of the date and time
stamp is MMDDYYHHMMSS. MM is the month. DD is the day of the month. YY are the
last two digits of the year. HH is the hour in military time. MM are minutes. SS are
seconds. You can open this file with the Excel™ application.

For a wavelength/absorbance method, the file contains the absorbance values for the spectral
scan and the discrete channel wavelengths at the moment that you clicked Snapshot.

For an intensity/diode method, the file contains the intensity values for the scan of the
diode array and the intensity values for up to three individual diodes.
Note The Snapshot button is available only after you click the Start Data button and the
graphical display has started updating.
Zero Data Zeros the absorbance data.

After you click Zero Data, the Current Method status box displays the message Zeroed Data
Display.
Note This button is only available in the wavelength/absorbance mode.
Stop Data Stops the updating of the graphical display.

After you click Stop Data, the Current Method status box displays the message Stopped
Data Display.
Levels (mAU)
Channel A/B/C level This graphical display shows the intensity or absorbance level of each discrete channel, A, B,
or C, specified in the method.
Lamp Lifetimes (hours)
Deuterium Displays the cumulative time in hours that the Deuterium lamp has been in the On state
since you clicked the Reset button.
Note Click Reset Lifetime on the Configuration page whenever you replace the
deuterium lamp. This resets the Last Reset readback to the current date and time and sets
the Lifetime readback to zero.
Tungsten Displays the cumulative time in hours that the tungsten lamp has been in the On state since
you clicked Reset Lifetime.
Note Click the Reset Lifetime button on the Configuration page whenever you replace
the tungsten lamp. This resets the Last Lifetime Reset readback to the current date and
time and restarts the Lifetime readback to zero.

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Table 49. Display page parameters (Sheet 3 of 4)

Parameter Description
Status (bottom left)
Status area Displays the status of the PDA detector and the lamps.
Connection Displays the communication status of the PDA detector. Depending on whether the data
system can connect to the PDA detector, the status displays Connected or Not Connected.

If this readback displays Not Connected, make sure that the PDA detector is powered on.
Check the Ethernet connections and the instrument configuration settings for the PDA
detector.
Diode array scan rate Displays the current configuration setting for the diode array scan rate. The possible diode
array scan rates are 20, 40, and 80 Hz.
PDA status Displays the current state of the PDA detector. The possible states are Not Ready for a Run
and Ready for a Run. This readback displays Not Ready for a Run if both lamps are off or if
the deuterium lamp is warming up.
Wavelength calibration Displays whether the wavelength calibration has been applied.
Dark current Displays whether the dark current calibration has been applied.
calibration
Method validity Displays whether a method has been downloaded to the PDA detector.
Filter wheel position Displays the position of the filter wheel. The filter wheel has two positions: 1 and 2. When
the filter wheel is in position 1, the readout displays Run Position. When the filter wheel is
in position 2, the readout displays Calibration Position.
Deuterium lamp Displays whether the deuterium lamp is on or off.
Tungsten lamp Displays whether the tungsten lamp is on or off.
Current method (top right)
Current method Displays the status of the current method.
Spectrum
Spectrum Plot Depending on the method type (.meth or .spda), these scan plots are displayed:
• For display methods (.spda), the scan plot shows intensity (counts) normalized to
100 percent on the y axis and diode number (2 to 511) on the x axis.
• For instrument methods (.meth), the scan plot shows absorbance (mAU) normalized to
100 percent on the y axis and wavelength (nanometers) on the x axis.

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Table 49. Display page parameters (Sheet 4 of 4)

Parameter Description
Channels
Channels Plot Depending on the method type (.meth or .spda), these discrete channel plots are displayed:
• For display methods (.spda), the plot shows intensity (counts) normalized to
100 percent on the y axis and time on the x axis.
• For instrument methods (.meth), the scan plot shows absorbance (mAU) normalized to
100 percent on the y axis and time on the x axis.

Each discrete channel is color coded. Channel A is yellow, Channel B is purple, and
Channel C is blue.

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Information Page
Use the Information page to monitor the chronological run log, instrument version, and
system date and time. The error log is an ongoing record of critical and non-critical errors in
the PDA detector. The log is generated and stored in the detector. This data is useful for
troubleshooting hardware and software problems.

 To open the Information page

1. Open the Direct Control dialog box for the PDA detector (see “PDA Detector Direct
Controls” on page 162).
2. Click the Information tab.
The Information page appears (see Figure 102).
Figure 102. Information page

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Information Page Parameters

Table 50 describes the parameters on the Information page.
Table 50. Information page parameters
Parameter Description
Error Log
Error Log Displays errors that are generated by the PDA detector. The error log can hold up to 100
errors. When the error log is full, the newest error log entry replaces the oldest error log
entry. The error log is protected by a backup battery when the detector is turned off.
Tip For best results, save the error log (print to file) before you clear it. The error log is
useful during preventive and problem maintenance.
Buttons
Request Log Downloads the error log that is stored in the PDA detector and displays the results in the
Error Log box.
Clear Log Erases the current error log.
Tip For best results, save the error log (print to file) before you clear it. The error log is
useful during preventive and problem maintenance.
Export Log Exports the log to a comma-separated values file that you can open with the Excel
application.
Versions
Versions display box Displays the version number for the detector firmware. This information is useful to
determine if firmware upgrades are necessary. Have this information handy whenever you
contact your Thermo Fisher Scientific service representative.
Date and Time
Date and time Displays the current system date and time. This is the time that the data system uses for
entries in the error log and the time stamp on the snapshot file.

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UV-Vis Detector Direct Controls

UV-Vis Detector Direct Controls

Use the Direct Control dialog box for the UV/Vis detector to turn the lamps on or off and to
zero the chromatographic baseline.

 To turn the UV/Vis detector’s lamps on or off

1. Open the Surveyor UV/Vis Instrument Setup view.

2. From the menu bar, choose Surveyor UV/Vis > Direct Control.
The Direct Control dialog box for the UV/Vis Detector appears (see Figure 103).
Figure 103. Direct Control dialog box for the UV/Vis Detector

3. In the Deuterium Lamp area, click Lamp On.

 To zero the absorbance

Click Zero.

UV/Vis Direct Control Parameters

Table 51 describes the buttons and readbacks in the Direct Control dialog box for the UV/Vis
detector.
Table 51. Direct control parameters for the UV/Vis detector (Sheet 1 of 2)
Parameter Description
Deuterium Lamp
Lamp On Turns the deuterium lamp on.
Lamp Off Turns the deuterium lamp off.

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Table 51. Direct control parameters for the UV/Vis detector (Sheet 2 of 2)
Parameter Description
Tungsten Lamp
Lamp On Turns the tungsten lamp on.
Lamp Off Turns the tungsten lamp off.
Other Options
Zero Zeros the absorbance reading from the detector.
Readbacks
Status Displays the state of the UV/Vis detector:
Ready The detector is ready to start data acquisition.
Off The detector is not ready to start data acquisition
because one or both lamps are off.

Depending on the acquisition wavelengths

specified in the downloaded instrument method,
one or both lamps must be on.
• For the UV range, the deuterium lamp must
be on.
• For the visible range, the tungsten lamp
must be on.
• When the wavelength table specifies
wavelengths in both the UV and visible
ranges, both lamps must be on.
Running The detector is acquiring data.
AU1 Displays the current absorbance value for the first wavelength
channel.
AU2 Displays the current absorbance value for the second wavelength
channel.

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Pump Direct Controls

Pump Direct Controls

The Surveyor product line includes the Surveyor LC Pump Plus and the Surveyor MS Pump
Plus.

These topics describe the direct controls for your Surveyor Plus pump:
• Surveyor LC Pump Plus Direct Controls
• Surveyor MS Pump Plus Direct Controls

Surveyor LC Pump Plus Direct Controls

Use the Surveyor LC Pump Direct Control dialog box to quickly draw fresh solvent through
the solvent lines, clear an error condition, download new solvent conditions to the pump, and
start and stop the solvent flow from the pump.

For information on opening the Direct Control dialog box and using the direct controls for
the Surveyor LC Pump Plus, see these topics:
• Opening the Direct Control Dialog Box for the Surveyor LC Pump Plus
• Operation - Surveyor LC Pump Direct Control Parameters
• Removing Air from the Solvent Lines Connected to the Surveyor LC Pump Plus
• Downloading New Solvent Conditions to the Pump
• Starting and Stopping the Solvent Flow
• Clearing an Error Condition for the Pump

Opening the Direct Control Dialog Box for the Surveyor LC Pump Plus
In the pump view, the direct controls are on the Operation - Surveyor LC Pump Direct
Control dialog box. In the Tune window for your Thermo Scientific mass spectrometer, the
direct controls for the pump are on the pump page of the Inlet Direct Control dialog box.

 To open the Operation - Surveyor LC Pump Direct Control dialog box

1. Open the pump view.

2. From the menu bar, choose Surveyor LC Pump > Direct Control > Operation.
The Operation - Surveyor LC Pump Direct Control dialog box appears.

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Pump Direct Controls

 To access the direct controls for the pump from the Tune window

1. Open the Tune window for your Thermo Scientific mass spectrometer.
2. Choose Setup > Inlet Direct Control.
The Inlet Direct Control dialog box that contains tabbed pages for each configured LC
device appears.
3. Click the Surveyor LC Pump tab.

Operation - Surveyor LC Pump Direct Control Parameters

Table 52 describes the direct control parameters for the Surveyor LC Pump Plus.
Table 52. Operation - Surveyor LC Pump Direct Control parameters (Sheet 1 of 2)
Parameter Description
Pump
Pump On Turns on the solvent flow from the pump.
Pump Off Turns off the solvent flow from the pump.
Error Condition
Clear Clears the error log. You must clear the error log before you can restart the solvent flow from
the pump.
Method
Flow Rate Specifies the flow rate, in mL/min.

Range: 0.000 to 9.999 mL/min

Component A, B, C, Specifies the percent composition of solvent A, B, C, or D.
or D
Download Downloads the new mobile phase settings to the on-board CPU of the Surveyor LC Pump
Plus.
Purge
Purge Time Specifies the length of time that the pump draws solvent through the system at
approximately 10 mL/min.

Range: 0.1 to 9.9 minutes

Solvent Valve Specifies the solvent proportioning valve that is activated. The pump draws solvent from the
solvent line connected to this proportioning valve.
Note The Surveyor LC Pump Plus is a quaternary gradient pump that can be set up to
pump four solvents. The solvent lines are labeled A, B, C, and D. You must purge each
separately.

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Pump Direct Controls

Table 52. Operation - Surveyor LC Pump Direct Control parameters (Sheet 2 of 2)

Parameter Description
Purge Draws the specified solvent at a speed of approximately 10 mL/min through the pump for
the specified purge time.
CAUTION Before you click the Purge button, open the drain valve by turning the drain
valve knob 180° counterclockwise.
Stop Purge Stops the solvent flow from the pump.
Tip After you finish purging the pump, close the drain valve by gently turning the drain
valve knob clockwise until you feel resistance.

Removing Air from the Solvent Lines Connected to the Surveyor LC Pump Plus
Use the purge feature to remove air bubbles from the solvent lines or the pump heads. If the
solvent line connecting the solvent reservoir bottle to the degassing assembly is completely
dry, attach a syringe to the drain line and open the drain valve. Make sure that the pump
power is on, and then draw the syringe barrel back, pulling solvent into the line.

Tip Cyclical baseline noise can be an indication of air in the pump heads.

 To remove air from the solvent lines or the pump head assemblies

1. Open the drain valve by turning it counterclockwise 180° to the purge position. Look for
the word DRAIN to appear upside down on the knob (see Figure 104).
Figure 104. Drain valve knob in the closed and open positions
Closed position Open position

DRAIN
SE
O
PE

LO
N

C
C

N
LO

PE
SE

DRAIN
O

2. Open the view for the Surveyor LC Pump Plus.

3. From the menu bar, choose Surveyor LC Pump > Direct Control > Operation.
The Operation - Surveyor LC Pump Direct Control dialog box appears (see Figure 105).

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Pump Direct Controls

Figure 105. Operation page of the Surveyor LC Pump Direct Control dialog box

4. In the Purge area, do the following:

a. In the Purge Time box, type an appropriate purge time.
The range is 0.1 to 9.9 minutes. Each solvent line holds approximately 3 mL of
solvent.
b. From the Solvent Valve list, select the solvent valve for the solvent line that you want
to draw solvent through.
c. Click Purge.
The pistons of the pump begin to move rapidly, increasing the flow rate to
9.99 mL/min.
5. After drawing fresh solvent through the solvent lines, close the drain valve.

Downloading New Solvent Conditions to the Pump

 To download new solvent conditions to the pump

1. Open the Surveyor LC Pump Plus view.

2. From the menu bar, choose Surveyor LC Pump > Direct Control > Operation.
The Operation - Surveyor LC Pump Direct Control dialog box appears.

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Pump Direct Controls

3. In the Method area, do the following:

a. In the Flow rate box, type the flow rate.
The range is 0.001 to 9.999 mL/min.
b. In the Component A, B, C, and D boxes, type the solvent composition.
c. Click Download.

Starting and Stopping the Solvent Flow

 To start or stop the solvent flow

1. Open the Operation - Surveyor LC Pump Direct Control dialog box (see “Surveyor LC
Pump Plus Direct Controls” on page 185).
2. Do one of the following:
• To start the solvent flow, click Pump On.
• To stop the solvent flow, click Pump Off.

Clearing an Error Condition for the Pump

When an error condition occurs, the solvent flow from the pump stops. Before you can restart
the solvent flow, you must clear the error condition.

 To clear an error condition for the pump

1. Open the Surveyor LC Pump Plus view.

2. From the menu bar, choose Surveyor LC Pump > Direct Control > Operation.
The Operation - Surveyor LC Pump Direct Control dialog box appears.
3. Click Clear.

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Pump Direct Controls

Surveyor MS Pump Plus Direct Controls

Use the Direct Control dialog box to download new solvent conditions to the pump, start and
stop the solvent flow from the pump, and change the global pressure limits.

Tip To open the direct controls for the pump from the Tune window, choose Setup >
Inlet Direct Control from the menu bar. Then click the pump tab.

 To download new solvent conditions to the pump

1. Turn on the power to the pump.

Tip When the power to the pump is off, the proportioning valves are closed. Before
you take the LDA apart to perform maintenance, turn off the power to the pump to
prevent solvent from leaking out of the proportioning assembly.

2. To open the Direct Control dialog box from the pump view, do the following:
a. From the menu bar of the pump view, choose Surveyor MS Pump Plus >
Direct Control.
The Direct Control dialog box for the pump appears (see Figure 106).
Figure 106. Direct Control dialog box for the Surveyor MS Pump Plus

3. In the Direct Control dialog box, do the following:

a. Select the Take Pump Under Control check box.
b. In the Flow box, type an appropriate flow rate for the pump. If you are drawing fresh
solvent through the lines and the liquid displacement assembly, type the maximum
flow rate for the pump.

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Pump Direct Controls

The maximum flow rate for the Surveyor MS Pump Plus is 1000 μL/min.
c. Type percentages for the solvent lines that you want to draw solvent through in the
Inlet boxes (A, B, C, and D).

 To start the solvent flow

Click (Start).

 To stop the solvent flow

Click (Stop).

 To change the global pressure limits

1. Click Pressure Limits.

The Pressure Limits dialog box appears (see Figure 107).
Figure 107. Pressure Limits dialog box

2. In the Min. Pressure box, type the minimum operating pressure for the pump.
3. In the Max. Pressure box, type the maximum operating pressure for the pump.
The maximum pressure for the Surveyor MS Pump Plus is 1000 bar (100 MPa or
14 504 psi).
4. Click OK to accept the settings and close the dialog box.

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Autosampler Direct Controls

Autosampler Direct Controls

The On/Off switch is the only manual control provided with the autosampler. To perform
tasks such as moving the XYZ arm to the back of the tray compartment, use the direct control
commands in the autosampler view or the tune application for your Thermo Scientific mass
spectrometer.

These topics describe the direct controls for the autosampler:

• Applying a Direct Command
• Direct Control Commands for the Autosampler
• Flushing the Autosampler Syringe
• Removing and Installing Sample Trays
• Controlling the Tray and Oven Compartment Temperatures

You can access the direct control commands for the autosampler from the autosampler view of
your data system or the tune application for your mass spectrometer.

 To open the Inlet Direct Control dialog box from the tune application

1. In the Tune window, choose Setup > Inlet Direct Control.

The Inlet Direct Control dialog box appears with tabbed pages for each configured LC
device.
2. Click the Surveyor AS tab.
The Surveyor AS page appears (see Figure 108).

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Autosampler Direct Controls

Figure 108. Inlet Direct Control dialog box for the Surveyor pump and autosampler

 To open the Direct Control dialog box

1. Open the autosampler view.

2. From the menu bar, choose Surveyor AS > Direct Control.
The Direct Control dialog box appears (see Figure 109).
Figure 109. Direct Control dialog box (Instrument Setup window)

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Autosampler Direct Controls

Applying a Direct Command

 To apply a direct command

1. Select a command from the list of commands.

If the command requires additional parameters, these parameters appear below the list.
Make the appropriate entries and selections.
2. To execute the command, click Apply.

Direct Control Commands for the Autosampler

Table 53 describes the direct control commands for the autosampler.
Table 53. Direct control commands for the autosampler (Sheet 1 of 3)
Command Description
Position Arm to Moves the XYZ arm to the back of the tray compartment so that you can remove trays from
Access Tray or place trays into the tray compartment.
Note. If the tray compartment door is open and you selected the Verify Door Is Closed
check box when you configured the autosampler, the autosampler does not execute this
command until you close the tray compartment door.
Flush Syringe Flushes the needle tubing and the interior of the needle with flush solvent.
Parameter Selections or range
Reservoir RV1, RV2, RV3, RV4, or Bottle
Volume 0 to 6000 μL
Flush Speed Depends on the syringe type as follows:
Syringe type Range
Concentric syringes 1.65 to 661.38 μL/s
Standard 2500 μL syringe 0.83 to 330.85 μL/s
Flush Syringe at Flushes the needle tubing, the interior of the needle, and the sample loop with flush solvent.
Fill Position For the parameter descriptions, see Flush Syringe.
Wash Needle Washes the exterior of the needle with solvent.
Parameter Selections or range
Reservoir RV1, RV2, RV3, RV4, or Bottle
Volume 0 to 6000 μL

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Autosampler Direct Controls

Table 53. Direct control commands for the autosampler (Sheet 2 of 3)

Command Description
Needle Removal Sets the needle to the needle removal position. Apply this command before you remove the
needle from the XYZ arm.
Set Oven Temperature Sets the temperature of the column oven compartment without downloading an instrument
method.
Parameter Range
Temperature 5 to 95 °C
IMPORTANT Avoid setting the temperature above the boiling point of the mobile
phase.
Set Tray Temperature Sets the temperature of the tray compartment without downloading an instrument method.
The temperature range is 0 to 60 °C.
Parameter Range
Temperature 0 to 60 °C
Turn Off Turns off the oven temperature control, allowing the temperature of the column oven
Oven Temperature compartment to return to ambient.
Turn Off Turns off the tray temperature control, allowing the temperature of the tray compartment to
Tray Temperature return to ambient.
Inject Sample Injects a sample.
Parameter
Vial The vial or well entries depend on the tray configuration:
Tray type Vial locations
Conventional trays A:01 to E:40
96-well plates A:A1 to C:H12
384-well plates A:A1 to C:P24
Volume For the no waste and partial loop injection modes, the minimum injection
volume is 0.1 μL.

