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Openlynx

Software Manual

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0% found this document useful (0 votes)

17 views

Openlynx

Software Manual

Uploaded by

Oliver Müller

We take content rights seriously. If you suspect this is your content, claim it here.

Available Formats

Download as PDF, TXT or read online on Scribd

You are on page 1/ 130

OpenLynx Users Guide

Version 3.5
th
15 August 2000

Page i
OpenLynx Users Guide

OpenLynx Users Guide

The software described in this book is furnished under a licence agreement and
may be used only in accordance with the terms of that agreement.

Micromass Ltd believes that the information in this publication is accurate.

However the information is subject to change without notice and should not be
construed as a contractual undertaking by Micromass Ltd. Despite the care that has
been given to the preparation of this publication, Micromass Ltd accepts no
responsibility for any loss or any other matter that may arise from any error or
inaccuracy that may inadvertently have been included.

Copyright (C) 1993-2000 Micromass Ltd. All Rights Reserved.

No part of this publication may be copied without the express written permission of
Micromass Ltd.

Trademarks

Micromass ® is a registered trade mark of Micromass Limited

(Reg. U.S. Pat. & Tm. Off.).

MassLynx and OpenLynx are registered trademarks of Micromass Ltd.

Windows is a trademark of Microsoft Corporation. Other product names mentioned

in this manual may be trademarks or registered trademarks of their respective
companies and are hereby acknowledged.

Page ii
OpenLynx Users Guide

Table of Contents
Introduction 1
The Life Cycle of a Sample 3
OpenLynx Modes of Operation 4

Initial Installation and Test 5

Installing the MSPC software 5
Checking the Instrument and LC System 5
Setting up the network connection 6
Installing the Login Software 7
Installing the Browser Software 8

OpenLynx Setup 11
Introduction 11
Accessing OpenLynx Setup 12
The OpenLynx Setup Toolbar 12
Getting Started 13
Walk-up Page 14
Input Fields 16
Printing Page 18
MS Data Page 19
DAD Data Page 21
Analog Data Page 23
Instrument Page 25
MS Process Page 27
Combine Parameters 28
Isotope Modelling 30
MaxEnt 30
Mass Measure 31
AFAMM Parameters 32
Isotopic Cluster Analysis 33
Spectrum Test Page 35
Chromatogram Test Page 37
Quality Control Page 38
Quantify Page 40
Library Page 41
Elemental Page 45
Acquisition Process Page 47

OpenLynx Browser 51
Overview 51
Creating Report Files 51
The OpenLynx Browser Screen 51
Accessing OpenLynx Browser 52
The OpenLynx Browser Toolbar 53
Getting Started 54
Report Schemes 56
Report Scheme Settings 56
Print Control Page 56
Report Column Selection Pages 58
View Options 61
Spectrum Page 61
Chromatogram Page 63
Default Plate Page 65

Page iii
OpenLynx Users Guide

Colors Page 67
Copy Control Page 68
Column Pages 69
Fraction Display Page 70
Other Display Options 72
Other Menu Options 73
File Menu 73
View Menu 75
Window Menu 75
The Plate Pane 76
The Sample Description Pane 77
The Fraction Results List Pane 77
The Results Table Pane 78
The Spectrum Pane 80
The Elemental Composition Results List/Library Search
Results List Pane 81
The Elemental Composition Results List 81
The Library Search Results List 82
The Chromatogram Pane 83

OpenLynx Manager 87
Overview 87
The OpenLynx Manager Dialog 87
The File Menu 88
Report Location 88
Print Report Format 89
The Administration Menu 90
Set Bed Layout 90
Clear Job Queue 91
Reset Bed Status 91
E-Mail 92

OpenLynx Login 95
Overview 95
The OpenLynx Login Dialog 95
The Status Bar 96
QC Setup 97
Reset Login Position 99
Sample Login 99
Plate Login 100
Single Shot Login 105
The File Menu 108
Methods 108
Status 108
HLPC File Location 109
Options 110
The Security Menu 112
Swap Mode 112
Timeout 113

Page iv
OpenLynx Users Guide

Registry Settings 117

Introduction 117
Initial Settings 117
OpenLynx Browser 117
OpenLynx 117
To Edit a Registry Setting 118
The Initial Registry Settings 119
OpenLynx 119
Batch Manager 119
Login 120

Index 123

Page v
OpenLynx Users Guide

Conventions
The MassLynx Users Guide follows these typographic conventions

This Represents

bold Anything you must type exactly as it appears

italic Place holders for information you must provide. For example
if you are asked to type filename, type the actual name for a
file instead of the word shown in italic type.

ALL Directory names, filenames and acronyms.

CAPITALS

Keyboard Formats

Key combinations and key sequences appear in the following formats.

KEY1+KEY2 A plus sign (+) between key names means to press and hold
down the first key while you press the second key. For
example, "press ALT+ESC" means to press and hold down the
ALT key and press the ESC key. Then release both keys.