The maximum volume depends on the syringe type:

Syringe Maximum volume
100 μL concentric syringe 20 μL
250 μL concentric syringe 125 μL
500 μL concentric syringe 300 μL
2500 μL standard syringe 1250 μL
Injection Full Loop, Partial Loop, and No Waste.
Mode

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Autosampler Direct Controls

Table 53. Direct control commands for the autosampler (Sheet 3 of 3)

Command Description
Move Needle Moves the XYZ arm to a specific vial or well location.
Set Injector Position Switches the position of the injection valve. The injection valve has two positions: fill and
inject.
Set Syringe to Sets the syringe to its removal position.
Removal Position
Set Syringe to Sets the syringe to its home position.
Home Position
Set Arm to Moves the XYZ arm to its home position, which is just above the injection port.
Home Position
Button
Apply Executes the command.

Flushing the Autosampler Syringe

To ensure the proper performance of the autosampler, remove air from the wash bottle tubing
and the autosampler syringe before you make your first injection. Once you have your system
running, periodically check the level of solvent in the wash bottle and remove air from the
syringe as needed.

Tip During a flush operation, the autosampler draws wash solvent into the syringe and
then pushes wash solvent through the needle tubing and the injection port to waste.
If you want to remove residual sample from the sample loop, use the Flush Syringe at Fill
Position command.

 To flush air out of the wash bottle tubing and the autosampler syringe

1. Open the view for the autosampler.

2. From the menu bar, choose Surveyor AS > Direct Control.
The Direct Control dialog box for the Surveyor Autosampler Plus appears
(see Figure 110).

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Autosampler Direct Controls

Figure 110. Flush syringe direct control command

3. Initiate the Flush Syringe command:

a. Select Flush Syringe from the list of commands.
The parameters for the command appear below the list.
b. In the Reservoir list, select Flush Bottle.
c. In the Volume box, type an appropriate flush volume.
The maximum flush volume is 6000 μL.
d. Click Apply to download the command to the autosampler.
4. Verify that the wash bottle tubing and syringe are free of air (see Figure 111).
5. Close the Direct Control dialog box.

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Autosampler Direct Controls

Figure 111. Solvent path for flushing the syringe

2-way
syringe valve
Needle tubing
assembly

Outer plunger moves upward, pushing

solvent out of the needle tubing, into the
injection port of the autosampler, through
Wash the transfer tube, and into the 6-port
tube injection valve.

Concentric
syringe

Solvent path for Solvent path for

Flush Syringe at Fill Position command Flush Syringe command

Injection port of Injection port of

autosampler autosampler

Transfer tube Transfer tube

To To
Waste
2 1 column 2 1 column
tube
6 6
3 3

4 5 4 5
From From
pump pump

Injection valve in Injection valve in

the inject position the inject position

Waste Waste
container container

Mobile phase
Wash solvent

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Autosampler Direct Controls

Removing and Installing Sample Trays

If you did not select the Verify Door Is Closed check box when you specified the
configuration options for the autosampler, the XYZ arm does not move to the back of the tray
compartment when you open the tray compartment door.

For information on specifying the configuration settings for the Surveyor Autosampler Plus,
see “Surveyor Autosampler Plus Configuration Settings” on page 45.

 To remove or install a sample tray

1. Open the Direct Control dialog box for the autosampler.

2. In the Direct Command list, select Position Arm to Access Tray.
3. Click Apply.
The XYZ arm moves to the back of the tray compartment.

Controlling the Tray and Oven Compartment Temperatures

The autosampler has two controlled temperature zones: the tray compartment and the
column oven compartment. Before you start a sequence run, equilibrate the controlled
temperature zones at the temperature specified in the instrument method.

Use the direct commands in the Direct Control dialog box or the Inlet Direct Control dialog
box to control the oven and tray compartment temperatures. For information about opening
the Direct Control and Inlet Direct Control dialog boxes, see “Autosampler Direct Controls”
on page 192.

 To download a new column oven temperature

1. Select Set Oven Temperature from the list of commands.

2. In the Temperature box, type an appropriate value for the column oven temperature.
The range is 5 to 95 °C.

IMPORTANT Do not set the oven temperature above the boiling point for the
mobile phase solvent.

3. Click Apply.

 To turn the column oven off

1. Select Turn Off Oven Temperature from the list of commands.

2. Click Apply.

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Autosampler Direct Controls

 To download a new tray compartment temperature

1. Select Set Tray Temperature from the list of commands.

2. In the Temperature box, type an appropriate value for the tray compartment temperature.
The range is 0 to 60 °C.
3. Click Apply.

 To turn the column oven off

1. Select Turn Off Tray Temperature from the list of commands.

2. Click Apply.

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 7

Sequence Setup
This chapter describes how to acquire and view chromatographic and PDA spectral data using
the Xcalibur data system.

Contents
• Creating a Single Sample Sequence
• Equilibrating the Chromatographic Column
• Loading the Autosampler
• Starting Data Acquisition
• Working with the Real Time Plot View

Creating a Single Sample Sequence

To set up a sequence to inject a single sample, follow these procedures in order:
1. Opening the Sequence Setup Window
2. Creating the Sequence
3. (Optional) Selecting the Vial Locations Interactively
4. Saving the Sequence

Opening the Sequence Setup Window

 To open the New Sequence Template dialog box

1. Click the Sequence Setup icon on the Home Page.

The Thermo Xcalibur Sequence Setup window appears (see Figure 112).

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7 Sequence Setup
Creating a Single Sample Sequence

Figure 112. Sequence Setup window

2. From the Sequence Setup window, choose File > New.

The New Sequence Template dialog box appears (see Figure 113). Go to the next topic,
“Creating the Sequence” on page 203.
Figure 113. New Sequence Template dialog box

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Creating a Single Sample Sequence

Creating the Sequence

 To create a new sequence

1. If it is not already open, open the New Sequence Template dialog box (see “Opening the
Sequence Setup Window” on page 201).
2. In the General area, make the following entries and selections:
a. In the Base File Name box, type a name for the raw data file.
b. Browse to the data file directory where you want to store your raw data files.
The data system adds the .raw file extension to the data files that contain the
chromatographic and spectral data.
c. Browse to the instrument method that you want to use to acquire your raw data files.
Instrument methods have a .meth file extension. The Instrument Setup view for the
Surveyor Plus devices is described in Chapter 3, “Instrument Method Setup.”
d. If you have not yet created a processing method that contains the information needed
to quantitate your unknowns, do not select a processing method.
You can create a processing method and reprocess your stored data files at a later date.
Processing methods have a .pmd file extension. For information about performing
tests to determine the suitability of your chromatographic method and on creating
calibration curves to quantitate your unknowns, refer to the Thermo Xcalibur
Quantitative Analysis User Guide.
3. In the Samples area, specify the vial locations by doing one of the following:
• To specify a contiguous set of sample vials or well locations:
– In the Number of Samples box, type the number of samples that you want to
analyze.
– In the Initial Vial Position box, type the vial position.
The vial positions for the conventional trays are shown in Figure 114.

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Creating a Single Sample Sequence

Figure 114. Vial positions for conventional sample trays

Slot for tray
Tray runner

Vial position Vial position

A:20 E:40

RV4

RV3

Standard RV2
1.8 mL vial
RV1

Vial position Vial position

A:1 E:21

A B C D E

Tray handle

For more information about the vial locations for conventional trays and the well
locations for microwell plates, see “Vial and Well Notation” on page 6.
• To select a non-contiguous set of sample vials or well locations, click Select Vials, and
then select the vial or well locations by using the Vial Selection dialog box.
For information about using the Vial Selection dialog box, see “Selecting the Vial
Locations Interactively” on page 206.
4. In the Injections per Sample box, type the number of injections per sample that you want
the autosampler to make per vial or well location.
5. In the Base Sample ID box, type an identifying name for the sample.
Base sample IDs are optional. If you do not enter a sample identification, the data system
automatically uses the vial position as the sample identification. If you enter a sample
identification, the data system automatically appends the vial position to your entry.
6. Click OK to display your sequence spreadsheet (see Figure 115).

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 7 Sequence Setup
Creating a Single Sample Sequence

The injection volume displayed in the Inj Vol column matches the injection volume
contained in your instrument setup method. You can override this injection volume
value.
7. To change the injection volume, double-click the spreadsheet cell containing the injection
volume value that you want to change, highlight the current value, and then type a new
value in the cell.
For full details of all the parameters in the New Sequence Template dialog box, refer to
the Help or the Xcalibur manual set.
Figure 115. Sequence Setup view, showing newly created one-line sequence

8. To alter the current column arrangement:

a. Click the Column Arrangement toolbar button.
The Column Arrangement dialog box appears (see Figure 116).
Figure 116. Column Arrangement dialog box

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Creating a Single Sample Sequence

b. Do one of the following:

• To add a column to the sequence, select the column from the Available Columns
list, and click Add.
• To remove a column from the sequence, select the column from the Displayed
Columns list, and click Remove.
• To alter the position of the columns in the sequence, select the column from the
Displayed Columns list, and click either Move Up or Move Down as
appropriate.

Selecting the Vial Locations Interactively

Use the Vial Selection dialog box to select specific vials for the sequence template.

 To interactively select vial or well locations for the sequence list

1. In the Sequence Setup window, choose File > New.

The New Sequence Template dialog box appears.
2. In the Samples area, click Select Vials.
The Vial Selection dialog box appears (see Figure 117).

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Creating a Single Sample Sequence

Figure 117. Vial Selection dialog box

3. Click on a vial position to add it to the sequence template.

4. When you have finished making your selection, click OK.
The vial or well locations appear in the position column in the order that you selected
them.

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Creating a Single Sample Sequence

Saving the Sequence

 To save the sequence

1. Choose File > Save As.

The File Summary Information dialog box appears (see Figure 118).
Figure 118. File Summary Information dialog box

2. In the Description box, type an appropriate description. Then click OK.

The Save As dialog box appears (see Figure 119).
Figure 119. Save As dialog box, showing the file extension for a sequence file

3. Browse to the appropriate folder where you want to save the sequence.

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 7 Sequence Setup
Equilibrating the Chromatographic Column

4. In the File Name box, type a file name.

5. Click Save.

Equilibrating the Chromatographic Column

Warming up the deuterium lamp and equilibrating the LC column reduces baseline drift. For
information about warming up the D2 lamp, see “Turning the Lamps On or Off ” on
page 163.

An LC column requires 10 to 20 column volumes to equilibrate to the initial mobile phase

\

conditions of an instrument method. For example, it takes approximately 17 mL of mobile

phase to equilibrate a typical 4.6 mm ID×10 cm length column.

To calculate the volume of an LC column, use the following equation:

Vm = Πr2 × L
Where:
Vm = volume in mL
r = column radius in cm (radius = inner diameter/2)
L = column length in cm

 To equilibrate your LC column

1. From the Thermo Xcalibur Roadmap menu, choose GoTo > Instrument Setup to
display the Instrument Setup window.
2. Download the same solvent percentages and flow rate as those contained in your method
to the pump:
• For information on downloading new solvent conditions to the Surveyor LC Pump
Plus and starting the solvent flow, see “Surveyor LC Pump Plus Direct Controls” on
page 185.
• For information on downloading new solvent conditions to the Surveyor MS Pump
Plus and starting the solvent flow, see “Surveyor MS Pump Plus Direct Controls” on
page 190.
3. In the status view for your pump (available on the Status page of Info View), monitor the
readings in the Pressure Status area to ensure that the pressure is appropriate for your
application. See “Viewing the Status of Each Device” on page 137.

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Loading the Autosampler

Loading the Autosampler

Before you load your samples into the autosampler, ensure that your samples are completely
soluble in the mobile phase and that you have filtered your samples through a 0.5 μm filter (if
necessary). These techniques minimize sample precipitation in the lines and remove
particulate matter that could obstruct the flow through the autosampler’s injection valve or
the LC column. In addition, make sure that the vial caps are securely fastened onto the vials.

Before you start a sequence run, ensure that you have samples in the locations specified in
your sequence.

Note To trigger the vial sensor, make sure to position custom vials in the tray so that the
top of the vial reaches the minimum height of 1.55 inches. If you place vials that fall
below this minimum height in the tray, the vial sensor does not detect them. When the
sequence reaches a vial that is below the minimum height, the sequence halts, and the Vial
Not Found message appears.

 To load a conventional tray into the autosampler

1. Open the left door of the autosampler.

If you configured the Surveyor AS device driver to verify that the tray compartment door
is closed, the XYZ arm automatically moves to the back of the tray compartment.
Figure 37 on page 53 shows the location of the Verify Door Is Closed check box, available
in the Instrument Configuration window.
2. If necessary, use the direct controls to move the XYZ arm to the back of the tray
compartment (see “Autosampler Direct Controls” on page 192).
3. Hold the tray handle, tilting the back end of the tray down. Insert the tray runner into
the slot at the rear of the tray compartment. Lower the front of the tray into place. Then
press down firmly to seat the tray.

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Starting Data Acquisition

Starting Data Acquisition

 To inject a sample and start data acquisition

1. Open the sequence file containing the information for the sample that you want to inject:
a. From the Sequence Setup view, choose File > Open.
The Open dialog box appears (see Figure 120).
Figure 120. Open dialog box, showing the selection of a sequence file

b. Browse to the appropriate folder.

c. Select the sequence that contains the sample you want to run.
You can identify sequence files by their .sld file extension.
d. Click Open.
The selected sequence appears.
2. Highlight the sequence row that you want to run. Do this even if the sequence contains
just one row. Figure 121 shows a highlighted sequence row.

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7 Sequence Setup
Starting Data Acquisition

Figure 121. Sequence Setup view, showing the first row selected

3. Confirm that you have a vial in the position specified in the sequence row.
4. From the toolbar, click the Run Sample button.
The Run Sequence dialog box appears (see Figure 122).
The User box contains your login name, and the Run Rows box contains the row number
that you selected in the sequence spreadsheet.
Figure 122. Run Sequence dialog box

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 7 Sequence Setup
Starting Data Acquisition

5. Confirm the following:

• The MS detector and LC components are configured for operation as Xcalibur
devices in the Instrument list.
• The autosampler is specified as the start instrument. Yes is displayed in the
Start Instrument column next to Surveyor AS (see Figure 123).
Figure 123. Surveyor AS specified as the start instrument

After the autosampler injection valve switches to the inject position, the autosampler
sends a signal to the detector to begin data acquisition.
6. Set up how the run is started as follows:
• To start the run automatically, select the Start When Ready check box.
After you complete the entries and selections in the Run Sequence dialog box and
click OK, the run begins after the pump sends a pump ready signal to the
autosampler. The pump does not indicate the Ready state until it monitors a stable
backpressure as defined in your instrument method.
• To start the run manually, clear the Start When Ready check box.
7. In the After Sequence Set System area, select one of these three options:
• To keep the devices in the On state, select the On option.
• To automatically turn off the solvent flow from the pump and the detector’s lamps at
the end of the sequence run, select the Off option.
• To turn off the solvent flow from the pump but keep the lamps at the end of the
sequence run, select the Standby option.
8. Keep the parameters in the other areas at their defaults.
You can use the Instrument Method and Programs areas in the Run Sequence dialog box
to specify particular acquisition or processing requirements. For full details of these
features, refer to the Xcalibur Help.
9. Start the run as follows:
• For automated runs, click OK to start the run.
• For manual runs, click OK, and then choose Actions > Start Analysis from the
Sequence Setup menu. To subsequently control the acquisition, choose Actions >
Pause Analysis or Actions > Stop Analysis.

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7Sequence Setup
Working with the Real Time Plot View

Working with the Real Time Plot View

To view and review data as it is being acquired in the Real Time Plot view, follow these
procedures:
• Viewing Data Acquisition
• Reviewing Real-Time Data
• Adding Cells to the Display

Viewing Data Acquisition

 To view the data as it is acquired

1. Choose View > Real Time Plot View, or click the Real Time Plot View button on the
Home Page toolbar.

2. If the display is not already locked, click the Lock Display button to lock the display.
Locked
Locking the display lets you monitor the real-time progress of your run.
In the unlocked position, you cannot monitor the real-time progress of your run, but you
Unlocked can review your data. For example, you can display the spectrum for a particular peak that
has already eluted. Data collection continues off screen as you review your data.
If you are collecting PDA scan data, a view similar to that shown in Figure 124 is
displayed. The view contains three cells: a chromatogram cell, a spectrum cell, and a Total
Scan cell.

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Working with the Real Time Plot View

Figure 124. Real Time Plot view, showing the acquisition of PDA scan data and one discrete channel
Lock display button

Reviewing Real-Time Data

You can review the data as it is being collected.

 To view the spectrum for a particular peak in the chromatogram

1. To unlock the display, click the Lock Display button.

After you unlock the display, data collection continues off screen.
2. Pin the spectrum cell by clicking the pin in the upper-right corner of the cell.
The pin in the upper-right corner of the spectrum cell turns green. Cursor actions in
other cells, such as the chromatogram cell, affect the view displayed in the pinned
spectrum cell.

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7Sequence Setup
Working with the Real Time Plot View

3. In the chromatogram cell, click the peak of interest.

In the spectrum cell, a spectrum appears for the time point that you clicked.
4. Click the Lock Display button to resume monitoring real-time data acquisition.
5. Pin the chromatogram cell by clicking the pin in the upper-right corner of the cell.
The pin in the upper-right corner of the chromatogram cell turns green. Cursor actions
in other cells such as the spectrum cell affect the view displayed in the pinned
chromatogram cell.
6. In the spectrum cell, click the wavelength of interest.
In the chromatogram cell that contained the Total Scan chromatogram, a scan
chromatogram appears for the specific wavelength that you clicked.
7. Click the Lock Display button to resume monitoring real-time data acquisition.

Adding Cells to the Display

You can display multiple cells in the Real Time Plot view.

 To display multiple chromatogram cells

1. Click the chromatogram cell to make it the active cell with a gray border.
2. Choose View > Ranges.
The Chromatogram Ranges dialog box appears (see Figure 125).

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Working with the Real Time Plot View

Figure 125. Chromatogram Ranges dialog box

3. For each cell that you want to add, do the following:

a. In the Type column, select its corresponding check box.
b. In the Detector list, select a detector.
c. In the Plot Type list, select a plot type.
4. Click OK to close the Chromatogram Ranges dialog box.
5. Choose View > Lock Display to resume monitoring real-time data acquisition.

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 8

Qual Browser
This chapter provides an introduction to the Xcalibur Qual Browser functions that you can
use to review the PDA data contained in your .raw data files.

Contents
• Opening a Raw Data File in Qual Browser
• Working with the Cell Grid
• Changing the Font Size of the Display
• Viewing a Report of the Instrument Method
• Creating a Layout for PDA Data
• Viewing the Spectrum for a Specific Time Point
• Viewing the Chromatogram for a Specific Wavelength
• Determining Peak Areas
• Calculating the Purity of the Chromatographic Peaks

Opening a Raw Data File in Qual Browser

Data files containing the raw chromatographic and spectral data have the .raw file extension.

 To open a .raw file in Qual Browser

1. Click the Qual Browser icon in the Roadmap view of the Homepage window, or choose
GoTo > Qual Browser.
The empty Qual Browser window appears (see Figure 126).