KEY1,KEY2 A comma sign (,) between key names means to press and
release the keys one after the other. For example, "press
ALT,F" means to press and release the ALT key and then press
the F key.

Mouse Buttons

Unless otherwise specified, use the left mouse button as default.

Page vi
Introduction

Introduction
Chapter 1

This document covers the installation, configuration and use of the OpenLynx
software. OpenLynx provides an easy to use interface to a Micromass UK Ltd
liquid chromatography-mass spectrometry system (LC-MS) for people who are not
familiar with operating such an instrument.

There are two separate parts of OpenLynx : the LC-MS system, which is controlled
using the MSPC (mass spectrometry computer); and the LoginPC, where samples
are logged in. The two computers are linked via a network (see Figure 1.1). Whilst
anybody can log in samples, only trained mass spectrometry operators should set up
the LC-MS.

When the system is fully operational, the LoginPC provides a list of methods which
contain all the information required for analysis. To analyse a sample, the submitter
must select the appropriate method and enter some sample information. The sample
analysis is then fully automated: the LoginPC tells the chemist where to place the
sample in the autosampler rack; and the sample method is downloaded to the MSPC.
The system works on a first in, first out (FIFO) principle. When the sample has
been analysed, the data is processed and the results can be printed, e-mailed and
viewed in the OpenLynx Browser. Thus, within a short time, the chemist obtains
detailed information about the sample.

LC-MS System Login System

Mass Spectrometer
HPLC

Printer

MSPC LoginPC

Figure 1.1 OpenLynx LC System

Page 1
Introduction

Assumptions

It is assumed in this document that the person installing and configuring OpenLynx
has a working knowledge of the following:

1. Microsoft Windows NT

2. LC-MS and MassLynx

3. Networking PCs

4. Sharing disk drives and directories across a network

5. Connecting to network disk drives and directories

6. Sharing printers across a network

7. Connecting to network printers.

Page 2
Introduction

The Life Cycle of a Sample

A sample begins at the Login workstation. The OpenLynx login program produces
an OpenLynx Batch File with a .OLB extension. The OpenLynx batch file is read
and validated by the OpenLynx Manager and an internal “Sample List” is produced.
This “Sample List” is then submitted to the MassLynx queue, which can be viewed
from the main MassLynx screen.

Once the Sample Batch is in the MassLynx sample queue then the MassLynx
process manager waits for the sample list to be acquired and processed. (The
MassLynx process manager is the component of MassLynx that executes MassLynx
sample lists and is different to the OpenLynx manager). The Processing is
performed on each sample in turn after it has been acquired. The OpenLynx.exe
program performs the post acquisition processing. It creates or appends to the
OpenLynx report file depending on if it is the first sample in the batch.

An OpenLynx batch file is able to hold from one to n samples where n is the number
of unallocated sample positions on the current autosampler. For example, a Gilson
215 running ten 96 well micro titre plates, it is possible to submit 960 samples in
one batch. Please be warned that if this was to be attempted it will take several
minutes before the first sample is injected due to the validation which takes place on
the batch.

On processing a batch the OpenLynx Batch file is moved to an

Openlynx\BatchDB\Processed folder. Depending on the configuration of the
OpenLynx Manager an automatic printout of the sample batch may occur. The
OpenLynx report file *.rpt is written to the location specified by the OpenLynx
Manager and can be viewed using the OpenLynx Browser.

Reprocessing Samples

It is possible to reprocess a previously acquired sample and generate a printed

report. For each batch / sample acquired OpenLynx generates a file with the
extension .OLB in the directory C:\MASSLYNX\OpenLynx\BatchDB\Processed as
described above. To reprocess a sample (without reacquiring the data)

From the Sample List choose Import Worksheet from the File menu. For the
sample you want to process select the
C:\MASSLYNX\OpenLynx\BatchDB\Processed \filename.olb that corresponds to
the sample and choose OK. This will automatically configure the correct columns
in the Sample List. An example is shown below.

Column Value

File Name LOOP01

Process C:\MASSLYNX\OPENLYNX.EXE

Parameter File C:\MASSLYNX\LOOP.OLP

Process Options

This will reprocess the data using the Loop.olp OpenLynx method. If the current
sample list is called OLTEST.SPL then the results will be saved to the
\sampledb\oltest.rpt file in the current MassLynx project.

Page 3
Introduction

OpenLynx Modes of Operation

The main modes of operation for OpenLynx are:

Open Access Walk Up Single Sample Loop

This OpenLynx Method file can be used to acquire and automatically printout the
results of a loop injection. All the user has to do is select Loop processing and a
Loop time on the Walk-Up page of the OpenLynx Setup as well as reporting MS
Spectra on the MS Data page. An example OpenLynx method file called
LOOP.OLP is distributed with MassLynx.

Open Access Walk Up Single Sample LC

Here the user will not select Loop or a loop time but will select the chromatograms
they wish to peak detect by editing the MS data, DAD Data and Analog Data pages.
An example OpenLynx method file called LC.OLP is distributed with MassLynx.
The ability to automatically process various chromatograms of interest i.e. TIC,
Masses and DAD traces to target and hence report Mass Spectra or Diode Array
Spectra for the chemist in an Open Access environment is perhaps the most
powerful tool OpenLynx has to offer the walk up chemist.

Open Access Walk Up Micro Titre Plate Login (Loop)

This is typically used in Combinatorial Drug Discovery. The samples are entered
via a TAB delimited text file or clipboard import from within the OpenLynx Login
software. The format of this file is set by the Input Fields section of the Walk-up
page of the OpenLynx setup program. The Report formats of the OpenLynx using
Plate login are generally modified over the Single Sample reports to include Plate
and Sample summaries.

Batch/Single Shot entry is enabled via the OpenLynx Manager.

OpenLynx is configured to report the presence or not of target compounds/masses

by the Spectrum Test Page of the OpenLynx setup. Pressing the Diversity button
enables this “target mass” reporting.

Open Access Walk Up Micro Titre Plate Login (LC)

The same as Single sample walk up, but this will acquire and automatically peak
detect the chromatogram traces the user specifies in the OpenLynx method.

All the above but not walk up

The user is able to generate MassLynx sample lists if they wish. The OpenLynx.exe
program is able to process the samples and the user must select the correct
OpenLynx method files and acquisition parameters. This mode is similar to the
MassLynx 2.3 version of OpenLynx Diversity for acquiring and processing data.
The OpenLynx Manager would not be active in this mode.

Page 4
Introduction

Initial Installation and Test

This section describes the steps involved in installing the OpenLynx software and
testing the system with the default files.

The OpenLynx disk set contains the following 3 disks:

OpenLynx disk — When you install MassLynx from the MassLynx CD and select
the OpenLynx option you will be asked to insert this disk.

OpenLynx Login disk — OpenLynx can be run with or without the Login program.
If you want to login samples, using the Login program then you need to install this
software by running the Setup program on the OpenLynx Login disk (see page 7 for
details). The Login software can either be installed on the same PC as MassLynx, or
on a separate Login PC.

OpenLynx Browser disk — This disk contains a stand-alone copy of the

OpenLynx Browser program. This is supplied so that you can install the Browser on
other PCs, to view and print OpenLynx reports without having to install the whole
of MassLynx. You do not need to install the Browser on a PC which already has the
OpenLynx disk installed, as the Browser will already have been installed as part of
OpenLynx.

Installing the MSPC software

The MSPC (Mass Spectrometry PC) should be using the Windows NT operating
system. Install MassLynx on the MSPC from the MassLynx CD, see the
"Introduction" chapter of the MassLynx User's Guide.

During the installation you will be asked to select the Options you wish to install.
You should select Software, OpenLynx, OpenLynx Data and any other options
you wish to install.

Checking the Instrument and LC System

Check the instrument and the LC system are working correctly and that you can
acquire multiple samples from the MassLynx Sample List.

Page 5
Introduction

Setting up the network connection

Note: The network connection must be set up before the Login software is installed.
If it is not then the installation of the software will fail.

The MSPC and LoginPC must be connected using the TCP/IP network protocol.

When the network has been installed:

1. Open Windows NT Explorer on the MSPC.

2. Click with the right mouse button on the C:\ directory.

3. Select Sharing… from the pop-up menu to display the Properties dialog.

Figure 1.2 Properties dialog

4. On the sharing tab check the Shared As option and press the New Share
button.

Figure 1.3 The New Share dialog

Page 6
Introduction

5. Enter a Share Name, C is recommended.

6. For the User Limit, check Maximum Allowed or Allow and enter the number
of users allowed.

7. Press the Permissions button and ensure that Full Control is enabled.

8. Press OK on the New Share dialog and on the Properties dialog.

9. From the OpenLynx Logon window of the LoginPC, in Administrator mode,

choose Status from the File menu and select the appropriate OpenLynx Status
(*.ols) file.

On the MSPC, load MassLynx. Open the tune page to initialise communications
and load the OpenLynx LC Control program.

Installing the Login Software

The LoginPC should be using the Windows NT operating system.

n To install the Login software under Windows NT

1. Insert the main MassLynx CD into the CD drive.

2. Press the Start button to display the Start menu.

3. Select Run…

4. In the Command Line text box, enter a:\oalogin\setup

5. Press the OK button.

6. Wait for the OpenLynx Login installation set-up window to be displayed and
select the default destination directory.

7. Insert the OpenLynx Login disk into drive a:\ as prompted.

The files will be copied onto the LoginPC.