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8 Qual Browser
Opening a Raw Data File in Qual Browser

Figure 126. Empty Qual Browser window

2. Choose File > Open.

The Open Raw Data File dialog box appears (see Figure 127).
Figure 127. Open Raw File dialog box

3. Select the .raw file that you want to review.

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Opening a Raw Data File in Qual Browser

4. Select the layout from the list at the bottom of the dialog box.
The available selections are Default Layout and Current Layout. Select Current Layout if
the current layout for the Qual Browser window is different from the default layout and
you want to apply it to your data file.
5. Click Open.
If the default layout has not been modified and your raw file contains MS data in
addition to PDA or UV data, the data file opens with the MS TIC chromatogram in the
upper cell and a mass range spectrum in the lower cell. For an explanation of cells, see
“Working with the Cell Grid” on page 224. The y axis for these cells is set to relative
absorbance (see Figure 128).
Figure 128. Qual Browser view with a chromatogram cell displaying MS TIC data and a spectrum cell displaying
mass range data

6. To apply a custom window layout to the Qual Browser view, do the following:
a. Choose File > Layout > Apply.
The Open Layout File dialog box appears (see Figure 129).

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8 Qual Browser
Opening a Raw Data File in Qual Browser

Figure 129. Open Layout File dialog box

b. Select a layout file from the list.

Layout files have the .lyt file extension.
c. Click Open to apply the layout to the raw data file.
Figure 130 shows a custom layout file applied to a raw data file containing both MS
data and PDA data. The custom layout replaces the MS TIC chromatogram with a
Total Scan chromatogram for the PDA data. It also replaces the mass range spectrum
data from the MS detector with the spectral data from the PDA detector.
For instructions on how to create a Layout file for your PDA data, see “Creating a
Layout for PDA Data” on page 233.

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Opening a Raw Data File in Qual Browser

Figure 130. Qual Browser view with a chromatogram cell displaying a Total Scan from the PDA detector and a spectrum cell
displaying the spectral data from the PDA detector for time 0

Spectrum for time = 0 minutes

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8Qual Browser
Working with the Cell Grid

Working with the Cell Grid

To use the Qual Browser facility, you must understand the concept of cell states and the effect
of cursor actions in a cell. This section contains the following topics:
• Cell States
• Cursor Actions

Cell States
When you open a raw data file in the Qual Browser window, the information within the data
file is displayed as a grid of cells.

There are three hierarchal states for a cell within the grid:
• Inactive Cells
• Active but Unpinned Cells
• Active and Pinned Cells

The grid always contains either one active but unpinned cell or one pinned cell. If the grid
contains more than one cell, only one cell can be active and the rest of the cells are inactive.

An unpinned cell has a gray pin icon in its upper-right corner.

A pinned cell has a green pin icon in its upper-right corner.

Inactive Cells
Inactive cells are not highlighted with a gray border and the pin icon in their upper-right
corners is gray. The cell in the lower portion of Figure 131 is inactive as indicated by the
absence of a gray border. Menu commands, toolbar buttons, and cursor actions do not affect
inactive cells. To zoom in on the contents of a cell or access its shortcut menu, you must make
the cell active.

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 8 Qual Browser
Working with the Cell Grid

Figure 131. Qual Browser window, displaying an active chromatogram cell and an inactive PDA spectrum cell
Gray border

Active cell

Unpinned

Inactive cell Shortcut

menu for
chromatogram
cell

Active but Unpinned Cells

An active but unpinned cell is highlighted with a gray border, and the pin icon in its
upper-right corner is gray. The cell in the upper portion of Figure 131 is active but unpinned.
Menu commands, toolbar buttons, and cursor actions affect the active cell. If the grid does
not contain a pinned cell, clicking an inactive cell in the grid makes it the active cell.

Active and Pinned Cells

Clicking the pin in the upper-right corner of a cell makes it the pinned cell within the grid. A
pinned cell is an active cell that cannot be made inactive by clicking in another cell. Instead,
actions performed in the inactive cells affect the pinned cell as described in the next topic,
“Cursor Actions” on page 226. The lower cell in Figure 132 is a pinned cell.

To automatically change the range of a cell by clicking in the grid, you must pin the cell. For
example, to display the spectrum for the 1 minute time point without opening the Spectrum
Ranges dialog box, pin the spectrum cell, and then click the 1 minute time point in the
inactive chromatogram cell.

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8Qual Browser
Working with the Cell Grid

Figure 132. Qual Browser window, displaying an inactive cell and a pinned cell

Inactive cell

Pinned cell

Cursor Actions
Within the cells of the grid, you can use the cursor in three ways:
• A click selects a point on the cell.
• A line dragged parallel to any axis selects a range.
• A line dragged in any diagonal direction selects an area.

The effect of these actions depends on the state of the cell. Within an active cell, cursor
actions rescale the plot (see Table 54).
Table 54. Effect of cursor action in an active cell
Cursor action Effect
Drag parallel to x axis Rescales graph showing selected x-axis range only, same
y-axis range.
Drag parallel to y axis Rescales graph showing selected y-axis range only, same
x-axis range.
Dragged area Rescales graph showing both the selected x-axis and y-axis
ranges.

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Working with the Cell Grid

If one of the cells is pinned, the cursor action in any of the inactive cells affects the pinned cell
(see Table 55).
Table 55. Effect of cursor action in an inactive cell on the pinned cell
Pinned cell Cursor action Effect
Spectrum Click in a chromatogram cell The spectrum cell displays the
spectrum at that retention time.
Chromatogram Click in a spectrum cell The chromatogram cell displays the
chromatogram for the wavelength
selected in the spectrum cell.

In Figure 133, the spectrum cell on the bottom of the view is pinned. Clicking the 1.8 minute
time point in the unpinned chromatogram cell causes the spectrum of benzene, which elutes
at 1.8 minutes, to appear in the pinned spectrum cell.
Figure 133. Qual Browser window with a pinned spectrum cell and an unpinned chromatogram cell
In the chromatogram cell, the pointer is
set to 1.8 minutes, the peak apex for
benzene.

In the spectrum cell, the spectrum of benzene, which elutes

at 1.8 minutes under the chromatographic conditions used,
is displayed.

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8Qual Browser
Working with the Cell Grid

In Figure 134, the chromatogram cell on the top of the view is pinned. Clicking a specific
wavelength in the unpinned spectrum cell displays the chromatogram of the scan wavelength
in the pinned chromatogram cell.
Figure 134. Qual Browser window with a pinned chromatogram cell and an unpinned spectrum cell

In the chromatogram cell,

the chromatogram of the 251 nm
scan wavelength is displayed.

In the spectrum cell,

the pointer is set to 251 nm.

Clicking (Full Size) in the toolbar sizes the active or pinned cell to the full width and
height of the window as shown in Figure 135.

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 8 Qual Browser
Working with the Cell Grid

Figure 135. Spectrum cell sized to full size of window

Dragging across a region in the active or pinned cell zooms in on that region as shown in
Figure 136.
Figure 136. Full size view of the spectrum cell zoomed in on the 320 to 380 nm region

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8 Qual Browser
Changing the Font Size of the Display

Changing the Font Size of the Display

Occasionally, you might want to change the font size of the data displayed in the Xcalibur
data system. For example, you might want to increase the font size for screen captures that you
plan to use for presentations.

 To increase the font size

1. From the Thermo Xcalibur Roadmap window, choose Tools > Configuration.
The Thermo Xcalibur Configuration dialog box appears.
2. Click the Fonts tab.
The Fonts page appears (see Figure 137).
Figure 137. Fonts page in the Thermo Xcalibur Configuration dialog box

3. To increase the font size of the chromatogram, spectrum, and map axis labels, in the
Proportional Pitch Font area, select a larger font size from the Max list, and select a larger
font size from the Min list.
4. To increase the font size for the Spectrum List, Scan Header, Scan Filters, or Report, in
the Fixed Pitch Font area, select a larger font size from the Max list, and select a larger
font size from the Min list.
Figure 138 shows the chromatogram axes labeled with a font size of 8. Figure 139 shows
the chromatogram axes labeled with a font size of 16.

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 8 Qual Browser
Changing the Font Size of the Display

Figure 138. Proportional pitch font size = 8

Figure 139. Proportional pitch font size = 16

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8 Qual Browser
Viewing a Report of the Instrument Method

Viewing a Report of the Instrument Method

After you open a data file, you might want to check the instrument parameters that were used
to acquire it.

 To view a report that lists the instrument control parameters

1. Choose View > Report > Instrument Method.

The instrument method is displayed in the top cell of the window. The instrument
method is divided by device, with the parameters for each device displayed on a separate
page (see Figure 140).
2. Click (Show Previous and Show Next) to move through the pages of your
Instrument Method.
Figure 140. Instrument Method Report (PDA page) in the Qual Browser view

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 8 Qual Browser
Creating a Layout for PDA Data

Creating a Layout for PDA Data

This section describes how to view chromatograms and spectral information acquired by the
PDA detector. In addition, it describes how to save the range and display settings for the PDA
data in a layout file.

To create a layout file for PDA data, follow these procedures in order:
1. Specifying the Chromatogram and Spectrum Ranges
2. Specifying the Display Options for the Chromatogram and Spectrum Cells
3. (Optional) Inserting Cells
4. Saving the New Layout

Specifying the Chromatogram and Spectrum Ranges

When you open a .raw data file in the Qual Browser application using the default layout, the
data file opens with the MS TIC chromatogram in the upper cell and a mass range spectrum
in the lower cell.

Follow these topics to change the upper cell to a chromatogram and the lower cell to spectral
data acquired by the PDA detector:
• Specifying the Chromatogram Ranges
• Specifying the Spectrum Range

Note You can modify the cells in any order.

Specifying the Chromatogram Ranges

There are two types of chromatograms for the PDA detector: chromatograms acquired from
any of the three discrete channels and chromatograms interpolated from the scan data. Follow
these procedures to display the two types of chromatograms acquired by the PDA detector in
the Qual Browser window:
• Displaying Scan Wavelength Chromatograms
• Displaying Discrete Wavelength Chromatograms

Displaying Scan Wavelength Chromatograms

 To display a scan chromatogram for the PDA detector data

1. Open a data file (.raw) that has PDA data and MS data (see “Opening a Raw Data File in
Qual Browser” on page 219).
The data file opens with the MS TIC chromatogram in the upper cell and a mass range
spectrum in the lower cell.

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8 Qual Browser
Creating a Layout for PDA Data

2. Pin the chromatogram cell (see “Active and Pinned Cells” on page 225).
3. Right-click the chromatogram cell.
4. From the shortcut menu, choose Ranges.
The Chromatogram Ranges dialog box appears (see Figure 141).
Figure 141. Chromatogram Ranges dialog box with the default layout settings

5. In the Range area, set the displayed time range of the chromatogram:
• For a generic layout file, leave an asterisk in the Time Range box.
When you open a .raw data file, the x axis of the chromatogram is scaled to the run
time for your detector in the instrument setup method used to acquire the data.
• To specify a specific time range, type a beginning time point and an ending time
point separated by a dash in the Time Range (minutes) box.

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Creating a Layout for PDA Data

6. In the Plot Properties area (see Figure 142), make the following selections:
a. In the Detector list, select PDA.
b. In the Peak Algorithm list, select Avalon.
c. In the Plot Type list, select a plot type:
• Select Wavelength to display the chromatogram for a specific wavelength within
your scan range or to display the averaged results from a range of wavelengths in
your scan range.
• Select Total Scan to display the average absorbance for each time point of all the
wavelengths in your scan range.
• Select Spectrum Maximum to display a plot of the maximum absorbance values
in your scan range for each time point.
d. Select a wavelength range (if you selected the Total Scan plot type, this box is
unavailable):
• To display the chromatogram for a specific scan wavelength, type the wavelength
number in the Range(s) box.
• To display a plot of the average absorbance values for a range of wavelengths, type
the beginning wavelength number and the ending wavelength number separated
by a dash in the Range(s) box. For example, type 200-300 to display a plot of the
average absorbance values for the scanned wavelengths from 200 to 300 nm.
Figure 142. Plot Properties area of the Chromatogram Ranges dialog box

7. Click OK to close the dialog box and view your scan chromatogram.
Figure 143 shows a chromatogram for a wavelength in the PDA scan.

To modify the layout for the spectrum cell, go to “Specifying the Spectrum Range” on
page 238.

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8 Qual Browser
Creating a Layout for PDA Data

Figure 143. Chromatogram view with a chromatogram for a PDA scan wavelength
220 nm
scan wavelength

Displaying Discrete Wavelength Chromatograms

 To display a discrete chromatogram for the PDA data

1. If you have not already done so, open a data file (.raw) that has PDA data and MS data
(see “Opening a Raw Data File in Qual Browser” on page 219).
The data file opens with the MS TIC chromatogram in the upper cell and a mass range
spectrum in the lower cell.
2. Pin the chromatogram cell (see “Active and Pinned Cells” on page 225).
3. Right-click the chromatogram cell.
4. From the shortcut menu, choose Ranges.
The Chromatogram Ranges dialog box appears. Figure 141 on page 234 shows the
default settings. Figure 144 shows the settings for a discrete channel wavelength.

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Creating a Layout for PDA Data

Figure 144. Chromatogram Ranges dialog box with the selection of a discrete channel wavelength

5. In the Range area, set the displayed time range of the chromatogram:
• For a generic layout file, leave an asterisk in the Time Range box.
When you open a .raw data file, the x axis of the chromatogram is scaled to the run
time for your detector in the instrument setup method used to acquire the data.
• To specify a specific time range, type a beginning time point and an ending time
point separated by a dash in the Time Range box.
6. In the Plot Properties area, select the following:
a. In the Detector list, select UV.
b. In the Peak Algorithm list, select Avalon.
c. In the Plot Type list, select Channel A, Channel B, or Channel C.
7. Click OK to exit the dialog box and view your discrete chromatogram.
Figure 145 shows a discrete channel chromatogram.

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8 Qual Browser
Creating a Layout for PDA Data

To modify the layout for the spectrum cell, go to “Specifying the Spectrum Range” on
page 238.
Figure 145. Chromatogram view with a chromatogram for a PDA discrete channel
Discrete Channel B
wavelength

Specifying the Spectrum Range

 To display a spectrum for the PDA data

1. If you have not already done so, open a data file (.raw) that has PDA data and MS data
(see “Opening a Raw Data File in Qual Browser” on page 219).
The data file opens with the MS TIC chromatogram in the upper cell and a mass range
spectrum in the lower cell.
2. Pin the spectrum cell.
3. Right-click the spectrum cell.
4. From the shortcut menu, choose Ranges.
The Spectrum Ranges dialog box appears (see Figure 146).
5. In the Plot Properties area, select PDA in the Detector list.

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 8 Qual Browser
Creating a Layout for PDA Data

6. For a generic layout file for PDA data, keep the other settings in the Spectrum Ranges
dialog box at their defaults as shown in Figure 146.
Figure 146. Spectrum Ranges dialog box with the PDA detector selected

If you have not already done so, modify the layout for the chromatogram cell as described in
“Specifying the Chromatogram Ranges” on page 233.

If you have specified the ranges for the chromatogram cell and the spectrum cell, go to the
next procedure, “Specifying the Display Options for the Chromatogram and Spectrum Cells.”

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8 Qual Browser
Creating a Layout for PDA Data

Specifying the Display Options for the Chromatogram and Spectrum Cells
After you specify the chromatogram and spectrum ranges, specify the display options for the
chromatogram and spectrum cells as described in these topics:
• Setting the Display Options for the Chromatogram Cell
• Setting the Display Options for the Spectrum Cell

Setting the Display Options for the Chromatogram Cell

 To set the display options for the chromatogram cell

1. Pin the chromatogram cell.

2. Right-click the pinned chromatogram cell.
3. From the shortcut menu, choose Display Options.
The Display Options dialog box appears.
4. Specify the Normalization parameters:
a. Click the Normalization tab.
The Normalization page appears (see Figure 147).
Figure 147. Normalization page in the Display Options dialog box

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Creating a Layout for PDA Data

b. In the Normalize Method area, select the Auto Range option.

Selecting Auto Range ensures that the entire dynamic range of the chromatogram is
displayed in the active view, normalized over the full range of the y axis.
c. In the Normalize Each Plot To area, select the Largest Peak in Selected Time Range
option.
5. Specify the Axis parameters as follows:
a. Click the Axis tab.
The Axis page appears (see Figure 148).
b. In the Units area, select the Absolute option.
Selecting Absolute sets the y axis to the absolute units of μAU.
Figure 148. Axis page in the Display Options dialog box

6. Specify the labels for the peaks in the chromatogram as follows:

a. Click the Labels tab.
The Labels page appears (see Figure 149).

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Creating a Layout for PDA Data

Figure 149. Labels page in the Display Options dialog box

b. Select the check boxes associated with the labels that you want to display, such as
retention time, area, height, and name.
7. Click OK to accept the settings and close the Display Options dialog box.

Setting the Display Options for the Spectrum Cell

 To set the display options for the spectrum cell

1. Pin the spectrum cell.

2. Right-click the pinned spectrum cell.
3. From the shortcut menu, choose Display Options.
The Display Options dialog box appears.
4. Specify the Normalization parameters as follows:
a. Click the Normalization tab.
The Normalization page appears (see Figure 150).

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Creating a Layout for PDA Data

Figure 150. Normalization page in the Display Options dialog box

b. In the Normalize Method area, select the Auto Range option.

Selecting Auto Range ensures that the entire dynamic range of the spectrum is
displayed in the active view, normalized over the full range of the y axis.
c. In the Normalize Spectrum To area, select the Largest Peak in Range option.
5. Specify the Axis parameters as follows:
a. Click the Axis tab.
The Axis page appears (see Figure 151).
b. In the Units area, select the Absolute option.
Selecting Absolute sets the y axis to the absolute units of μAU.
6. Click OK to close the Display Options dialog box.

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Creating a Layout for PDA Data

Figure 151. Axis page in the Display Options dialog box

Inserting Cells
Occasionally, you might want to add more cells to the Qual Browser window. For example,
you might want to add a cell containing a map plot (contour or 3D) to the view screen, or you
might want to display several discrete or scan wavelengths in separate cells.

 To add a cell containing a map plot to the window

1. Click a cell to make it the active cell.

2. Choose Grid > Insert Cells > Left, Right, Above, or Below.
The location of the new cell is relative to the active cell. Initially, the new cell contains the
same information as the existing cell (see Figure 152).

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 8 Qual Browser
Creating a Layout for PDA Data

Figure 152. Qual Browser window with three cells

Chromatogram cell

Spectrum cell

Spectrum cell

3. Change the lower cell so that it displays the Map view (see Figure 153) as follows:
a. Pin the cell by clicking its pin button.
b. Click the View Map button in the toolbar.

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8 Qual Browser
Creating a Layout for PDA Data

Figure 153. Qual Browser window with a chromatogram cell, spectrum cell, and map cell

4. Select the appropriate range options for the map cell as follows:
a. Right-click the map cell.
b. From the shortcut menu, choose Ranges.
The Map Ranges dialog box appears (see Figure 154).
Figure 154. Map Ranges dialog box

c. In the Wavelength box, type the wavelength range that you want to display.
d. In the Time box, type the time range that you want to display.

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Creating a Layout for PDA Data

5. Select the appropriate display options for the map cell as follows:
a. Right-click the map cell.
b. From the shortcut menu, choose Display Options.
The Display Options dialog box appears.
c. Click the Axis tab.
The Axis page appears (see Figure 151 on page 244).
d. In the Units area, select the Absolute option.
e. Click the Normalization tab.
The Normalization page appears.
f. In the Normalize Method area, select the Auto Range option.
g. Click the Style tab.
The Style page appears (see Figure 155).
Figure 155. Style page in the Display Options dialog box for the map cell

h. Select the appropriate style.

i. Click OK to save your settings and close the Display Options dialog box.

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Creating a Layout for PDA Data

Saving the New Layout

Now that you have created a layout for displaying your PDA data, save the layout so that you
can apply it to other data files containing PDA data.

 To save the layout

1. From the Qual Browser window, choose File > Layout > Save As.
The Save Layout File dialog box appears (see Figure 156).
Figure 156. Save Layout File dialog box

2. Type a file name in the File name box.

3. Click Save.

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 8 Qual Browser
Viewing the Spectrum for a Specific Time Point

Viewing the Spectrum for a Specific Time Point

 To view a spectrum for a specific time point

1. Open a raw data file with PDA data and apply an appropriate layout file (see “Opening a
Raw Data File in Qual Browser” on page 219).
2. Pin the spectrum cell.
3. Click a time point in the chromatogram cell.
The spectrum for the selected time point appears in the spectrum cell (see Figure 157).
Figure 157. Qual Browser window with a chromatogram of the PDA test mixture and a
spectrum for the 7.42 minute time point

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8 Qual Browser
Viewing the Chromatogram for a Specific Wavelength

Viewing the Chromatogram for a Specific Wavelength

 To view the scan chromatogram for a specific wavelength

1. Open a raw data file with PDA data and apply an appropriate layout file (see “Opening a
Raw Data File in Qual Browser” on page 219).
2. Pin the chromatogram cell.
3. Click a wavelength in the spectrum cell.
The scan chromatogram for the selected wavelength appears in the chromatogram cell as
shown in Figure 158.
Figure 158. Qual Browser window, displaying a chromatogram cell and a spectrum cell
334 nm
scan wavelength

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 8 Qual Browser
Determining Peak Areas

Determining Peak Areas

In a chromatogram, the area of an isolated peak is directly proportional to the concentration
of the analyte.

 To make a peak area determination using the Qual Browser application

1. Open the Qual Browser application.

2. Open the data file (.raw) of interest (see “Opening a Raw Data File in Qual Browser” on
page 219).
3. Ensure that the chromatogram cell is the active cell, as indicated by a gray border.
4. Select the chromatogram that you want to integrate as follows:
a. Right-click the chromatogram and from the shortcut menu choose Ranges.
The Chromatogram ranges dialog box appears.
b. In the Detector list, select the detector type:
• To integrate a scan wavelength, select PDA.
• To integrate a discrete wavelength channel, select UV.
c. Ensure that Avalon is selected as the Peak Algorithm.
d. Select the appropriate wavelength:
• To display the chromatogram for a scan wavelength, select Wavelength Range
from the Plot Type list, and then type a value for a wavelength within your scan
range in the Range box.
• To display the chromatogram for a discrete wavelength channel, select
Channel A, B, or C from the Plot Type list.
5. Turn on peak detection by right-clicking the chromatogram cell and choosing
Peak Detection > Toggle Detection in This Plot from the shortcut menu.
6. To display numerical values for areas of the chromatographic peaks, do the following:
a. Right-click the chromatogram cell and choose Display Options.
The Display Options dialog box appears.
b. Click the Labels tab.
The Labels page appears (see Figure 159).

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8 Qual Browser
Determining Peak Areas

Figure 159. Labels page in the Display Options dialog box

c. Select the Area check box.

d. Click OK to return to the chromatogram cell.
7. To set the integration parameters, do the following:
a. Right-click the chromatogram and choose Peak Detection > Settings from the
shortcut menu.
The Avalon Peak Detection Settings page appears on the left side of the window
(see Figure 160).

Note The Avalon Peak Detection Settings page appears only when Avalon is
selected as the peak algorithm in the Chromatogram Ranges dialog box.

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 8 Qual Browser
Determining Peak Areas

Figure 160. Avalon Peak Detection Settings page

b. Click Auto Calc Initial Events to force the Avalon peak integration algorithm to
determine the “best” values for the following initial events: Start Threshold,
End Threshold, Peak Threshold, P-P Threshold, Bunch Factor, Negative Peaks, and
Tension.
Figure 161 shows a chromatogram for the 239 nm scan wavelength that is integrated
with the “best” initial integration values as determined by the Avalon peak integration
algorithm. The peaks areas are shown above the apexes of the integrated peaks.

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8 Qual Browser
Calculating the Purity of the Chromatographic Peaks

Figure 161. Avalon Peak Detection Settings page displaying a chromatogram acquired
with the PDA detector

Calculating the Purity of the Chromatographic Peaks

The data system can calculate the spectral purity of your chromatographic peaks by
comparing the similarity of the spectra across the peak to a spectrum from the peak apex. The
calculation is affected by the integration of the scan chromatogram and by the scan threshold,
peak coverage, and scan wavelengths that you set in the Peak Purity Settings dialog box.

 To display the purity values for the integrated peaks

1. Select a chromatogram for a scan wavelength (see “Displaying Scan Wavelength

Chromatograms” on page 233).
2. Set the integration parameters for the chromatogram (see “Determining Peak Areas” on
page 251).
3. Right-click the chromatogram cell and choose Peak Purity from the shortcut menu.
The Peak Purity Settings dialog box appears (see Figure 162).

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 8 Qual Browser
Calculating the Purity of the Chromatographic Peaks

Figure 162. Peak Purity Settings dialog box

4. Select the Enable check box.

5. In the Scan Threshold (μAU) box, type an appropriate scan threshold.
The scan threshold limits the portion of the peak included in the analysis to spectral slices
that have a lambda max above the scan threshold. You can set this limit to eliminate noise
from the analysis. The limits for this box are 0 to 2 000 000 μAU.
6. In the Peak Coverage % box, type an appropriate value for your application. The limits
for this parameter are 1 to 100% coverage.
At a setting of 100%, the data system compares all the spectral slices that fall within the
beginning and ending tick marks of the integrated peak. To limit the peak purity
calculation to a specific range of wavelengths in the scan, select the Limit Scan
Wavelength check box, and then enter a wavelength range in the Wavelength Range box.
7. Click OK to close the Peak Purity Settings dialog box, and then view the effect of your
peak purity settings.
The following figures show the effect of various settings on peak purity:
• Figure 163 shows the effect of the scan wavelength on peak purity.
• A comparison of Figure 164 and Figure 165 on page 257 demonstrates the effect of
integration on peak purity.
• Figure 166 on page 258 shows the effect of the scan threshold setting on peak purity.
• Figure 167 on page 258 shows the effect of the peak coverage setting on peak purity.

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Calculating the Purity of the Chromatographic Peaks

Figure 163. Comparison of peak purity results for two different scan wavelengths

225 nm scan wavelength

3 uAU scan threshold
95% peak coverage

239 nm scan wavelength

3 uAU scan threshold
95% peak coverage

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Calculating the Purity of the Chromatographic Peaks

Figure 164. Chromatogram for the 225 nm scan wavelength with default integration parameters

Benzene

Impurity

Figure 165. Chromatogram for the 225 nm scan wavelength with Auto calc integration parameters

3 uAU scan threshold

95% peak coverage

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8 Qual Browser
Calculating the Purity of the Chromatographic Peaks

Figure 166. Effect of scan threshold on peak purity calculation

3 uAU scan threshold

95% peak coverage

500000 uAU scan threshold

95% peak coverage

Figure 167. Effect of peak coverage on peak purity calculations

3 uAU scan threshold

50% peak coverage

Peak start Peak stop

3 uAU scan threshold

5% peak coverage

Peak start Peak stop

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 9

LC Pump Calibration and Record Keeping

This chapter describes the calibration and record keeping procedures for the Surveyor LC
Pump Plus.

Contents
• Calibrating the Surveyor LC Pump Plus
• Recording Maintenance Information for the Surveyor LC Pump Plus
• Firmware Version Information for the Surveyor LC Pump Plus

The Surveyor LC Pump Plus is factory calibrated to produce an accurate flow rate while
pumping water at 1 mL/min. Its ability to accurately proportion binary mobile phases is also
tested at a flow rate of 1 mL/min.

The Surveyor LC Pump Plus does not require calibration upon arrival at its shipping
destination. However, over time, the pressure readings from its built-in pressure transducer
can drift and require re-zeroing. If you are running the LC pump at high backpressures, you
might notice an increase in its pressure pulsation. You can reduce this pressure pulsation by
adjusting the compressibility setting of the LC pump.

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Calibrating the Surveyor LC Pump Plus

Calibrating the Surveyor LC Pump Plus

Two calibration options for the Surveyor LC Pump Plus affect its performance: the alpha
setting, which affects the flow rate; and the compressibility setting, which affects the pressure
pulsation of the system. The alpha setting is factory calibrated to produce an accurate flow
rate for water. The compressibility setting is set to 0.45 GPa–1, which is the compressibility
value for water.

If you are pumping solvents other than water and your application is sensitive to pressure
pulsation, you might want to optimize the compressibility setting. After you optimize the
compressibility setting, check the flow rate accuracy. If adjusting the compressibility setting
has affected the flow rate accuracy, adjust the alpha setting.

In addition to the alpha setting and the compressibility setting, the pressure transducer that is
attached to the back of the purge manifold assembly is also factory calibrated. If you replace
the pressure transducer, you must update the pressure sensor adjustment setting. Even if you
never replace the pressure sensor, you must occasionally re-zero its output, as the readout
tends to drift under normal usage.

These topics provide information on calibrating the LC pump:

• Accessing the Calibration Options for the Surveyor LC Pump Plus
• Calibration Options for the Surveyor LC Pump Plus
• Calibration Procedures for the Surveyor LC Pump Plus

Accessing the Calibration Options for the Surveyor LC Pump Plus

You can fine-tune the performance of the Surveyor LC Pump from the Calibration – Surveyor
LC Pump Direct Control dialog box.

 To open the Calibration – Surveyor LC Pump Direct Control dialog box

1. Turn on the power to the Surveyor LC Pump.

2. Open the Surveyor LC Pump view in the Instrument Setup window.
3. Choose Surveyor LC Pump > Direct Control > Calibration.
The Calibration – Surveyor LC Pump Direct Control dialog box appears (see
Figure 168).

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 9 LC Pump Calibration and Record Keeping
Calibrating the Surveyor LC Pump Plus

Figure 168. Calibration page for the Surveyor LC Pump

Default value

Calibration - Surveyor LC Pump Direct Control Parameters

Table 56 describes the calibration parameters for the Surveyor LC Pump Plus.
Table 56. Calibration parameters for the Surveyor LC Pump Plus (Sheet 1 of 2)
Parameter Description
Settings
Compressibility Specifies the compressibility of the mobile phase (see “Compressibility” on page 262).

For information on determining the appropriate value for your solvent conditions, see
“Updating and Optimizing the Compressibility Setting” on page 266.
Pressure Recorder Full Specifies the full-scale range of the recorder connected to the pressure terminals on the back
Scale panel of the pump (see “Pressure Recorder Full Scale” on page 264).

Range: 1 to 10, in integer steps

For information on setting the full-scale range for the pressure recorder, see “Scaling the
Output of the Pressure Recorder Terminals” on page 268
Flow Rate Adjustment Makes fine adjustments to the flow rate (see “Flow Rate Adjustment (Alpha)” on page 265).
(Alpha)
For information on calibrating the alpha value, see “Updating the Flow Rate Adjustment
Setting” on page 268.

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Calibrating the Surveyor LC Pump Plus

Table 56. Calibration parameters for the Surveyor LC Pump Plus (Sheet 2 of 2)
Parameter Description
Pressure Sensor Adjusts the pressure sensor reading (see “Pressure Sensor Adjustment” on page 265).
Adjustment
For information on adjusting the pressure sensor reading, see “Updating the Pressure Sensor
Adjustment Setting” on page 269.
Set Downloads the new setting to the pump.
Pressure Transducer
Zero Calibrates the current pressure reading as the zero point (see “Pressure Transducer Zero” on
page 265).

For information on setting the zero point for the pressure transducer, see “Zeroing the
Pressure Transducer” on page 269.

Calibration Options for the Surveyor LC Pump Plus

The Xcalibur data system provides the following calibration options (see Figure 168) for the
Surveyor LC Pump Plus:
• Compressibility
• Pressure Recorder Full Scale
• Flow Rate Adjustment (Alpha)
• Pressure Sensor Adjustment
• Pressure Transducer Zero

Compressibility
The compressibility of a liquid is a measure of its resistance to a decrease in volume caused by
an increase in pressure. Compared to gases, most liquids are relatively incompressible. Water, a
commonly used mobile phase solvent, is even less compressible than most organic solvents
because of its extensive hydrogen bonding and cluster structure.

For information on updating the compressibility setting, see “Updating and Optimizing the
Compressibility Setting” on page 266.

Effect of the Compressibility Setting

Even though liquids are relatively incompressible, the compressibility of the mobile phase can
affect your chromatography if you are running the LC pump at the upper limit of its pressure
range. You can use the compressibility setting for the Surveyor LC Pump to compensate for
the compressibility of the mobile phase. However, changing the compressibility setting
simultaneously affects both the pressure pulsation of the Surveyor LC Pump and the flow rate
of the mobile phase.

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The compressibility effect is caused by the portion of the cam cycle where the pistons are
compressing the mobile phase. The compressibility portion of the cam cycle extends from the
time when the primary piston starts discharging until the time the secondary piston reaches
full intake—approximately 80° of the cam cycle. To minimize the pressure pulsation and
maintain a constant flow rate, the on-board CPU compensates for this compression by
making fine adjustments to the speed of the stepping motor. If the compressibility setting is
incorrect, the LC pump cannot effectively minimize the pressure pulsation.

Figure 169 shows the overlaid pressure traces for three runs of water pumped at a nominal
flow rate of 3 mL/min. The compressibility settings for the three runs were 0.45 GPa–1,
1.25 GPa–1, and 3.0 GPa–1, as labeled. The compressibility of water is 0.45 GPa–1.
Figure 169. Overlaid LC pump pressure traces, showing the effect of the compressibility setting

3.0 GPa-1

1.25 GPa-1

0.45 GPa-1

Table 57 lists the calculated pressure pulsation and the empirically determined flow rates for
the three different compressibility settings. The pressure pulsation as well as the actual flow
rate increased as the compressibility setting increased.

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Table 57. Measured flow rate and pressure pulsation versus compressibility setting
Compressibility % Pressure Actual flow rate
% Rel diff
setting pulsation (mL/min)
0.45 GPa–1 ± 0.2% 3.01 + 0.3%
1.25 GPa–1 ± 0.4% 3.05 + 1.8%
3.0 GPa–1 ± 1% 3.18 + 5.9%

Compressibility Ratios for Common Solvents

Because most mobile phases are made up of a mixture of solvents, you must determine the
correct compressibility setting for a given mobile phase empirically. Table 58 lists the
compressibility ratios for a few common solvents.
Table 58. Measured flow rate and pressure pulsation versus compressibility setting
Solvent Compressibility ratio (GPa-1)
Water 0.45
Acetonitrile 1.20
Methanol 1.25
Hexane 1.60

Pressure Recorder Full Scale

The pressure recorder full-scale calibration option sets the scaling factor for the pressure trace
if you choose to monitor the pressure with a chart recorder. The pressure recorder terminals
are located on the back of the Surveyor LC Pump Plus (see Figure 170). Integer values from
1 to 10 are within the allowable range.
Full scale = Set value × 4.9 MPa (50 kgf/cm2) (full-scale voltage = 1 mV)

For example:
When the set value = 1, the full scale is 4.9 MPa (50 kgf/cm2)
When the set value = 10, the full scale is 49.0 MPa (500 kgf/cm2)
4.9 MPa = 50 kgf/cm2 = 49 bar = 711 psi

Note The value for the scaling factor is stored until you change it or until you turn off the
power to the Surveyor LC Pump.

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Figure 170. Terminals located on the back of the Surveyor LC Pump Plus
Pressure terminals

UNIT ID ENET

+5V @ 150mA

NC
PROG. START
PUMP READY
INJECT HOLD
GND
PUMP ON
GND

NC

FW DOWNLOAD
NC
NC
GND

+5V @ 15OmA

PRESSURE+
PRESSURE -
For information on setting the scaling factor for the pressure recorder, see “Scaling the Output
of the Pressure Recorder Terminals” on page 268.

Flow Rate Adjustment (Alpha)

The alpha value for your Surveyor LC Pump Plus is factory calibrated based on a flow rate of
1.000 mL/min for distilled water. A sticker containing the factory calibration value is located
inside the pump on the motor casing. You can optimize the alpha value for your application
by updating the alpha setting. The range for alpha values is 1 to 9.9. If you are pumping
water, decreasing the alpha value by 1 decreases the flow rate by 1 percent. Increasing the
alpha value by 1, however, increases the flow rate by 1 percent.

For information on setting the alpha value, see “Updating the Flow Rate Adjustment Setting”
on page 268.

Pressure Sensor Adjustment

Reset the Pressure Sensor Adjustment parameter when you replace the pressure sensor. Each
pressure sensor is labeled with a data sticker that contains a “0.XXXX” value for the pressure
sensor adjustment setting. Multiply this value by 10 000 and then update the pressure sensor
adjustment setting for your Surveyor LC Pump Plus.

For information on updating the pressure sensor adjustment, see “Updating the Pressure
Sensor Adjustment Setting” on page 269.

Pressure Transducer Zero

The pressure readout for the Surveyor LC Pump Plus is produced by a cell type
potentiometer. This type of device tends to drift by small increments, requiring you to
occasionally re-zero the readout. To update the pressure transducer zero value, turn off the
pump flow and open the drain valve knob. Then click the pressure transducer zero button in
the data system that operates your pump.
For information on zeroing the pressure transducer, see “Zeroing the Pressure Transducer” on
page 269.

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Calibration Procedures for the Surveyor LC Pump Plus

You fine-tune the performance of the Surveyor LC Pump Plus from the
Calibration - Surveyor LC Pump Direct Control page (Figure 168 on page 261).

For instructions on opening the Calibration page, see “Accessing the Calibration Options for
the Surveyor LC Pump Plus” on page 260.

To fine-tune the performance of the Surveyor LC Pump Plus, follow these procedures:
• Updating and Optimizing the Compressibility Setting
• Scaling the Output of the Pressure Recorder Terminals
• Updating the Flow Rate Adjustment Setting
• Updating the Pressure Sensor Adjustment Setting
• Zeroing the Pressure Transducer

Updating and Optimizing the Compressibility Setting

If you have already determined the best compressibility setting for your application, update
the compressibility setting of the Surveyor LC Pump Plus.

For information on compressibility, see “Compressibility” on page 262.

 To update the compressibility setting

1. Open the Calibration page for the Surveyor LC Pump (see “Accessing the Calibration
Options for the Surveyor LC Pump Plus” on page 260).
2. Type a new value into the Compressibility setting box. Then click Set.

 To optimize the compressibility setting for your application

1. Set up your system:

a. Set up a device to record the pressure output from the back panel pressure terminals.
See “Pressure Recorder Full Scale” on page 264.
b. Scale the output of the pressure terminals as described in “Scaling the Output of the
Pressure Recorder Terminals” on page 268.
2. Download the mobile phase parameters specified in your application:
a. If it is not already on, turn on the power to the Surveyor LC Pump Plus.
b. From the Surveyor LC Pump view, choose Surveyor LC Pump > Direct Control >
Operation.
The Operation - Surveyor LC Pump Direct Control dialog box appears
(see Figure 171).

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Calibrating the Surveyor LC Pump Plus

Figure 171. Operation - Surveyor LC Pump Direct Control dialog box

c. In the Method area, enter the specified flow rate in the Flow Rate box and enter the
specified mobile phase composition in the Component A through Component D
boxes.
d. Click Download to send these parameters to the onboard CPU of the Surveyor LC
Pump Plus.
e. Click Pump On to turn on the pump flow.
3. Record the pressure trace.
4. If the pressure pulsation is too high for your application, change the compressibility
setting. Then, repeat steps 2 and 3. Continue to change the compressibility setting until
the level of pump pulsation is adequate for your application.

Note Changing the compressibility setting affects the flow rate.