When the installation is complete there will be a new program group, OpenLynx
Login, with one item in, OpenLynx Login.

n To set up a shortcut

1. Press Start button, choose Programs and then Windows NT Explorer.

2. Select the OpenLynx Login folder then click on the OALogin.exe icon and
drag it out onto the desktop

To start OpenLynx Login in future just double click on the shortcut to OALogin
icon on the desktop. Alternatively, press the Start button, choose Programs,
OpenLynx Login and then OpenLynx Login.

Page 7
Introduction

Installing the Browser Software

The OpenLynx Browser can also be installed as a separate program. This may be
useful for viewing and generating reports from a different PC.

n To install the Browser software under Windows NT

1. Insert the main MassLynx CD into the CD drive.

2. Press the Start button to display the Start menu.

3. Select Run… and enter a:\diverse\setup in the Command Line text

box.

4. Press the OK button.

5. Wait for the OpenLynx Browser installation set-up window to be displayed

and select the default destination directory.

6. Insert the OpenLynx Browser disk into drive a:\ as prompted.

When the installation is complete there will be a new program group, MassLynx
OpenLynx Browser, containing the OpenLynx Browser item.

Page 8
Introduction

Notes
................................................................................................................................................................

................................................................................................................................................................

Page 9
Introduction

Notes
................................................................................................................................................................

................................................................................................................................................................

Page 10
OpenLynx Setup

OpenLynx Setup
Chapter 2
Introduction
OpenLynx Setup is used to develop OpenLynx methods for use by MassLynx. The
OpenLynx methods describe how a sample will be acquired and the processing to be
applied to the sample. The OpenLynx methods have .olp file extensions and can be
found in the main MassLynx installation directory.

The setup of the OpenLynx method files allows the operator to configure OpenLynx
for a variety of applications.

The OpenLynx Setup has the following pages:

• Walk-up — allows method files to be selected.

• Printing — allows the required report scheme to be selected.

• MS Data — allows Integration parameters for TIC, BPI and Mass

Chromatograms to be defined.

• DAD Data — allows Integration parameters for DAD Data to be defined.

• Analog Data — allows Integration parameters for Analog Data to be defined.

• Instrument — allows positive and negative Adducts, Charges and Multimers to

be defined.

• MS Process — allows parameters for processing spectra. (Combine, Mass

Measure and Isotope Modeling) to be defined.

• Spectrum Test — allows parameters that decide if spectra are acceptable to be

defined.

• Chromatogram Test — allows an area threshold to be defined, the

chromatogram peak area must be greater than this to be displayed as found in
the OpenLynx Browser.

• Quality Control — allows quality control procedures to be defined.

• Quantify — allows quantification parameters to be defined.

• Library — allows users to define libraries to search results against or to create

new ones from results acquired.

• Elemental — allows elemental composition calculations to be performed.

• Acquisition Process — allows an acquisition processes to be defined.

Page 11
OpenLynx Setup

Accessing OpenLynx Setup

To access the OpenLynx Setup pages select OpenLynx Setup from the OpenLynx
menu from the top level MassLynx window. To view an individual page click with
the left mouse button on the relevant tab.

The OpenLynx Setup Toolbar

Toolbar Menu equivalent Purpose
button

File… New Create a new OpenLynx parameter file.

File… Open Open an existing OpenLynx parameter file.

File… Save or Save an OpenLynx parameter file.

File… Save As

File… Print Print a summary of the Setup file.

Edit… Cut Cut the selection and put it on the clipboard.

Edit… Copy Copy the selection and put it on the

clipboard.

Edit… Paste Paste the contents of the clipboard.

Help… About Display program information, version

OpenLynx number and copyright.

Page 12
OpenLynx Setup

Getting Started
Before the user can create an OpenLynx parameter file, the acquisition method files
must be created in MassLynx. See the relevant sections in the MassLynx User’s
Guide and the Guide to Data Acquisition for details.

1. In MassLynx, create a new project.

2. Within this project create the relevant acquisition files. MS Tune, MS Method
and Inlet Method.

3. Select OpenLynx Setup from the OpenLynx menu on the top level MassLynx
Screen.

n To Create an OpenLynx Parameter File

1. Press the Toolbar button, or select New from the OpenLynx Setup File
menu.

2. Enter the required data on each page of the OpenLynx Setup.

3. Press the toolbar button, or select Save or Save As from the OpenLynx
Setup File menu. Enter a name for the new OpenLynx parameter file and press
OK.

n To Open an Existing OpenLynx Parameter File

1. Press the Toolbar button, or select Open from the OpenLynx Setup File
menu.

2. Select the required OpenLynx file (*.olp) and press Open.

n To Print an OpenLynx Parameter File

1. Press the Toolbar button, or select Print from the OpenLynx Setup File
menu. The standard Windows Print dialog is displayed.

2. Enter the number of copies to print and press OK.

Page 13
OpenLynx Setup

Walk-up Page

Figure 2.1 The Walk-up page

Description Enter a description of the method.