5. After you change the compressibility setting to minimize the pressure pulsation, check the
flow rate. If necessary, adjust the flow rate adjustment setting as described in “Updating
the Flow Rate Adjustment Setting” on page 268.

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Scaling the Output of the Pressure Recorder Terminals

For information on using the pressure terminals on the pump’s back panel, see “Pressure
Recorder Full Scale” on page 264.

 To set the full-scale output of the pressure recorder terminals

1. Open the Calibration page for the Surveyor LC Pump (see “Accessing the Calibration
Options for the Surveyor LC Pump Plus” on page 260).
2. Enter a value from 1 to 10 in the Pressure Recorder Full Scale box (see Figure 168 on
page 261). Then click Set. For information on scaling the output of the pressure recorder
terminals, see “Pressure Recorder Full Scale” on page 264.

Updating the Flow Rate Adjustment Setting

If you change the compressibility setting for the Surveyor LC Pump, you might also need to
change its flow rate adjustment setting. Changing the flow rate adjustment setting can
compensate for minor deviations in the flow rate of approximately ±5 percent from the
expected value.

 To update the flow rate adjustment setting

1. Open the Calibration page for the Surveyor LC Pump (see “Accessing the Calibration
Options for the Surveyor LC Pump Plus” on page 260).
2. In the Flow Rate Adjustment (alpha) box (see Figure 168 on page 261), type a new value:
• If the actual flow rate is below the set value, increase the alpha value. If you are
pumping water, increasing the alpha value by 1increases the flow rate by 1%.
For example, if the pump is set to deliver a flow rate of 1 mL/min and the actual flow
rate is 0.96 mL/min, which is 4 percent below the set rate, raise the current setting
by 4. If the current setting is 5.0, enter a new setting of 9.0.
• If the actual flow rate is above the set value, decrease the alpha value. If you are
pumping water, decreasing the alpha value by 1 decreases the flow rate by 1%.
For example, if the pump is set to deliver a flow rate of 1 mL/min and the actual flow
rate is 1.04 mL/min, which is 4 percent above the set rate, lower the current setting
by 4. If the current setting is 5.0, enter a new setting of 1.0.
3. Click Set.

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Calibrating the Surveyor LC Pump Plus

Updating the Pressure Sensor Adjustment Setting

Reset this parameter when you replace the pressure sensor. Each pressure sensor is labeled with
a data sticker that contains a “0.XXXX” value for the pressure sensor adjustment setting.
Multiply this value by 10 000 and enter the result in the Pressure Sensor Adjustment
setting box.

 To update the pressure sensor adjustment setting

1. Open the Calibration page for the Surveyor LC Pump (see “Accessing the Calibration
Options for the Surveyor LC Pump Plus” on page 260).
2. In the Pressure Sensor Adjustment box (see Figure 168 on page 261), type the value on
the data sticker “0.XXXX” multiplied by 10 000.
3. Click Set.

Zeroing the Pressure Transducer

The offset error of the pressure transducer is the value that is displayed when it should be zero,
such as when the purge manifold knob is set to the open position. You can correct for this
offset error by re-zeroing the pressure readout of the pressure transducer when the purge
manifold knob is open.

 To re-zero the output of the pressure transducer

1. Stop the flow of solvent from the LC pump:

a. From the Instrument Setup window, choose Surveyor LC Pump > Direct Control >
Operation.
b. Click Pump Off.
2. Open the drain valve to ensure that the transducer is actually sensing zero system pressure
(see Figure 172). When the drain valve is in the open position, look for the word DRAIN
to appear upside down on the knob.
Figure 172. Drain valve in closed and open positions

Closed position Open position

DRAIN
SE
O
PE

LO
N

C
C

N
LO

PE
SE

DRAIN
O

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9 LC Pump Calibration and Record Keeping
Recording Maintenance Information for the Surveyor LC Pump Plus

3. Open the Calibration page of the Direct Control dialog box by choosing
Surveyor LC Pump > Direct Control > Calibration.
4. Click Zero in the Pressure Transducer area (see Figure 168 on page 261).
5. When you are finished zeroing the pressure transducer, close the drain valve by gently
turning the knob clockwise until you feel resistance.

Note Applying excessive force to the drain valve knob reduces the life span of its
O-ring.

Recording Maintenance Information for the Surveyor LC Pump Plus

Use the Direct - Control Maintenance dialog box to update the maintenance information for
the Surveyor LC Pump Plus and to set the pistons to the maintenance position.

Each pump head assembly contains a piston seal. The two seals can wear at different rates,
causing leaks to occur in one or both pump heads. Before dismantling the pump head
assemblies, attempt to determine the source of the leakage. To save time and materials, replace
only the piston seal in the pump head assembly that is leaking. Or, as a preventive measure,
replace the piston seals after pumping 120 L of mobile phase.

 To open the Direct Control - Maintenance dialog box

From the menu bar of the Surveyor LC Pump Plus view, choose Surveyor LC Pump >
Direct Control > Maintenance.
The Maintenance - Surveyor LC Pump Direct Control page appears (see Figure 173).
Figure 173. Direct Control - Maintenance dialog box

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 9 LC Pump Calibration and Record Keeping
Recording Maintenance Information for the Surveyor LC Pump Plus

 To reset the solvent volumes or the pump operating time

Perform the following tasks as specified:

• Every time you install a new piston seal, click the appropriate Reset button.
Clicking Reset sets the readback for the volume of liquid pumped by the respective
pump head assembly to zero.
• If you install a new motor, click the Reset button under Pump Operating Time.
Clicking Reset sets the recorded hours for the pump operating time to zero.

 To set the pistons to the maintenance position before removing the pump heads

Click Maintenance Position.

Maintenance -Surveyor LC Pump Direct Control Parameters

Table 59 describes the parameters in the Maintenance dialog box for the
Surveyor LC Pump Plus.
Table 59. Maintenance dialog box for the Surveyor LC Pump Plus
Parameter Description
Left Seal Volume
Reset Zeros the recorded volume of mobile phase pumped by the left pump head.

Every time you install a new piston seal in the left pump head, click Reset in the Left Seal
Volume area to set the recorded volume of liquid pumped by the left pump head assembly
back to zero.
Right Seal Volume
Reset Zeros the recorded volume of mobile phase pumped by the right pump head.

Every time you install a new piston seal in the right pump head, click Reset in the Right
Seal Volume area to set the recorded volume of liquid pumped by the right pump head
assembly back to zero.
Pump Operating Time
Reset Resets the recorded operating time for the Surveyor LC Pump Plus to zero.

If you install a new motor, click Reset in the Pump Operating Time area to set the recorded
Pump Operating Time back to zero.
Position Pistons
Maintenance Position Sets the pistons to the maintenance position.

Set the pump pistons to the maintenance position before removing the pump heads.

To set the pistons to the maintenance position, click Maintenance Position.

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Firmware Version Information for the Surveyor LC Pump Plus

Firmware Version Information for the Surveyor LC Pump Plus

Use the Configuration - Surveyor LC Pump Direct Control dialog box (see Figure 174) to
view the firmware versions of the pump’s Main board and Pump Converter board.
Figure 174. Configuration - Surveyor LC Pump Direct Control dialog box

 To view the firmware version of your Surveyor LC Pump Plus

1. Open the pump view.

2. From the menu bar, choose Surveyor LC Pump > Direct Control > Configuration.
The Configuration - Surveyor LC Pump Direct Control page appears.

Configuration Page Parameters

Table 60 describes the parameters on the Firmware page.
Table 60. Configuration - Surveyor LC Pump Direct Control page parameters
Parameter Description
Firmware Versions
Pump Main Board Displays the firmware version of the Pump Main printed circuit
board.
Pump Converter Displays the firmware version of the Pump Converter printed
Board circuit board.

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Autosampler Calibration and Record Keeping

This chapter describes the calibration and record keeping procedures for the autosampler.

Contents
• Calibrating the Autosampler
• Autosampler Maintenance Information
• Autosampler Validation Information

The autosampler does not require calibration upon arrival at its shipping destination.
However, if you use custom vials or custom microplates, you must perform the Well Bottom
Distance calibration, which determines the actual depth of a vial or microplate well (see “Well
Bottom Distance Calibration” on page 305). If problems occur with the column oven control,
the tray temperature control, or the arm positioning, contact a Thermo Fisher Scientific
service representative. This appendix includes calibration procedures for these items; however,
to calibrate the autosampler’s temperature zones and XYZ arm position, you must have the kit
that contains the necessary test fixtures.

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Calibrating the Autosampler

There are four calibration options for the autosampler:
• Column Oven Air Sensor Calibration
• Vial Tray Metal Sensor Calibration
• Arm Calibration
• Well Bottom Distance Calibration

The column oven and oven compartment temperature calibrations and the arm calibration
are typically performed by a Thermo Fisher Scientific field service representative. To perform
these calibrations yourself, you must have the service kit that contains the temperature test
fixtures. In addition, to calibrate the temperature sensors for the autosampler’s
temperature-controlled zones, your Thermo Scientific application must be capable of
providing feedback for these sensors.

Note Typically, a Thermo Fisher Scientific field service representative calibrates the
controlled temperature zones and the XYZ arm position. To perform the temperature
calibrations yourself, order the Field Service Calibration Kit (P/N 60053-62001). To
calibrate the XYZ arm, order the LED light fixture and the non-reflective target port
fixture.

If you choose to use custom vials or custom microwell plates, you must perform the
Well Bottom Distance calibration, which determines the depth of the custom vial or
microplate well. Perform this calibration you select a new custom tray configuration and each
time you use a new type of custom vial or custom microwell plate.

Note If you are controlling the autosampler from a Thermo Scientific data system other
than the Xcalibur data system, refer to the Help provided with your data system for
information about accessing the Calibration dialog box for the autosampler.

 To open the Calibration dialog box for the autosampler

1. Open the view for your autosampler.

2. In the menu bar, choose Surveyor AS > Calibration.
The Calibration dialog box appears (see Figure 175).

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Figure 175. Calibration dialog box for the autosampler

Column Oven Air Sensor Calibration

To calibrate the column oven temperature, you must have the oven sensor test fixture
provided in the Field Service Calibration Kit (P/N 60053-62001) for the autosampler.

CAUTION Because the column oven compartment can reach temperatures as high as
95 °C (203 °F), ensure that the column oven is off and that the column oven
compartment is at room temperature before you install the oven sensor test fixture.

To calibrate the column oven temperature, follow these procedures in order:

1. Preparing to Calibrate the Column Oven Temperature
2. Specifying the Internal Set Target for the Column Oven Calibration Temperature
3. Adjusting the Temperature Calibration for the Column Oven

Preparing to Calibrate the Column Oven Temperature

 To set up the system for a temperature calibration

1. Open the status view for the autosampler’s oven temperature.

To open the Oven page from the Xcalibur data system, do the following:
a. If the Information view is closed, click the Information View button ( ) to
open the view.
The Information view opens with the Status page displayed.

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b. Verify that the status reads Ready to Download.

For information about checking the status, see “Checking the Status of the LC
Devices” on page 136.
c. Click Surveyor AS in the directory tree.
The status pages for the autosampler appear at the bottom of the Status page.
d. Click the Oven tab.
The Oven status page appears.
2. On the Oven page, check the column oven status.
3. If the column oven is on and set to a high temperature, turn the column oven off, open
the column oven door, and wait for the column oven to cool to room temperature.
For information about using the direct controls to turn the column oven on or off, see
“Controlling the Tray and Oven Compartment Temperatures” on page 199.
4. Install the oven sensor test fixture (869C thermometer or equivalent) as follows:
a. If it is not already open, open the column oven door.
b. Loosen the top thumbscrew that holds the column clamp.
c. With the sensor facing down, slide the metal cable protector under the right side of
the clamp.
d. Verify that the sensor is between the upper and lower column clamps and that it is
not touching any metal.
e. Tighten the thumbscrew on the sensor, route the cable of the sensor so as not to
interfere with the door, and then close the column oven door.
5. Open the Calibration dialog box for the autosampler. For information about accessing
the Calibration dialog box from the Xcalibur data system, see “Calibrating the
Autosampler” on page 274.

Specifying the Internal Set Target for the Column Oven Calibration Temperature
Use the Internal Set Target page of the Column Oven Air Sensor Calibration wizard to specify
the calibration temperature.

 To specify the internal set target for the calibration temperature

1. Set up the system to perform the column oven calibration (see “Preparing to Calibrate the
Column Oven Temperature” on page 275).
2. Select the Column Oven Air Sensor Calibration option, and then click Next.
The Diagnostic - Internal Set Target page of the Column Oven Air Sensor Calibration
wizard appears (see Figure 176). The default calibration temperature is 50.0 °C.

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Figure 176. Diagnostic - Internal Set Target page of the Column Oven Air Sensor Calibration
wizard with the default temperature setting of 50.0 °C

The default temperature for the calibration of

the column oven temperature is 50.0 °C.

3. In the Calibration Target Temperature (C) box, type 30 (see Figure 177).
Figure 177. Diagnostic - Internal Set Target page of the Column Oven Air Sensor Calibration
wizard with the user setting of 30 °C

User setting. The range is 5 to 95 °C.

4. Click Start Calibration.

The data system turns on the column oven and downloads the target temperature.
The Next button becomes available.
5. Click Next.

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The Diagnostic - External Standard page of the Column Oven Air Sensor Calibration
wizard appears (see Figure 178). The default calibration temperature for the external
standard is 50 °C.
Figure 178. Oven page and the Diagnostic - External Standard page of the Column Oven Air
Sensor Calibration wizard

The oven control is on and the

set temperature is 30 °C.

The default temperature for

the calibration of the column
oven temperature is 50.0 °C.

Adjusting the Temperature Calibration for the Column Oven

 To adjust the temperature calibration for the column oven

1. Specify the calibration temperature and start the Column Oven Air Sensor Calibration
wizard (see “Specifying the Internal Set Target for the Column Oven Calibration
Temperature” on page 276).
2. Wait for the current temperature readback on the Oven page to reach 30.0 °C
(see Figure 179).
The Current temperature readback displays the temperature recorded by the
autosampler’s internal temperature sensor.

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Figure 179. Oven page, showing that the current temperature has reached the set temperature

The current temperature is 30 °C.

3. When the current temperature readback on the Oven page (autosampler view on the
Status page of the Information view) reaches exactly 30.0 °C (see Figure 179), do the
following:
a. Type the reading from the 869C thermometer in the External Standard
Temperature (C) box (see Figure 180).
For example, if the thermometer reading is 29.8 °C, type 29.8 in the External
Standard Temperature (C) box. The range is 0 to 110.0 °C.

Note The external standard is the thermometer.

Figure 180. Diagnostic - External Standard page of the Column Oven Air Sensor
Calibration wizard

Type the temperature reading

from the thermometer that you
temporarily installed in the
column oven compartment.
b. Verify that the current temperature on the Oven page is still displaying 30.0 °C.
c. On the Diagnostic - External Set Target page (see Figure 180), click Adjust.

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The data system downloads the temperature calibration to the autosampler and the
Finish button becomes available (see Figure 181).
Figure 181. Diagnostic - External Standard page of the Column Oven Air Sensor
Calibration wizard

Finish button

d. Repeat step 3a through step 3c until the readings from the 869C thermometer and
the current temperature readout agree within ±0.2 °C.
4. When the temperatures on the 869C thermometer and the Current Temperature
readback are within ±0.2 °C of each other, click Finish (see Figure 181).
5. On the Oven page, verify that the Current Temperature readback is stable at 30.0 °C with
a maximum temperature drift of ±0.2 °C.
6. After you verify the stability of the column oven temperature, turn off the column oven
using the autosampler direct controls and remove the temperature probe.
For information about the autosampler direct controls, see “Controlling the Tray and
Oven Compartment Temperatures” on page 199.

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Vial Tray Metal Sensor Calibration

Use the Vial Tray Metal Temperature Sensor Calibration wizard and an external temperature
sensor to calibrate the vial tray temperature control.

To perform the vial tray metal sensor calibration procedure, you must have the following
items provided in the Field Service Calibration Kit (P/N 60053-62001):
• Calibrated Omega 869C RTD thermometer or equivalent
• A/S vial tray sensor

To calibrate the column oven temperature, follow these procedures in order:

1. Preparing to Calibrate the Tray Compartment Temperature
2. Specifying the Internal Set Target for the Tray Compartment Temperature
3. Adjusting the Tray Temperature Calibration

Preparing to Calibrate the Tray Compartment Temperature

 To set up the system to calibrate the temperature of the tray compartment

1. Install the tray temperature sensor as follows:

a. Open the door to the tray compartment.
b. Install the tray temperature sensor into location E of the tray compartment.
The tray temperature sensor is a standard tray with a temperature sensor cemented
into a middle vial location of the tray.
c. Route the cable of the sensor through the notch at the top on the tray compartment
so that it does not interfere with the door closure.
d. Close the door to the tray compartment.
2. Open the status page for the tray temperature.
To open the Tray page from the Xcalibur data system, do the following:
a. If the Information view is closed, click the Information View button ( ) to
open the view.
The Information view opens with the Status page displayed.
b. Verify that the status reads Ready to Download. For more information, see
“Checking the Status of the LC Devices” on page 136.
c. Click the listing for the autosampler in the directory tree.
The status pages for the autosampler appear at the bottom of the Status window.

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3. Click the Tray tab.

The Tray page appears (see Figure 182).
Figure 182. Tray page

4. Open the Calibration dialog box for the autosampler (see “Calibrating the Autosampler”
on page 274).
5. Select the Vial Tray Metal Sensor Calibration option (see Figure 183).
Figure 183. Calibration dialog box

6. Click Next.
The Diagnostic - Internal Set Target page of the Vial Tray Metal Sensor Calibration
wizard appears (see Figure 184).
The default external standard temperature is 40.0 °C.

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Specifying the Internal Set Target for the Tray Compartment Temperature
Use the Diagnostic – Internal Set Target page (see Figure 184) of the Vial Tray Metal Sensor
Calibration wizard to specify the calibration temperature.
Figure 184. Diagnostic - Internal Set Target page of the Vial Tray Metal Sensor Calibration wizard

Default temperature

 To specify the target calibration temperature for the tray compartment and start the
calibration
1. Prepare the system for the temperature calibration (see “Preparing to Calibrate the Tray
Compartment Temperature” on page 281).
2. In the Calibration Target Temperature box, type 30.0, and then click Start Calibration
(see Figure 185).

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Figure 185. Diagnostic -Internal Set Target page of the Vial Tray Metal Sensor Calibration
wizard

User setting

The data system turns on the tray temperature control and downloads the set temperature
of 30.0 °C. The Next button becomes available.
3. Click Next.
The Diagnostic - External Standard page appears (see Figure 186). The default external
standard temperature is 40.0 °C. The range is 0 to 110.0 °C.
Figure 186. Tray page and the Diagnostic - External Standard page of the Vial Tray Metal
Sensor Calibration wizard

Tray temperature control is on.

The set temperature is 30.0 °C. Default setting

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Adjusting the Tray Temperature Calibration

Use the Diagnostic – External Standard page of the Vial Tray Metal Sensor Calibration
wizard, the status readout on the Tray page, and the external temperature sensor to adjust the
temperature calibration of the tray compartment.

 To adjust the calibration temperature of the tray compartment

1. When the current temperature readback on the Tray page reaches exactly 30.0 °C
(see Figure 187), do the following:
a. In the External Standard Temperature (C) box (see Figure 187) on the External Set
Target page, type the reading from the thermometer.
Figure 187. Tray page (status view) and the Diagnostic - External Standard page of the Vial Tray
Metal Sensor Calibration wizard

Type the temperature reading

Current temperature has from the test fixture that you
reached the set temporarily installed in the
temperature of 30.0 °C. tray compartment.

b. On the Tray page, verify that the Current Temperature readback still displays
30.0 °C.
c. On the Diagnostic - External Standard page (see Figure 187), click Adjust.
The data system downloads the calibration to the autosampler and the Finish button
becomes available (see Figure 188).

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Figure 188. Diagnostic - External Standard page of the Vial Tray Metal Sensor Calibration
wizard with an available Finish button

d. Repeat step 1a through step 1c until the temperatures on the thermometer and the
current temperature readout (see Figure 187) agree within ± 0.2 °C.
2. When the temperatures on the 869C thermometer and the Current Temperature readout
are within ±0.2 °C of each other, click Finish at the bottom of the Diagnostic - External
Set Target page.
3. On the Tray status page, verify that the Current Temperature readout is stable at 30.0 °C
with a maximum temperature drift of ± 0.2 °C.
4. After you have verified the stability of the oven tray temperature, remove the temperature
probe.

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Arm Calibration
During an injection, the XYZ arm moves between the specified vial or well location and the
injection port. When you move the autosampler, you can jar the XYZ arm, causing it to lose
alignment.

Performing the arm calibration procedure requires you to visually align the XYZ arm over the
injection port. To make this visual alignment, you must replace the needle with an LED light
fixture that shines a small beam of red light onto the port and replace the stainless steel
injection port with a non-reflective target fixture. These test fixtures do not come with the
autosampler; you must order them from Thermo Fisher Scientific.

After following the instructions in the Arm Calibration wizard to adjust the XYZ arm
alignment, test the alignment by making a set of injections from one or two 384-well
microplates. The microplate carrier and the 384-well microwell plates are provided in the
Autosampler Accessory Kit.

To calibrate the XY position of the XYZ arm, you must have these items:
• LED light fixture (P/N 60357-60021)
• Target port fixture (P/N 60357-20021)
• Microplate carrier
• One or two 384-well microtitre plates
• Masking tape

Figure 189 shows the LED light and the target port fixtures.
Figure 189. Arm calibration fixtures available by special order

8-pin connector LED holder

Target port fixture

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To calibrate XY position of the XYZ arm and verify the calibration, follow these procedures:
1. Modifying the Autosampler Instrument Configuration
2. Starting the Arm Calibration Wizard
3. Moving the Arm to the Needle Removal Position
4. Installing the LED Light Fixture and the Target Port Fixture
5. Moving the XYZ Arm to the Home Position
6. Aligning the Light Beam with the Target
7. Applying the Arm Calibration Setting
8. Checking the Arm Calibration Offset Values
9. Testing the Alignment of the XYZ Arm

Modifying the Autosampler Instrument Configuration

To calibrate the arm position, turn off the feature that prevents control of the autosampler
when the tray compartment door is open.

 To modify the instrument configuration for the autosampler

1. Open the Surveyor Autosampler Configuration dialog box.

The dialog box opens with the Tray page displayed (see Figure 190).

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Figure 190. Tray page with the 384-well microplate tray type selected

2. Select the 384-well plate tray type.

3. In the A1 Well Position area, select the Top Left option.
4. Click the Communication tab.
The Communication page appears.
5. Clear the Verify Door Is Closed check box (see Figure 191).

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Figure 191. Communication page with the Verify Door Is Closed check box cleared

Clear this check box.

When the Verify Door Is Closed check box is selected, the data system prevents you from
starting an injection sequence or using some of the direct control commands for the
autosampler when the tray compartment door is open.
6. Click OK at the bottom of the dialog box to accept the settings and close the dialog box.
7. Click Done to close the Thermo Foundation Instrument Configuration window.

Go to the next procedure, “Starting the Arm Calibration Wizard.”

Starting the Arm Calibration Wizard

Use the Arm Calibration wizard to adjust the home position of the XYZ arm.

For information about the LED light and non-reflective needle port fixtures that you must
have to perform the Arm Calibration wizard, see “Arm Calibration” on page 287.

 To start the Arm Calibration wizard

1. If you have not already done so, modify the autosampler instrument configuration as
described in “Modifying the Autosampler Instrument Configuration” on page 288.
2. Open the view for the autosampler.
3. From the Surveyor AS menu, choose Calibration.
The Calibration dialog box appears (see Figure 192).
4. Select the Arm Calibration option.

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Figure 192. Calibration dialog box with the Arm Calibration option selected

The Arm Calibration wizard appears (see Figure 193).

The Current Calibration Values area displays the current calibration values for the x-axis
and y-axis position of the XYZ arm over the autosampler injection port.
Figure 193. Current Calibration Values page

Note The user interface specifies the x- and y-axis offsets in microns, which is another
term for micrometers.

1000 micrometers = 0.04 inches

The diameter of the hole in the center of the target port fixture is 0.047 inches.

5. Click Next to proceed to the next page of the wizard.

Go to the next procedure, “Moving the Arm to the Needle Removal Position.”

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Moving the Arm to the Needle Removal Position

Use this page of the Arm Calibration wizard to move the arm to the needle removal position
(see Figure 194).
Figure 194. Move the Arm to Needle Removal Position button page

 To move the XYZ arm to the needle removal position

1. Click Move the Arm to Needle Removal Position.

The XYZ arm moves to the center front of the tray compartment and the needle holder
moves down 1 inch.
2. Click Next to proceed to the next page of the wizard.

Go to the next procedure, “Installing the LED Light Fixture and the Target Port Fixture.”

Installing the LED Light Fixture and the Target Port Fixture
This page of the Arm Calibration wizard instructs you to remove the needle and install the
calibration light source (see Figure 195).
Figure 195. Request to install the LED light fixture page

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The needle assembly is a welded piece of 0.012 in. ID stainless steel tubing with an externally
threaded fitting, a needle flag, a latch, and a compression spring (see Figure 196). It slides into
the needle mount on the XYZ arm and is secured with the latch. The needle tubing assembly
has an internally threaded fitting that connects to the 10-32 externally threaded fitting of the
needle assembly.
Figure 196. Needle assembly

Latch
10-32 fitting
Compression
spring
Needle flag

Needle mount on
the XYZ arm

 To install the light fixture and the target port fixture

1. Remove the needle assembly from the needle mount as follows:

a. Unscrew the needle tubing assembly from the needle assembly.
b. For the Surveyor Autosampler Plus, remove the syringe drive assembly (refer to the
instructions in the Surveyor Autosampler Plus Hardware Manual).
c. Pull the latch nut of the needle assembly forward.
d. Pull the needle up from the needle mount on the XYZ arm.
2. Install the LED light fixture as follows:
a. Connect the 8-pin connector of the light fixture cable to the timed events connector
on the back panel of the autosampler (see Figure 197). The red wire with the resistor
connects to the +5V autosampler pin and the black wire connects to the autosampler
ground pin.

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Figure 197. Cable connection for the light fixture

Resistor

Light fixture connector

8-pin connector on the back panel of

the autosampler

b. Verify that the LED is brightly lit.

c. Insert the LED holder into the needle mount (see Figure 198).

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Figure 198. Inserting the LED holder into the needle mount

LED holder

Needle mount

d. Push the LED holder down until it meets resistance from the needle mount.
e. Make sure that the light fixture cable is routed so that it does not obstruct the
movement of the XYZ arm.
3. Install the target port fixture as follows:
a. Remove the aluminum retention clip (see Figure 199) from the wash station housing,
pull it forward, and then upward.
Figure 199. Retention clip for the autosampler injection port

Retention clip

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b. Pull the injection port out from the wash station (see Figure 200).
Figure 200. Autosampler injection port connected to the transfer tube nut

Injection port

Transfer tube nut

4. Insert the target port fixture (see Figure 189 on page 287) into the position previously
held by the injection port.
5. Click Next to proceed to the next page of the wizard.

Go to the next procedure, “Moving the XYZ Arm to the Home Position.”

Moving the XYZ Arm to the Home Position

Use this page of the Arm Calibration wizard (see Figure 201) to move the XYZ arm to the
home position. In the home position, the XYZ arm is aligned over the autosampler injection
port.
Figure 201. Move the Arm to the Home Position button page

 To move the XYZ arm to the home position

1. Click Move the Arm to the Home Position.

The XYZ arm moves to the home position. The Next button becomes available.
2. Click Next to proceed to the next page of the Arm Calibration wizard.

Go to the next procedure, “Aligning the Light Beam with the Target.”

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Aligning the Light Beam with the Target

Use this page of the Arm Calibration wizard (see Figure 202) to adjust the fine position of the
XYZ arm.

Two lead screws and two stepper motors control the x-axis and y-axis position of the XYZ arm
(see Figure 203).

The Left and Right buttons move the XYZ arm along the x axis. The Forward and Backward
buttons move the XYZ arm along the y axis.
Figure 202. Alignment buttons page

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Figure 203. XYZ arm of the Surveyor Autosampler Plus

x-axis
stepper motor
y-axis
stepper motor
XYZ arm

x-axis
y-axis
lead screw
lead screw

y axis

x axis

 To align the light beam over the hole in the target port fixture

1. In the Step list of the Arm Calibration wizard, select 25x (793.75 microns).
This selection moves the arm 793.75 micrometers (0.03125 inches) each time you click
Left, Right, Forward, or Backward.
1 micrometer = 3.937 × 10–5 inches
2. Click Left, Right, Forward, and Backward to align the position of the light beam with
the hole in the center of the target port fixture.
3. In the Step list, select a smaller step size, and continue aligning the position of the
light beam.
4. After you align the light beam with the hole in the center of the target port fixture,
click Next to proceed to the next page of the wizard.

Go to the next procedure, “Applying the Arm Calibration Setting.”

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Applying the Arm Calibration Setting

Use this page of the Arm Calibration wizard (see Figure 204) to download the new arm
calibration settings.
Figure 204. Set Calibration button page

 To apply the current calibration settings for the arm position

1. Ensure that the light beam is centered over the hole in the target port fixture
(see Figure 205).
Figure 205. LED light beam centered over the hole in the target port fixture

LED light beam aligned with the

hole in the target port fixture

2. Click Set Calibration.

The Next button becomes available.
3. Click Next to proceed to the final page of the wizard.

Go to the next procedure, “Checking the Arm Calibration Offset Values.”

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Checking the Arm Calibration Offset Values

Use this page of the Arm Calibration wizard to check the calibration values and close the
wizard (see Figure 206).
Figure 206. Final page of the Arm Calibration wizard with the Finish button

 To verify the calibration setting

1. In the Current Calibration Values area, verify the following:

• The X Offset readback displays a value from +900 to –900 μm.
• The Y Offset readback displays a value from 1500 to 2500 μm.

Tip 1000 microns = 1000 micrometers = 0.04 inches

The diameter of the hole in the center of the target port fixture is 0.047 inches.

2. Click Finish to accept the settings and close the Arm Calibration wizard.
3. Remove the LED and target port calibration fixtures.
4. Reinstall the injection port as follows:
a. Insert the injection port into the port in front of the wash station.
b. Align the retention clip with the slot located in front of the wash station.
c. Using the retention clip to push the injection port down, align the circular cutout in
the retention clip over the alignment screw.
d. Insert the end of the retention clip into the wash station slot as far as it will go.
Figure 207 shows the installation of the retention clip.

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Figure 207. Retention clip installation

Slot in wash station

Injection port

Alignment screw

Retention clip
installed

5. Reinstall the needle assembly as follows:

a. Remount the syringe drive assembly.
b. Slide the needle into the needle mount on the XYZ arm.
c. Turn the latch to the right.
d. Reconnect the needle tubing assembly to the needle assembly.

Leave the autosampler view of the Instrument Setup view open and go to the next procedure,
“Testing the Alignment of the XYZ Arm.”

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Testing the Alignment of the XYZ Arm

To test the alignment of the XYZ arm, make injections from the four corners of two 384-well
microplates.

 To test the alignment of the XYZ arm

1. Cover columns 1, 2, 23, and 24 of two 384-well microplates with tape (see Figure 208).
Figure 208. 384-well microplate positions
A1 A24
A

P P1 P24

1 24
2. Place the microplates in each end of the microwell carrier, leaving the middle position
empty.
3. Load the microwell carrier into the tray compartment of the autosampler as follows:
a. From the menu bar, choose Surveyor AS > Direct Control.
The Direct Control dialog box appears (see Figure 209).

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Figure 209. Direct Control dialog box for the autosampler

b. Select Position Arm to Access Tray, and then click Apply.

The XYZ arm moves to the back of the tray compartment.
c. Insert the microwell carrier into the tray compartment.
d. Verify that the microwell carrier sits flat and is properly installed.
4. Send the XYZ arm to the home position as follows:
a. In the Direct Control dialog box, select Go to Home Position.
b. Click Apply.
The XYZ arm moves to the home position, which is above the injection port.
5. Make an injection from each corner of the microplate as follows:
a. In the Direct Control dialog box, select Inject Sample.
The sample injection parameters appear (see Figure 210).
Figure 210. Direct Control dialog box with the Inject Sample command selected

b. In the Vial box, type C:A1.

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c. Click Apply and wait for the injection to finish.

The XYZ arm moves to the location of the A:1 well of the (C) microplate at the back
of the tray compartment, and then lowers the needle through the masking tape and
into the well.
d. In the Vial box, type C: A24.
e. Click Apply and wait for the injection to finish.
f. In the Vial box, type C: P1.
g. Click Apply and wait for the injection to finish.
h. In the Vial box, type C: P24.
i. Click Apply and wait for the injection to finish.
6. Remove the microplate and check the location of the injections as follows:
a. In the Direct Control dialog box, select Position Arm to Access Tray.
The XYZ arm moves to the back of the tray compartment.
b. Remove the tray from the tray compartment, and inspect the holes in the tape. Verify
that the holes are at or near the center of the microplate wells. Each hole must be at
least 0.05 cm (0.02 inches) from the edge of the well.
7. If the results are not satisfactory, repeat the arm calibration, and then repeat the alignment
test with the second (A) microplate, located at the front of the tray compartment.

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Well Bottom Distance Calibration

The autosampler supports custom vials and well plates in addition to the standard 1.8 mL
vials, 96-well plates, and 384-well plates. However, to use custom vials or well plates, you
must first determine how far the autosampler needle must travel to reach the bottom of the
vials or wells.

Use the Well Bottom Distance wizard to determine the distance that the needle must travel to
reach the bottom of a vial or well. The XYZ arm uses this value when you select one of the
custom tray configurations.

IMPORTANT Because the autosampler stores only one value for the custom well bottom
distance, you must perform a well bottom distance calibration each time you select a new
custom tray type configuration and each time you use a different type of custom vial or
custom microwell plate.

To perform a well bottom distance calibration, follow these procedures in order:

1. Starting the Well Bottom Distance Wizard
2. Selecting the Calibration Method for the Well Bottom Distance
3. Depending on the selected calibration method, follow one of these procedures:
• Manually Entering the Well Bottom Distance
–or–
• Using the Needle Sensor to Determine the Well Bottom Distance

Starting the Well Bottom Distance Wizard

 To start the Well Bottom Distance wizard

1. Open the status view for the autosampler.

For information about opening the status view from the Xcalibur data system, see
“Checking the Status of the LC Devices” on page 136.
2. Verify that the autosampler status reads Ready to Download.
3. Open the view for the autosampler.
4. From the Surveyor AS menu, choose Calibration.
The Calibration dialog box appears (see Figure 211).

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Figure 211. Calibration dialog box with the Well Bottom Distance option selected

5. Select the Well Bottom Distance option, and then click Next.
The Select Calibration Method page appears (see Figure 212).
Figure 212. Select Calibration Method page

Go to the next procedure, “Selecting the Calibration Method for the Well Bottom Distance”
on page 306.

Selecting the Calibration Method for the Well Bottom Distance

Use the Select Calibration Method page of the Well Bottom Distance wizard to select a
calibration method. You can manually enter a bottom distance value for your custom vials or
microplates, or you can use the autosampler’s needle sensor feature to determine the correct
distance value.

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 To select the calibration method for the well bottom distance

Do one of the following:

• Select the Enter Value Manually option if you want to enter a previously determined
value for the well bottom distance. Click Next. Then go to the next procedure,
“Manually Entering the Well Bottom Distance.”
–or–
• Select the Calibrate to Find Value option to perform an active calibration. Click
Next. Then go to “Using the Needle Sensor to Determine the Well Bottom Distance”
on page 308.

Note The autosampler stores only one well bottom distance value for custom tray
configurations. The number at the top of this dialog box is the current value for
the distance.

Manually Entering the Well Bottom Distance

 To manually enter a new value for the well bottom distance

1. In the Enter New Value (microns) box, type the new value in micrometers
(see Figure 213).
The range is 15 000 to 46 990 micrometers (15 to 46.9 mm).

Note The user interface specifies the bottom distance in microns, which is another
term for micrometers.

Figure 213. Manual calibration page

2. Click Set Calibration.

The new bottom distance value (in microns) appears at the top of the dialog box and the
Finish button becomes available.
1 micron = 1 micrometer
3. Click Finish to close the Well Bottom Distance dialog box.

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Using the Needle Sensor to Determine the Well Bottom Distance

The autosampler has a needle sensor that can determine the bottom distance of custom vials
or microplate wells.

 To determine the well bottom distance with the autosampler’s needle sensor

1. Remove the cap or lid from your vial or well plate.

IMPORTANT Remove vial caps or well plate lids before performing an active well
bottom distance calibration. As the needle pierces a vial cap or a well plate lid, the
spring in the needle mechanism is compressed, which can cause premature activation
of the needle sensor.

IMPORTANT Before placing a custom tray into the autosampler tray compartment,
check the height limitations for 96-well and 384-well plates listed in the hardware
manual for your autosampler. Tall objects will stall the autosampler arm.

2. Place the vial into a tray or the well plate into a carrier, and then place the tray or carrier
into the tray compartment of the autosampler.
3. In the Calibrate at Well/Vial position box (see Figure 214), type a vial or well location.

Note If you are calibrating the bottom distance of a vial, verify that you have placed a
vial in the selected location.

Figure 214. Calibrate to find page

4. Click Set Calibration to activate the autosampler.

After the XYZ arm moves to the selected location, the needle mechanism descends until it
detects the bottom of the vial or well. After it detects the bottom, the XYZ arm moves to
the home position. In the Well Bottom Distance wizard, the new bottom distance
calibration value appears at the top of the page.
5. Click Finish to accept the calibration.

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Autosampler Maintenance Information

Autosampler Maintenance Information

Use the Maintenance Information dialog box (see Figure 215) to set the scheduled
maintenance time (SMT) for the autosampler maintenance items: Injections, Valve Cycles,
Needle Cycles, and Syringe Cycles.
Figure 215. Maintenance Information dialog box

 To open the Maintenance Information dialog box

1. Open the view for your autosampler.

The Method page for your autosampler appears.
2. In the menu bar, choose Surveyor AS > Maintenance.

 To set a new usage limit

1. Click the tab for the page that contains the maintenance item that you want to change the
usage limit for.
2. In the Usage Limit box, type the usage limit.
3. Click Set New Limit.

 To reset the usage counter after performing the scheduled maintenance task

1. Click the tab for the scheduled maintenance task.

2. Click Zero Counter.

Note If you selected the Enable Maintenance Log check box on the Communication page
of the Surveyor AS Autosampler dialog box when you configured the Surveyor
Autosampler, you can set the scheduled maintenance times (see “Communication Page”
on page 52).

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Autosampler Maintenance Information

Maintenance Information Parameters

Table 61 describes the parameters on the Maintenance Information pages.

When anyone of these counters on the Maintenance Information pages exceeds the
user-specified usage limit, the Maintenance Due readback displays Yes and the data system
prevents the autosampler from making injections.