Input Fields These are the fields that will be displayed on the LoginPC for user
input. For example, Sample Id, Mass, Concentration etc. See Input Fields, on
page 16 for details on adding and deleting these fields.

Maximum Samples Enter the maximum number of samples that can be

processed in one OpenLynx login session.

Priority Process Check this box to define the job submitted from the
OpenLynx Login as a priority process. Note all processes using this method will be
priority processes. For more information see "The MassLynx User Guide,
Getting Started chapter".

Night Time Process Check this box to define the job submitted from the
OpenLynx Login as a night time process. Note: All processes using this method
will be night time processes. For more information see "The MassLynx User Guide,
Getting Started chapter".

HPLC File Check this box to allow users to define a gradient for the LC method
when logging on a sample. For more information see the OpenLynx Login chapter.

Page 14
OpenLynx Setup

Time of Analysis Enter the time to analyse one sample. This time is written to
the batch file.

MS Tune This is the tune parameters file. Select the required file from the drop
down list box.

MS Method This is the scanning parameters file. Select the required file from the
drop down list box.

Inlet Method This is the LC parameters file. File extensions will vary depending
on the type of inlet selected. Select the required file from the drop down list box.

Injection Volume Enter the volume of sample to be injected, in microlitres.

Pre-Run Method This is the pre-run parameters file that will be run to condition a
column. File extensions will vary depending on the type of inlet selected. Select the
required file from the drop down list box.

Post-Run Method This is the post-run parameters file that will be run to return
the column to a known state. File extensions will vary depending on the type of
inlet selected. Select the required file from the drop down list box.

Switch Method This is the method run when a column is switched. File
extensions will vary depending on the type of inlet selected. Select the required file
from the drop down list box. The switch method is run if the inlet method is
different from the previous one.

Fraction Method This is the fraction collection parameters file. Select the
required file from the drop down list box.

Loop Mode Checking this box will perform a loop injection and should only be
used for samples requiring no chromatography.

Loop Time This is the retention time at which spectral data will be taken during
processing.

Page 15
OpenLynx Setup

Input Fields

Input Fields are the fields that will be displayed on the LoginPC for users to enter.
E.g. Sample Id, Mass, Concentration etc.

Fields can be added or deleted via the Field Mapper dialog. To access this dialog
press the Edit Fields button or double click with the left mouse button on one of the
Input Fields, or ’-None-’ if no fields are displayed.

Figure 2.2 The Field Mapper dialog

n To Add a Field

1. Click on the required field, with the left mouse button, in the Available Fields
box.

2. Press the Append button.

3. Repeat steps 1 and 2 as required.

4. Press the OK button. The fields selected will appear in the Input Fields box.
Pressing the Cancel button will disregard these changes.

n To Insert a Field

1. Click on the required field, with the left mouse button, in the Available Fields
box.

2. In the Order of Fields to Use box, click on the field before which you want
to insert the new field.

3. Press the Insert button.

4. Repeat steps 1 and 2 as required.

5. Press the OK button. The fields selected will appear in the Input Fields box.
Pressing the Cancel button will disregard these changes.

Page 16
OpenLynx Setup

n To Delete a Field

1. Click on the required field, with the left mouse button, in the Order of Fields
to Use box.

2. Press the Remove button.

3. Repeat steps 1 and 2 as required.

4. Press the OK button. The fields selected will no longer appear in the Input
Fields box. Pressing the Cancel button will disregard these changes.

n To Delete All Fields

1. Press the Clear button.

2. Press the OK button. –None– will appear in the Input Fields box. Pressing
the Cancel button will disregard these changes.

n Field Alias

If the field name in the Available Fields list does not correspond to a description the
user will recognise, another name can be entered in the Field Alias box. E.g. Well
could be displayed on the LoginPC as Bottle Number. This field may also be used
to display field names in another language.

Page 17
OpenLynx Setup

Printing Page

Figure 2.3 The Printing page

Walk-up Batch Report Scheme Enter the name of the Report Scheme to be
used when printing results. If not specified, the currently selected scheme will be
used. For more information on Report Schemes, see the OpenLynx Browser
chapter.

Per Sample Printing Check this box to print information for each sample. Enter
the name of the Sample Report Scheme to be used when printing results. If not
specified then the currently selected scheme will be used. For more information on
Report Schemes, see the OpenLynx Browser chapter.

Page 18
OpenLynx Setup

MS Data Page

Figure 2.4 The MS Data page

This page allows users to define integration parameters for TIC, BPI and Mass
chromatograms.

Start Time This is the retention time at which the integration of data starts and the
time from which data is written to the report file.

End Time This is the retention time at which the integration of data stops and the
time from which data stops being written to the report file.

Note: If Start and End times are left at the default 0.00 then the whole trace will be
integrated and written to the report file.

Min Peak Separation If there are two acquisition functions, e.g. a positive and
negative, and a peak appears within this time of each other, the peaks are considered
to be the same peak. Only one peak time will be used for the peak top time and both
peaks will be reported as the same compound.