To enable the autosampler, you must zero the counter or change the usage limit. If the usage
limit is based on a scheduled maintenance plan, perform the scheduled maintenance.
Table 61. Maintenance Information dialog box pages and parameters
Page or Parameter Description
Page
Injections Use this page to set the scheduled maintenance time for the number of user-defined
injections (excluding any cancelled injections).
Valve Cycles Use this page to set the scheduled maintenance time for the number of user-defined valve
cycles for the injection valve (from Fill to Inject).
Needle Cycles Use this page to set the scheduled maintenance time (SMT) for the number of user-defined
needle cycles when the needle is inserted into a septum, injection port, or wash station.
Syringe Cycles Use this page to set the scheduled maintenance time (SMT) for the number of user-defined
syringe cycles where the syringe is put in the Ready position.
Parameter
Usage Limit Use this box to specify the new usage limit for the selected maintenance item.
Note When a counter exceeds the usage limit, the autosampler cannot start a run until
you reset the counter to zero, change the usage limit, or clear the Enable Maintenance Log
check box on the Communication page of the Surveyor Autosampler Configuration
dialog box (see “Communication Page” on page 52).
Set New Limit Downloads the new usage limit to the autosampler.
Current Counter and Displays the current count. When the counter exceeds the usage limit (scheduled
Zero Counter maintenance time), the autosampler cannot start a run until you perform the scheduled
maintenance or clear the Enable Maintenance Log check box on the Communication page
of the Autosampler Configuration dialog box.
Zero Counter Zeros the counter for the selected maintenance item.

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Autosampler Validation Information

Autosampler Validation Information

Use the Validation Information dialog box (see Figure 216) to enter the validation date for the
indicated parameter and the name of the person who performed the validation.
Figure 216. Validation Information dialog box

 To open the Validation Information dialog box

1. Open the view for your autosampler.

The Method page for your autosampler appears.
2. In the menu bar, choose Surveyor AS > Validation.
The Validation Information dialog box appears.

 To specify your user name and the validation date

1. In the Time box, type or select the validation date.

2. In the Initial Name box, type your initials.
3. Click Set.

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Validation Information Parameters

Table 62 describes the parameters on the Validation Information dialog box.
Table 62. Validation Information dialog box parameters
Parameter Description
Time To change the date that the validation was performed, click the
arrows to increase or decrease the value, and then click Set.
Initial Name To change the name of the person who performed the validation,
type the new value in the Initial Name box, and then click Set.
Current Values This readback displays the current time and initial name.
Button
Set Enter the appropriate values in the Time box and the Initial Name
box, and then click Set to set the values.

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 11

PDA Detector Performance Check and Calibration

This chapter describes the performance verification and calibration procedures for the PDA
detector.

Contents
• Verifying the Performance of the PDA Detector
• Calibrating the PDA Detector

The PDA detector is factory tested for linearity, noise, and drift. Because of the sensitivity of
its optical bench, adjust the light throughput to the diode array and recalibrate the PDA
detector after you install it, and each time you move it, change its flow cell, or replace either of
the lamps.

Verifying the Performance of the PDA Detector

Before you perform either calibration procedure, turn on both lamps (see “Turning the Lamps
On or Off ” on page 163), let the temperature of the detector stabilize for approximately
one hour, and adjust the light throughput to the diode array detector.

To adjust the light throughput to the diode array, follow these procedures:
• Creating a Display Method
• Adjusting the Light Throughput to the Diode Array

Creating a Display Method

Methods that display a plot of integrated light intensity versus diode number have a .spda file
extension.

 To create a display method for the PDA detector

1. In the view bar of the Instrument Setup window, click the Surveyor PDA Plus button.
The view for the PDA detector appears.
2. In the Units area, select the Diode/Intensity option (see Figure 217).

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Figure 217. Surveyor PDA Plus Method page with the Diode/Intensity option selected

3. Verify that the following parameters are specified on the Surveyor PDA Method page in
the Spectra area:
• Start Diode (diode num) = 2
• End Diode (diode num) = 511
• Diode Step (diode num) = 1

Note For a display method, the following parameters are not downloaded to the PDA
detector: run length, filter rise time, and sample rate.

4. Choose File > Save to save the display method.

An error message appears (see Figure 218).
Figure 218. Error message that appears when you attempt to save a display method

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5. Click OK.
6. From the menu bar, choose Surveyor PDA > Direct Control.
7. Click Yes.
The Save PDA Display Method dialog box appears.
8. Save the display method.
The data system saves the method with a .spda file extension.

Note The .spda file extension is a special file extension used for all method files based
on Diode/Intensity units. When you create a file with an .spda file extension, you can
only load and use it in the Direct Control dialog box.

After you save the method, the Direct Control dialog box appears with the Display page
open.
9. To adjust light throughput to the diode array, go to “Adjusting the Light Throughput to
the Diode Array.”

Adjusting the Light Throughput to the Diode Array

The PDA Detector has two attenuators that control the light throughput from the lamps.
Manually adjusting the position of the attenuators increases or decreases the amount of light
falling onto the array.

Adjust the light throughput to the diode array whenever you do the following:
• Observe an increase in the detector noise level.
• Move the detector.
• Replace either lamp or the flowcell.

The first time that you adjust the attenuators, you must create a display method that records
light intensities. You can identify display methods by their .spda file extension. After creating
the method for adjusting the attenuators, save it with a descriptive name, such as
diagnostics.spda, and store it for future use to simplify future adjustments of the attenuators.

Note Before you adjust the attenuators, replace the column with a flow restrictor, and set
the pump to deliver HPLC-grade water at a flow rate of 1 mL/min through the flowcell.

To adjust the light output from the lamps, follow these procedures in order:
1. “Preparing the LC System for an Attenuator Adjustment” on page 316
2. “Adjusting the Attenuators” on page 317
3. “Adjusting the Attenuators” on page 317

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Preparing the LC System for an Attenuator Adjustment

 To prepare the LC system for an attenuator adjustment

1. Ensure that the lamps are on.

You can view the lamp status from the Configuration page of the Direct Control dialog
box or from the PDA detector view of the Status page of the Information view. For
information about the Configuration page, see “Configuration Page” on page 171.
2. Replace the LC column with a flow restrictor.
3. Start pumping HPLC-grade water at a flow rate of 1 mL/min through the flowcell.

Go to the next procedure, “Accessing the Attenuators.”

Accessing the Attenuators

 To access the attenuators

1. Open the front doors of the detector.

2. Unscrew the captive screw, and then remove the flowcell cover.
The attenuators are located on the right side of the front panel. Two black tabs are
attached to the attenuators for manual adjustments (see Figure 219).
The left tab controls the light throughput from the deuterium lamp (UV region) and the
right tab controls the light throughput from the tungsten lamp (Visible region). Moving
an attenuator tab up increases the light throughput, and moving the tab down decreases
the light throughput to the diode array.
Figure 219. Attenuator tabs for the Surveyor PDA Plus Detector
Deuterium lamp
attenuator tab

Tungsten lamp
attenuator tab

Go to the next procedure, “Adjusting the Attenuators” on page 317.

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Adjusting the Attenuators

 To adjust the attenuators

1. If you have not already done so, create a display method to view the light intensity from
the lamps (see “Creating a Display Method” on page 313).
2. Load the display method to the detector as follows:
a. In the Direct Control dialog box for the PDA detector, click the Display tab.
The Display page appears.
b. In the Control area, click Load Method.
The Open Display Method dialog box appears (see Figure 220).
Figure 220. Open Display Method dialog box for the PDA detector

c. Choose your display method file (.spda).

d. Click Open.
The file name of the display method appears in the Current Method readback on the
Display page (see Figure 221 on page 318).
3. Start the data stream and adjust the attenuators as follows:
a. In the Control area, click Start Data.
The spectrum of light intensities appears in the top window (see Figure 221). For the
UV region, the diode of maximum intensity is between diode 10 and diode 50. For
the Visible region, the diode of maximum intensity is between diode 400 and
diode 500. Ignore the spike at approximately diode number 380. This spike is due to
the deuterium lamp.

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Figure 221. Display page for the PDA detector with an intensity spectrum

Start Data –or– Display method file name

SNAPSHOT button

b. Adjust the attenuators (see Figure 219 on page 316) as follows:

• Adjust the attenuator with the left tab on the PDA (UV range attenuation) to
achieve a maximum value from 400 000 to 900 000 intensity counts in the
region between diode number 10 and diode number 40.
• Adjust the attenuator with the right tab (Visible range attenuation) to achieve a
maximum value from 400 000 to 900 000 intensity counts in the region between
diode number 400 and diode number 500.
4. To record the light intensities, do the following:
• To save a picture of the scan to the Clipboard, press ALT+PRINT SCREEN. Paste
this picture into a text editor such as Microsoft™ Word. Keep this scan for future
comparisons to see if there is degradation in light intensity. Date the printout and
add it to your maintenance records.
• To save the data to a file, click SNAPSHOT.
The data system saves a comma-separated values file named PDASnapshot.csv to the
following folder on the data system computer:
drive:\Xcalibur\data
A date and time stamp are appended to the file name. The format of the date and
time stamp is MMDDYYHHMMSS. MM is the month. DD is the day of the
month. YY is the last two digits of the year. HH is the hour in military time. MM are
minutes. SS are seconds. You can open this file with the Excel application.

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For a wavelength/absorbance method, the file contains the absorbance values for the
spectral scan and the discrete channel wavelengths at the moment that you clicked
Snapshot.
For an intensity/diode method, the file contains the intensity values for the scan of
the diode array and the intensity values for up to three individual diodes.
5. After you finish adjusting the attenuators, replace the flowcell access cover, close the front
doors of the detector, and replace the flow restrictor with your LC column.

Calibrating the PDA Detector

For information about calibrating the PDA detector, see these topics:
• Calibration Page for the PDA Detector
• Performing a Dark Current Calibration
• Performing a Wavelength Calibration
• Creating and Editing a Custom Wavelength Calibration List

To calibrate the wavelength accuracy of the optical bench, the PDA detector uses a holmium
oxide reference solution, one of the four calibration files provided with the Xcalibur data
system, or your own custom wavelength calibration file.

IMPORTANT Before you perform a wavelength calibration, verify that the diode array is
not saturated (see “Adjusting the Light Throughput to the Diode Array” on page 315).

Figure 222 shows the holmium oxide spectrum.

Figure 222. Holmium oxide spectrum
Holmium Oxide Bands
537
Absorbance

451

641
417
241

287

361

485
278

333
345
250

230 270 310 350 390 430 470 510 550 590 630 670
Wavelength (nm)

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Calibration Page for the PDA Detector

Use the Calibration page (see Figure 223) to perform the dark current and wavelength
accuracy calibrations. Perform these calibrations on a regular basis and as part of the operation
verification procedure.
Figure 223. Calibration page, showing that the detector is not calibrated

Before you perform a wavelength calibration, verify that the diode array is not saturated (see
“Adjusting the Light Throughput to the Diode Array” on page 315).

 To open the Calibration page

1. From the PDA detector view, choose Surveyor PDA Plus > Direct Controls.
The Direct Control dialog box appears.
2. Click the Calibration tab.

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Note The diode array used in the PDA detector has a background count level at each
diode even when both lamps are off. This background count level is called the dark
current. This background or dark current must be subtracted from the intensity counts
before the intensity values are converted to absorbance units (AU). After you perform a
dark current calibration, the PDA detector corrects the spectrum intensity values for the
dark current.

 To start a dark current calibration

1. Turn on both lamps and wait one hour for the lamps to equilibrate (see “Turning the
Lamps On or Off ” on page 163).
2. In the Dark Current Calibration area, click Calibrate.
The Dark Current Calibration wizard appears.
3. Follow the instructions provided by the wizard. For more information, click Help at the
bottom of the Dark Current Calibration dialog box.

 To start a wavelength calibration

1. Disconnect the LC column from the system, and then pump HPLC-grade methanol
through the flowcell to remove any contaminants.
2. Turn on both lamps and wait one hour for the lamps to equilibrate (see “Turning the
Lamps On or Off ” on page 163).
3. Verify that the array is not saturated (“Adjusting the Light Throughput to the Diode
Array” on page 315).
4. In the Wavelength Calibration area, click Calibrate.
The Wavelength Calibration wizard appears.
5. Follow the instructions provided by the wizard. For more information, click Help at the
bottom of the Wavelength Calibration dialog box.

 To reset the wavelength or dark current calibration to the default values

• To reset the dark current calibration values, in the Dark Current Calibration area, click
Reset Dark Current Calibration To Default Values.
• To reset the wavelength calibration values, in the Wavelength Calibration area, click Reset
Wavelength Calibration To Default Values.

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Calibration Page Parameters

Table 63 describes the parameters on the Calibration page for the PDA detector.
Table 63. Calibration page parameters for the PDA detector
Parameter Description
Dark Current Calibration
Calibrate Starts the dark current calibration.
Last Calibration Indicates whether or not the PDA detector is currently calibrated. If the detector has not
been calibrated, the readback is Not Calibrated. If the detector has been calibrated, the date
and time of the last calibration are displayed.
Reset Dark Reloads the default instrument dark current calibration values. When you perform a dark
Current Calibration To current calibration, the Xcalibur data system compares the results to the last saved
Default Values calibration file. This can cause successive calibrations to deviate from the default.
Occasionally, you must reset to the default calibration values before performing a new dark
current calibration to get calibration values as close to the default as possible.
Wavelength Calibration
Calibrate Starts the wavelength calibration.
Last Calibration Indicates whether the PDA detector is calibrated. If the detector has not been calibrated,
[Wavelength] this readback displays Not Calibrated. If the detector has been calibrated, this readback
displays the date and time of the last calibration.
Reset Wavelength Reloads the default instrument wavelength calibration values. When you perform a
Calibration To Default wavelength calibration, the Xcalibur data system compares the results to the last saved
Values calibration file. This can cause successive calibrations to deviate from the default.
Occasionally, you must reset to the default calibration values before performing a new
wavelength calibration to get calibration values as close as possible to the default.

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Performing a Dark Current Calibration

The function of the array calibration is to measure and correct for the dark current produced
by the diodes of the photodiode array. The dark current is the small amount of background
signal that is produced by the diodes of the array even when both lamps are turned off.

The environmental conditions of your laboratory can cause the dark current of the diode
array to increase over time. For best results, perform an array calibration (dark current) after
any of the following events occur:
• After 100 hours of use or monthly, whichever comes first
• Whenever a 5 °C change in the operating environment occurs
• After you move the detector
• After you replace the lamp
• After you download a new firmware file

Because the dark current produced by the diodes rises as the temperature within the detector
rises, warm up the lamps for one hour before you perform a dark current calibration.
Warming up the lamps for one hour allows the detector to equilibrate to its normal operating
temperature.

The lamps turn off during the dark current calibration routine. After the dark current
calibration routine finishes, the lamps turn back on.

 To perform the dark current calibration

1. Pump methanol through the flow cell at 1 mL/min.

2. Turn on both lamps and wait one hour for the lamps to equilibrate.
3. Open the Calibration page for the PDA detector.
4. To start the wizard for the dark current calibration, click Calibrate in the Dark Current
Calibration area.
The preconditions page appears (see Figure 224).

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Figure 224. Preconditions page

5. Read the list of preconditions, and determine if the PDA detector is ready:
• If the detector meets all the preconditions, click Next to proceed with the calibration.
The status page appears.
• If the detector does not meet all the preconditions, click Cancel to exit the wizard.
Then prepare the PDA detector for calibration and begin this wizard again.
6. Observe the status pane as the calibration proceeds (see Figure 225).
Figure 225. Calibration status page

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7. When the calibration is complete, click Next.

The next page of the wizard appears (see Figure 226). You can export the results of the
calibration from this page.
Figure 226. Export results page

8. (Optional) To print a record of the dark current calibration, do the following:

a. Click Export Results.
The Save As dialog box appears (see Figure 227).
Figure 227. Save As dialog box, showing the file extension for a text file

b. Type a name in the File Name box, and then click Save.
Once you have saved the file with a name of your choice, you can view or print the
contents of the file using any text editing program (see Figure 228).

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11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

Figure 228. PDA dark current calibration text file

9. Click Apply to download the calibration results to the detector.

The wizard proceeds to the success confirmation page (see Figure 229).
Figure 229. Success confirmation page

10. Click Finish to close the wizard.

The calibration is saved and the date and time of calibration are displayed in the Dark
Current Calibration area of the Calibration page as the Last Calibration (see Figure 230).

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Figure 230. Calibration page, showing the Currently Calibrated status

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11 PDA Detector Performance Check and Calibration
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Performing a Wavelength Calibration

The alignment of the spectrum on the diode array depends on the physical alignment of
various components of the optical bench. The alignment can become offset if the detector is
sharply jolted, in shipping, for example. Such bumps and jars can slightly change the
wavelength of light reaching the photodiode array. The automated wavelength calibration
procedure determines the detector’s wavelength accuracy and adjusts the detector’s wavelength
algorithm to correct for any misalignment.

 To perform a wavelength calibration

1. Pump HPLC-grade methanol at 1 mL/min through the flowcell.

2. Turn on both lamps and wait one hour for the lamps to equilibrate as follows:
a. From the PDA detector view, choose Surveyor PDA Plus > Direct Controls.
The Direct Control dialog box appears.
b. Click the Configuration tab.
The Configuration page appears.
c. In the Deuterium Lamp area, click Lamp On to turn on the deuterium lamp.
d. In the Tungsten Lamp area, click Lamp On to turn on the tungsten lamp.
3. Start the Wavelength Calibration wizard as follows:
a. Click the Calibration tab.
The Calibration page appears (see Figure 231).

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 11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

Figure 231. Calibration page for the PDA detector

b. In the Wavelength Calibration area, click Calibrate.

Page 1 of the wizard appears. This page lists the preconditions required to perform a
wavelength calibration (see Figure 232).

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11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

Figure 232. Preconditions page

c. Read the preconditions, and determine if the detector meets these preconditions:
• If the detector meets all of the preconditions, click Next to proceed to the next
page of the wizard where you are prompted to select a wavelength file.
• If the detector does not meet all the preconditions, click Cancel to exit the
wizard and prepare the PDA detector for calibration.

Note On any page of the wavelength calibration wizard, you can click Cancel to
exit the procedure.

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4. Do the following:
a. Select a peak set from the list.
The peak set should span the wavelengths you use under normal operating
conditions.
Figure 233 shows the selection of the Holmium Oxide 5 peak set. This wavelength
list instructs the program to calibrate the detector at each of the five wavelengths
shown.

Note The data system has four calibration files to select from. For example, the
Holmium Oxide UV file contains five wavelengths in the UV region, while
the other files use sets of wavelengths from both the UV and visible wavelength
regions. The holmium oxide absorbance maxima are selected from a spectrum
published in “Holmium Oxide Solution Wavelength Standard from
240 to 640 nm - SRM 2034 (NIST Special Publication 260-54).”
Figure 233. Choose Calibration Peak List page

Click to create a
custom peak list.

Note For information about creating a custom peak list, see “Creating and
Editing a Custom Wavelength Calibration List” on page 337.

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11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

b. Click Next.
The next page of the wizard appears (see Figure 234).
5. Do the following:
a. Observe the status pane that tells you the wavelength file is being downloaded
(see Figure 234).
Figure 234. Download status for the selected peak list page
Instruction to click Next

b. After you see the message: Click the Next button to proceed with the wavelength
calibration, click Next.
The next page of the Wavelength Calibration wizard appears (see Figure 235). This
page instructs you to place the filter wheel in position 2.
Figure 235. Request to rotate the filter wheel to position 2 page

6. Rotate the Holmium Oxide filter wheel to position 2 as directed.

After you turn the wheel, the Next button becomes available (see Figure 236).