Report Chromatogram For all types of chromatogram, check this box to write
the chromatogram trace to the report file.

Page 19
OpenLynx Setup

Full Range For each chromatogram type, check this box to display the full
chromatogram in the OpenLynx Browser. If the full chromatogram is displayed, the
specified integration range remains the same.

For all types of chromatogram, pressing the button will invoke the Integrate
Chromatogram parameters dialog. For more information on integration parameters
see "The MassLynx User Guide, Chromatogram chapter".

Use all detected peaks Check this box to use all detected chromatography
peaks for targeting Spectra and in Browser reports. If not checked, then a value
should be entered into the Maximum peaks box. Maximum peaks specifies the
maximum number of peaks to be taken from each chromatogram trace. The largest
peaks, based on area, will be chosen.

Report MS Spectra For all types of chromatogram, check this box to write the
Spectrum, from the top of the peaks in the chromatogram trace, to the report file.

Fixed Mass Range Enter the Mass to search for and the ± Range in which to
search for the peak. This is used for generating a mass chromatogram for each
sample, without having to enter the same details for each sample on the LoginPC.

Page 20
OpenLynx Setup

DAD Data Page

Figure 2.5 The DAD Data page

This page allows the user to define integration parameters for TAC, BPI and
Wavelength chromatograms.

Start Time This is the retention time at which the integration of data starts and the
time from which data is written to the report file.

End Time This is the retention time at which the integration of data stops and the
time from which data stops being written to the report file.

Note: If Start and End times are left at the default 0.00 then the whole trace will be
integrated and written to the report file.

Offset Time The time in minutes used to align the Diode Array detector with the
MS data. Normally DAD data is ahead of the Mass Spectrometer and this offset
time is added to the raw DAD time therefore only positive values are valid.

Report Chromatogram For all types of chromatogram, check this box to write
this chromatogram trace to the report file.

Page 21
OpenLynx Setup

Use all detected peaks Check this box to use all detected chromatography
peaks for targeting Spectra and in Browser reports. If not checked, then a value
should be entered into the Maximum peaks box. The maximum peaks specifies the
maximum number of peaks to be taken from each chromatogram trace. The largest
peaks, based on area, will be chosen.

Report MS Spectra Check the box for each type of chromatogram, to write the
Spectra, from the top of the peaks in the chromatogram trace to the report file.

Report DAD Spectra Check the box for each type of chromatogram, to write the
DAD Spectra, from the top of the peaks in the chromatogram trace to the report file.

For Fixed Wavelength Range enter the Wavelength to look for and the ± Range
to look for the peak in. This is used for generating a wavelength chromatogram for
each sample, without having to enter the same details for each sample on the
LoginPC.

Page 22
OpenLynx Setup

Analog Data Page

Figure 2.6 The Analog Data page

This page allows the user to define integration parameters for up to four channels of
Analog chromatograms.

Start Time This is the retention time at which the integration of data starts and the
time from which data is written to the report file.

End Time This is the retention time at which the integration of data stops and the
time from which data stops being written to the report file.

Note: If Start and End times are left at the default 0.00 then the whole trace will be
integrated and written to the report file.

Offset Time This is time in minutes used to align the Analog detector with the MS
data. Normally Analog data is ahead of the Mass Spectrometer and this offset time
is added to the raw Analog time, therefore only positive values are valid.

Page 23
OpenLynx Setup

Press the button to invoke the Integrate Chromatogram parameters dialog. For
more information on integration parameters see "The MassLynx User Guide,
Chromatogram chapter".

Report Chromatogram Check this box to write this chromatogram trace to the
report file.

Report MS Spectra Check this box to write the Spectra, from the top of the
peaks in the chromatogram trace, to the report file.

Page 24
OpenLynx Setup

Instrument Page

Figure 2.7 The Instrument page

This page allows the user to define positive and negative ion series adducts, charges
and multimers.

Normally the unionised molecular weight is entered in the spreadsheet or on the

LoginPC, OpenLynx then adds the adducts specified on this page to determine the
target mass. If the ionised molecular weights have been entered then leave this page
blank.

n To Add an Adduct

1. If the and buttons are not next to the required ion type (positive or
negative), click on any of the column headings. The buttons will move so that
they appear to the right of the required ion type.

2. Click on the button. A new line will appear with default values of
Adduct = 0.0000, Charge = 1, Multimers = 1 and Desc = blank.

Page 25
OpenLynx Setup

3. To change the default values double click on the required Adduct field. The
display will change to allow the user to enter values as below.

4. Change values as required and press Enter. Note: For negative adducts the
minus sign must be entered.

n To Delete an Adduct

1. If the and button are not next to the required ion type (positive or
negative), click on any of the column headings. The buttons will move so that
they appear to the right of the required ion type.

2. Click on the required Adduct and press the button. The selected Adduct
will be deleted.

Page 26
OpenLynx Setup

MS Process Page

Figure 2.8 The MS Process page

This page allows users to process MS data. The processes available are Combine,
Mass Measure and Isotope Modelling.

Threshold Spectra

Filter Mode To define which spectral peaks to display in a Browser report, select
Absolute, Relative % or Most Intense Peaks from the drop down list box.

Value Enter the value above which the peaks must be to be displayed on the
spectrum.

Save Processed Spectra Check this box if you require the processed spectra to
be saved as processes within the data files.

Page 27
OpenLynx Setup

Combine Parameters

Figure 2.9 The combine regions of a chromatographic peak

Combine is used to generate a background subtracted mass spectrum from a

chromatographic peak.

Average Before Top The region of the chromatogram, from the Peak Start to the
Peak Top, to use in combine. Corresponds to in Figure 2.9.

Average After Top The region of the chromatogram, from the Peak Top to the
Peak End, to use in combine. Corresponds to in Figure 2.9.

Offset Before Top The time in minutes from the end of the background subtract
region to the Peak Start. Corresponds to in Figure 2.9.

Offset After Top The time in minutes from the Peak End to the start of the
background subtract region. Corresponds to in Figure 2.9.

Background Before Top The region of the chromatogram before the peak top to
use for background subtract in combine. Corresponds to in Figure 2.9.

Background After Top The region of the chromatogram after the peak top to use
for background subtract in combine. Corresponds to in Figure 2.9.

Minimum peak separation This is the spectral peak width in amu. For
centroided data the peak width can be determined from inspection of the tune peaks
in the tune page. The Combine algorithm combines peaks within a Minimum peak
separation window into a single peak. The default value is 1, this will need
reducing for accurate mass calculations as peaks will normally be resolved closer
together than this.

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OpenLynx Setup

Figure 2.10 The combine regions of a chromatographic peak

Background directly after average region The background can be taken

from immediately before the Average Before Top and immediately after the
Average After Top regions (as in Figure 2.10). Check this box and set both Offset
Before Top and Offset After Top to zero.

Use accurate mass spectra When running OpenLynx to determine accurate

mass (on LCT/QTOF) only those spectra in which the accurate mass calculations
were successful should be used. The lock mass and analyte peaks must be within
the count limits, specified in the upper/lower limits boxes and it applies to the
centroided data count, not the continuum data count. Checking this box means that
only those spectra which have successfully had dead time correction and lock mass
adjustment applied to them will be used. OpenLynx will search in the specified
Average retention time window for valid spectra, if processing continuum data the
first single spectrum that has valid accurate mass will be selected, if processing
centroided spectra all the valid scans in the specified retention time range will be
combined together. Accurate mass centroid files can be acquired real-time or
produced from continuum data using the All File Accurate Mass Measure program.

Upper Lock Mass Limit Enter the upper lock mass limit in counts. This is the
maximum intensity that a lock mass peak can have. If the value of the lock mass
peak for a spectrum is below this value then the spectrum can be used for accurate
mass determination.

Lower Lock Mass Limit Enter the lower lock mass limit in counts. This is the
minimum intensity that a lock mass peak can have. If the value of the lock mass
peak for a spectrum is above this value, then the spectrum can be used for accurate
mass determination.

Number of Spectra to Combine Enter the number of spectra to combine.

Upper Analyte Limit Enter the upper analyte limit in counts. This is the
maximum intensity that the analyte peak can have. If the value of the analyte peak
for a spectrum is below this value then the spectrum can be used for accurate mass
determination.

Lower Analyte Limit Enter the lower analyte limit in counts. This is the
minimum intensity that the analyte peak can have. If the value of the analyte peak
for a spectrum is above this value then the spectrum can be used for accurate mass
determination.

Page 29
OpenLynx Setup

Analyte Window Enter the size of the window, around the mass specified, that
the analyte peak must be found in for the spectrum to be used for accurate mass
determination. An analyte window of 2 is 1 Dalton around the mass entered.

Isotope Modelling

Press the Isotope button to display the Isotope modelling dialog, and enter the
required values. For more information on Isotope Modelling, see "The MassLynx
User’s Guide, Isotope Cluster Abundance Plots, in the Spectrum chapter".

Figure 2.11 The Isotope Modelling dialog

MaxEnt

The MaxEnt algorithm uses the method of maximum entropy to produce true
molecular mass spectra from multiply charged electrospray spectra.

Press the MaxEnt button to display the MaxEnt dialog, and enter the required
values. For more information on MaxEnt see "The MassLynx User’s Guide,
MaxEnt, in the Spectrum chapter".

Figure 2.12 The MaxEnt dialog

Page 30
OpenLynx Setup

Mass Measure

Mass Measure Check this box if you require the acquired data to be Mass
Measured.

Data type Select Standard or TOF from the dropdown list box.

Settings Press this button to invoke the Mass Measure parameters dialog, and
enter the required values. For more information on Mass Measure see "The
MassLynx User’s Guide, Spectrum chapter".