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 11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

Figure 236. Available Next button

7. Click Next.
The calibration status page of the wizard appears (see Figure 237).
Figure 237. Calibration status page

Instruction to click Next

8. Do the following:
a. Observe the status pane (see Figure 237).
The diagnostics program waits a few seconds for the rise time filter to equilibrate, and
then the detector takes a holmium oxide scan.
b. When you see the message: Click the Next button to proceed with calibration,
click Next.
The next page of the wizard appears (see Figure 238).

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11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

Figure 238. Request to rotate the filter wheel to position 1 page

9. Rotate the wheel back to position 1 (Open) as instructed.

After you rotate the wheel, the Next button becomes available (see Figure 239).
Figure 239. Available Next button

10. Click Next to proceed.

The results page for the wavelength calibration appears (see Figure 240).

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 11 PDA Detector Performance Check and Calibration
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Figure 240. Delta values page

Click to export the

Click to accept calibration results
the calibration to a text file (see
(see step 13). step 12).

11. Verify that the delta values are within ±1 nm:

• If the Delta values are acceptable, go to step 12.
• If the delta values are not within the range of ±1 nm, do not export the results.
Complete the calibration procedure. Then, repeat the wavelength calibration. After
applying a second calibration, if the Delta values are still not within the range
of ±1 nm, call your Thermo Fisher Scientific service representative for assistance.
12. (Optional) To print a report of the calibration results, do the following:
a. Click Export Results to print the results to a file.
The Save As dialog box appears (see Figure 241).

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11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

Figure 241. Save As dialog box

b. Type a name in the File Name box, and then click Save.
After you save the file with a name of your choice, you can view or print the contents
of the file using any text editing program (see Figure 242).
Figure 242. Wavelength Calibration file, viewed in Microsoft Notepad

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 11 PDA Detector Performance Check and Calibration
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13. To apply the calibration results to the detector, click Apply on the Delta Values page (see
Figure 240 on page 335).
The success confirmation page appears (see Figure 243).
Figure 243. Success confirmation page for a wavelength calibration

14. Click Finish to complete the wavelength calibration.

The calibration is saved. The date and time of the calibration are displayed in the
Wavelength Calibration area of the Calibration page (see Figure 231 on page 329).

Creating and Editing a Custom Wavelength Calibration List

Use the Custom List Name dialog box to name a custom wavelength calibration list
(WCL file).

 To open the Custom List Name dialog box and the Edit Peak List area

1. Start the Wavelength Calibration wizard (see “Performing a Wavelength Calibration” on

page 328).
2. Verify that the PDA detector meets the preconditions for a wavelength calibration and
click Next.
The wavelength list page appears (see Figure 233 on page 331).
3. Click Save As Custom List.
The Custom List Name dialog box appears (see Figure 244).

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11 PDA Detector Performance Check and Calibration
Calibrating the PDA Detector

Figure 244. Custom List Name dialog box

4. Type a name for the list in the box, and then click OK to add the name to the Choose
Calibration Peak List and close the dialog box.
The name of the custom list appears in the Choose Calibration Peak List box.
5. In the Choose Calibration Peak List box, click the custom list name.
The wavelength list becomes available.
6. In the wavelength list, click a wavelength that you want to edit.
The Edit Peak List area appears to the right of the wavelength list.

 To create a custom wavelength calibration list

1. Start the Wavelength Calibration wizard (see “Performing a Wavelength Calibration” on

page 328).
2. Click Save As Custom List.
The Custom List Name dialog box appears.
3. In the box, type a name.
4. Click OK.
The name of the new wavelength calibration list appears in the Choose Calibration Peak
List box.

 To edit the wavelength calibration list

1. Click the Crest/Window pane.

The Edit Peak List area appears.
2. To add a wavelength, type a wavelength in the Peak Crest box and a window in the Peak
Window box, and then click Add.
3. To delete a wavelength, select the wavelength, and then click Delete.

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 11 PDA Detector Performance Check and Calibration
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4. Click Save As Custom List to save the edited list.

The Custom List Name dialog box appears.
5. Type the name of the custom list in the box.
The Save As Custom dialog box appears (see Figure 245).
Figure 245. Save As Custom dialog box

6. Click Yes to save the wavelength calibration list.

Edit Peak List Area

Table 64 describes the parameters in the Edit Peak List area on the Choose Calibration Peak
list page of the Wavelength Calibration wizard.
Table 64. Edit Peak List area of the Wavelength Calibration wizard for the PDA detector
Parameter Description
Peak Crest Specifies a spectral band. The holmium oxide wheel contains a
solution of holmium oxide in perchloric acid.

Range: 190 to 800 nm

Peak Window Specifies the search window for the peak crest.

Start wavelength = peak crest – peak window/2

End wavelength = peak crest + peak window/2

Range: 0.1 to 611.0

Buttons
Modify Modifies the selected spectral band.
Add Adds a spectral band.
Delete Deletes a spectral band.

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 12

Making a Single Injection from the Tune Window

If you are using the Surveyor Plus LC system as an inlet to a Thermo Scientific mass
spectrometer, you can use the direct control dialog boxes available from the Tune window to
make a single injection and acquire data.

For information about setting up the LC/MS system, refer to the Getting Connected Guide
for your mass spectrometer. For information about acquiring raw data files from the tune
program for your mass spectrometer, refer to the Getting Started Guide for your mass
spectrometer.

Note You can use the PDA Direct Control dialog box to perform diagnostic tests such as
checking the performance of the deuterium lamp. To acquire PDA data for a single
injection, you must run a single row sequence from the Sequence window.

 To inject a single sample from the Tune window

1. Prepare the LC system for operation. See Chapter 5, “Daily Operation.”

2. From the Tune window for your Thermo Scientific mass spectrometer, choose Setup >
Inlet Direct Control.
The Inlet Direct Control dialog box that contains tabbed pages for each configured LC
device appears.
3. Start the solvent flow from the pump as follows:
• For the Surveyor LC Pump Plus, click the Surveyor LC Pump tab. In the Method
area (see Figure 246), enter the appropriate values for the flow rate and the solvent
percentages. Click Download. In the Pump area, click Pump On to start the solvent
flow.

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12 Making a Single Injection from the Tune Window

Figure 246. Surveyor LC Pump page of the Inlet Direct Control dialog box

• For the Surveyor MS Pump Plus, click the Surveyor MS Pump Plus tab. Select the
Take Pump Under Control check box (see Figure 247). Type the appropriate flow
rate in the Flow box. Type the appropriate solvent proportions in the Inlet boxes.
Select the Pump Ready check box. Click (Start) to start the solvent flow.
Figure 247. Direct Control dialog box for the pump

4. Start the injection as follows:

a. In the Inlet Direct Control dialog box, click the Surveyor AS tab.
The Surveyor AS page appears (see Figure 248).

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 12 Making a Single Injection from the Tune Window

b. In the list of commands, select Inject Sample.

The Inject sample parameters appear (see Figure 248).
Figure 248. Surveyor AS page of the Direct Inlet Control dialog box

c. In the Vial box, type the location of the sample. Ensure that you have placed a sample
in this location.
For information about the vial and well notation, see “Vial and Well Notation” on
page 6.
d. In the Volume (μL) box, type the volume that you want to inject.
e. Select the injection mode: Full, Partial, or No Waste. For more information, see
“Injection Modes” on page 19.
f. Click Apply.
The autosampler loads the sample into the sample loop connected to the injection
valve as follows:
The XYZ arm of the autosampler moves to the sample location, and then lowers
the needle into the sample vial. The syringe plunger descends, drawing sample
into the needle tubing. The XYZ arm moves back to the injection port, and then
lowers the needle into the injection port. The syringe plunger ascends, pushing
sample into the injection port, through the transfer tubing, and into the sample loop
of the injection valve.
5. On the Surveyor MS Pump Plus page, select the Release Injection check box.
The injection valve switches to the inject position, allowing mobile phase to backflush the
sample out of the sample loop and into the LC column.

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 I

Index
Numerics B
384-well microplates, well positions 10, 302 back panels
96-well microplates, well positions 7 Ethernet port location 24
unit ID location 42
baseline
A drift, reducing 209
absorbance level noise, reducing 187
zeroing for the PDA detector during a run 105 zeroing absorbance level
zeroing for the UV/Vis detector 23 PDA detector 103
zeroing on the Display page 178 UV/Vis detector 23
accessories
reservoir vials 5
solvent lines 23 C
standard vials 6 cables
wash bottle assembly 13 Ethernet 3, 41
active and pinned cells, Qual Browser 225 RS-232 serial 2
air bubbles, loaded into the sample loop 19 system interconnect 32
alpha values for flow rate adjustment 265, 268 calibration
analog outputs arm calibration, autosampler 287
changing the polarity 164 column oven 275
testing 165 dark current 323
LC pump 260
areas of peaks, displaying 242
tray temperature 281
arm calibration, autosampler 287
wavelength 328
attenuators, PDA 22 well bottom distance, custom vials or microplates 305
autosampler calibration curves, creating 203
automated sample preparation 113
cell grid, Qual Browser
busy status message 139
adding cells to the real-time display 216
calibrating 274
cell states 224
configuration parameters 45
cursor actions 226
custom vials or microplates, using 305
inserting cells 244
Direct Inlet Control dialog box 343
channels, instrument method 100
instrument method parameters 85
loading trays 210 chemicals, filtering 210
timed events table parameters 94 chromatograms
transfer tubing 17 cursor actions, cell grid 226
vial and well notation 6 labels (retention time, area, and so on) 241
autozero function for the UV/Vis detector 107 peak detection 252
UV data, displaying 250
Avalon integration algorithm 237
column
See LC column
column arrangement, sequence spreadsheet 205

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Index: D

column oven delta values, PDA calibration 335

description 21 Description box, LC column 69
direct control 199 detectors
temperature calibration 275 See PDA detector or UV/Vis detector
test fixture, installing 276 devices
Comm LED adding to the instrument configuration 44
autosampler 38 start instrument 213
LC pump 37 status, viewing 137
MS pump 36 turning into Standby mode 154
PDA detector 39 turning on/off 154
UV/Vis detector 40 dilutions, sample preparation example for automating 127
communication, Xcalibur data system 41 diode numbers 102
compliance diode voltage leakage 323
FCC vii Direct Control dialog box
regulatory iii autosampler 197
WEEE ix LC pump 188
compressibility MS pump 190
defined 262 PDA detector 162
updating 266 UV/Vis detector 183
values 264 discrete channel wavelengths, instrument method 100
concentric syringe display methods
See syringe, autosampler creating 313
configuration options saving 314
autosampler 45 display options
LC pump 63 chromatogram cell 240
MS pump 61 map cell 247
PDA detector 65 spectrum cell 242
UV/Vis detector 66
drain valve knob for LC pump 4, 187, 269
contact closure cable 32 dual wavelength program, UV/Vis detector 107
conventional vial trays 6
Custom List Name dialog box 337
custom vials and microplates E
calibrating the bottom distance of 305 electromagnetic compatibility vii
selecting tray options 47 error log
autosampler 144
PDA detector 182
D
event types, PDA detector timed event 103
dark current calibration 323 external devices, triggering 102
data acquisition
analyzing acquired data 219
starting 211 F
viewing real-time 214 FCC compliance vii
data files file types
naming 203 comma-separated values file (.csv) 318
opening 219 data file (.raw) 219
dead volume for transfer tubing, configuring 54 display method (.spda) 315
Degas LED layout file (.lyt) 222
LC pump 37 processing method (.pmd) 203
MS pump 36 sequence (.sld) 208
degassing unit, built-in 2, 23 fill position, injection valve 18
delay volume, LC pump 3 filter frit, LC pump 4
delay, PDA detector timed event 103 filter wheel, PDA detector 22

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 Index: G

firmware, upload version 60 PDA detector parameters 98

fixed loop injection saving 109
See full loop injection UV/Vis detector parameters 108
flow rate Instrument Setup window, opening 68
adjustment setting 268 integration
gradient program changes 79 auto calculation 253
range Avalon integration algorithm 252
LC pump 3 intensity
MS pump 2 counts, maximum light throughput 318
flush bottle location 13 data, recording 318
flush speeds 87, 89 intensity display 178
font size of display, changing 230 isocratic pump program
fraction collector, triggering 102 creating for LC pump 71
full loop injection creating for MS pump 81
description 20
instrument method parameter 90 L
Labels page, Display Options dialog box 241
G Lamp Startup Time dialog box 166
gradient delay volume lamps
autosampler preheat tubing 21 controls on the PDA detector Configuration page 163
LC pump pulse dampener 3 deuterium 22–23
MS pump 2 Information view Turn Device On command 154
gradient program lamp warm-up message 137
LC pump 71 safety interlock 23
MS pump 79 timed startup for PDA detector 166
Gradient Start signal, pump 35 tungsten 22–23
grinding sound, caused by high flush speeds 89 turning on, UV/Vis detector 183
usage hours, resetting for the PDA detector 164
wavelength range for the PDA detector 22
H Lamps LED
heights, chromatographic peak 242 PDA detector 39
UV/Vis detector 40
layout files for PDA data
I creating 233
inactive cells, Qual Browser 224 saving 248
initialization process for syringe 134 LC column
Initializing status message 137 damaging 77
inject position, injection valve 18 equilibrating 209
injection mode, description 19 LC pump
injection valve, description 18 components 3
injection volume in-line filter frit 4
full loop injections 20 instrument method parameters 69
no waste injections 19, 90 LED states 37
partial loop injections 20 purging 4, 187
instrument methods LEDs, device status 35
adding a sample preparation routine 113 level trigger 103
autosampler parameters 85 light fixture, arm calibration 287, 294
creating 67 light throughput to the diode array, adjusting 315
LC pump parameters 69 Load Method button 177, 317
MS pump parameters 74 Lock Display button 214
parameters report, data file 232

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Index: M

M PDASnapshot.csv 318
peaks, chromatographic
maintenance log, autosampler 54
areas, displaying 251
manuals, accessing xvi
peak detection 251
methods
purity settings 255
See instrument methods or display methods
polarity, active high or active low 164
microplates
Post-Injection Valve Switch Time box 89
384-well 10
Power LED
96-well 7
autosampler 38
description 6
LC pump 37
selecting tray options 47
MS pump 36
MS pump
PDA detector 39
instrument method parameters 74
UV/Vis detector 40
operating without solvent 77
power, turning on/off 134
pressure settings, minimum and maximum 77
pressure stability 77 precision, injection-to-injection 89
priming the pulse dampener 156 preheating tubing 21
Ready signal 77 Prep Operations list 116
pressure
minimum for LC pump 69
N recorder terminals 264
names, chromatographic peaks 242 sensor adjustment 269
needle and needle tubing assemblies, description 16 units for displaying backpressure 63
New Sequence Template dialog box 202 pressure recorder terminals, scaling the output 268
no waste injection pressure transducer
description 19 replacing 265
injection volume recommendation 91 zeroing 265, 269
instrument method parameter 90 processing method (.pmd) file type 203
noise, detector 170 pump
Normalization page, Display Options dialog box 240 See LC pump or MS pump
Pump Ready signal 35
O
On, Off, Standby shortcut menu 154 Q
On/Off switches for LC devices 135 Qual Browser
output signal terminals 164 accessing 219
Oven page readbacks, autosampler 142 cell grid 224
cursor actions 226
display options, UV chromatograms 240
P layout files, creating 233
partial loop injection
description 20
instrument method parameter 89
R
PCR plate, configuring 48 Ready signal, pump 77
PDA detector ready to download message 137
dark current calibration 323 real-time data
data acquisition parameters 95 locking 214
display method parameters 101 reviewing 215
functional description 22 regulatory compliance iii
instrument method parameters 98 removal position, needle 303
light throughput, adjusting 315 report, instrument method 232
parameters in method report 232 Reservoir Content page, autosampler solvent descriptions 93
timed events parameters 102 Reset Lifetime button 173
wavelength calibration 328

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 Index: S

retention times, chromatographic peak spectrum

displaying 242 chromatographic time point 249
effect of temperature control on reproducibility 87 cursor actions 226
rise time filter displaying 238
for the PDA detector 96 maximum absorbance 235
for the UV/Vis detector 106 speeds
Run LED flush speed setting 87
autosampler 38 loop loading 92
LC pump 37 no waste injections 19
MS Pump 36 stack address or stack number 24, 42, 63, 65
PDA detector 39 standard syringe (single plunger), size 14
UV/Vis detector 40 standby, Status page shortcut menu item 154
Start Data button 169
S status
checking the status of the LC devices 136
safety interlock, lamps 23
LEDs for LC devices 35
safety standards iii
Stop Data button 170
sample loop description 18
switches
sample preparation Ethernet 24
routines, creating 113
tray compartment door, magnetic 6
rules 115
synchronizing the LC devices 32
Sample Preparation page, opening 113
syringe valve, description and figure 13
sample rate, PDA detector 99
syringe, autosampler
sample trays
configuring 53
figure showing conventional trays 204
description 14
loading into the tray compartment 210
flushing 196
selecting tray options 47
sample preparation rules for 115
temperature control 21
vial and microplate well positions 6
Save PDA Display Method dialog box 315 T
scan threshold 255 target port fixture, arm calibration 299
screen saver, turning off 24 Temp LED 38
seals, piston, ruining 77 temperature control
sequences tray and LC column compartments 21
creating 201 Wait for Temperature Ready check box 54
saving 208 terminals, output signals 164
turning off the lamps and the solvent flow 213 Timed Events page, autosampler 94
Snapshot button 169, 178, 318 timed events, PDA detector 104
solvent composition total scan 235
gradient program linearity 79 tray compartment door
instrument method 79 magnetic switch 210
programming for LC pump 72 Verify Door Is Closed check box 54
solvent lines tray compartment temperature
four lines for mobile phase solvents 23 calibration 281
wash bottle 23 control 21
solvent platform 23 tray temperature sensor, installing 281
solvent reservoir bottles 23 trays
spectral light intensity (.spda) file type 315 See sample trays

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Index: U

tubing wavelength
behind column oven 21 accuracy, calibrating 328
degasser 2 calibration list, editing 338
needle tubing 13 data acquisition range
solvent lines 23 PDA detector 99
wash bottle 13 UV/Vis detector 108
Turn Device On command 154 WEEE compliance ix
well bottom distance calibration 305
U well position and well ordering, selecting 49

unit ID
description 42 X
relation to communication protocols 24 x- and y -axis offset values, arm calibration 300
unpinned cells, Qual Browser 225 Xcalibur data system
UV/Vis detector Instrument Setup Window, opening 68
configuring 66 Qual Browser, opening 219
direct controls 183 Roadmap view 135
instrument method parameters 108 Sequence Setup window, opening 201
lamp controls 183 XYZ arm
parameters in method report 232 description 15
wavelength modes 23 home position 296
moving to the back of the tray compartment 303
V position, calibrating 287

valves
six-port injection valve 18 Z
syringe two-position rotary valve 13 Zero DACs button 175
variable volume injections, types 20 Zero Data
Verify Door Is Closed check box 6, 54, 290 button on Display page 170
vial bottom sensing 54 event type, PDA detector 105
Vial Not Found message 210 zeroing, absorbance level
vial trays, notation 6 PDA detector 103
viscous flush solvents 89 UV/Vis detector 23, 107
volume
flush 197
full loop injections 20
gradient delay, pulse dampener in LC pump 3
no waste injections 19, 90
partial loop injections 20
preheat tubing 21
sample loops 18
sample preparation operations 115
standard needle tubing and needle tubing extension 13
tubing in chambers of vacuum degassing unit 2

W
Wait for Temperature Ready check box 54
wash bottle location 13

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