If TOF data type is selected two settings buttons are displayed. Press the
Settings MS+ for positive data and Settings MS- for negative data.

Figure 2.13 The Mass Measure dialog

Page 31
OpenLynx Setup

AFAMM Parameters

Figure 2.14 AFAMM Parameters dialog

Do AFAMM Check this box to process the data using All File Accurate Mass
Measure (AFAMM).

Process Type From the drop down list box, select the process type that you want
to apply to the data. You can select one of the following four options:

• Mass Measure

• Mass Measure with Peak Filter

• Secondary Reference Correction

• Peak Filter.

Depending on the Process Option selected, the following fields will be enabled:

Filter Reference File Press the Browse button and select a Filter Reference File
(*.ref) from the displayed dialog. This file removes peaks arising from the reference
compound from the acquired data file.

Filter Parameters Select Peak Window (ppm) or Peak Window (Da) and
enter the required window size.

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OpenLynx Setup

Secondary Reference Correction Parameters

Filter Reference File Press the Browse button and select a secondary Filter
Reference File (*.ref) from the Open dialog. This selects a reference file against
which data in an acquired data file can be adjusted.

Peak Match

Peak Window ppm Enter the range to search the data file for a peak that matches
one in the reference file. The window is +/- the entered value around the mass
defined in the reference file. This means that a value of 250ppm will result in a
search window of 500ppm.

Intensity Threshold Enter the percentage of the most intense peak in the
spectrum that a peak must be above to be considered as significant.

Lock Mass Peaks Found Enter the percentage of peaks (within the required
mass range) in the reference file that must be successfully located in the scan, for
that scan to be adjusted for accurate mass.

Select Largest Peak in Window to use the mass of the largest peak in the search
window, or select Closest Peak in Window to use the mass of the peak in the
data scan closest to that of the reference file.

Isotopic Cluster Analysis

Press the Isotope Cluster button to display the Isotopic Cluster Analysis dialog.

Figure 2.15 The Isotopic Cluster Analysis dialog

Page 33
OpenLynx Setup

Isotopic Cluster Analysis Check this box to perform Isotopic Cluster Analysis.

Select Use Mass Differences Only to use the mass differences in the cluster
analysis or select Use Mass Differences and ratios to use the mass differences
and ratios in the cluster analysis.

RT Start Time Enter the retention time in minutes to start Isotopic Cluster
Analysis.

RT End Time Enter the retention time in minutes to stop Isotopic Cluster
Analysis.

Start Mass Enter the mass at which to start Isotopic Cluster Analysis.

End Mass Enter the mass at which to stop Isotopic Cluster Analysis.

Mass Tolerance Enter the mass tolerance, this will be used with the First Mass
Difference and Second Mass Difference to find the next peak in the cluster. A
peak found at the first or second mass difference ± the Mass Tolerance will be
considered as part of the cluster.

Ratio Tolerance Enter a ratio tolerance, this will be used with the First Intensity
Ratio and Second Intensity Ratio to find the next peak in the cluster. A peak
found with the first or second ratio intensity ± the Ratio Tolerance will be
considered as part of the cluster.

Intensity Threshold Enter the minimum intensity threshold, peaks with an

intensity below this threshold will be ignored.

Use Second Mass Difference Check this box if the analyte is likely to have
three peaks within a cluster. The Mass 2 values are applied to the mass and intensity
ratio between the second and third peaks.

Mass 1

First Mass Difference Enter the expected mass difference for the next peak in
the cluster, the second peak should be found at this mass within the Mass Tolerance
window.

First Intensity Ratio Enter the expected intensity ratio (Intensity of peak 2/
Intensity of peak 1), the second peak should be found within the Ratio Tolerance
window. This only applies when Use Mass Differences and Ratios is selected.

Predefined Elements For some elements the First Mass Difference and First
Intensity Ratio have been defined, select the required element from the drop down
list box to automatically enter values in these fields.

Mass 2

These fields are the same as for Mass 1.

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OpenLynx Setup

Spectrum Test Page

Figure 2.16 The Spectrum Test page

This page allows the user to define parameters that decide if spectra acquired are
valid.

Overload The maximum intensity that the mass spectrometer can record is
4194304, if the detector becomes saturated values larger than this will be produced.
Check this box and enter a value over which spectra will be marked as overloaded.

Noise Check this box and enter a value above which spectra will be marked as
noise. E.g. if 10 is entered then if the noise is greater than 10% of the base peak
intensity then the spectrum will be mainly noise and so be rejected.

Peak Density Check the box and enter a value for the minimum number of peaks
which must appear per Dalton. If the number of detected peaks per Dalton is lower
than this, then the spectrum will be rejected.

Diversity These parameters are used to identify peaks in the OpenLynx Browser,
to enable these parameters click on the Diversity heading. A second click on the
heading will disable the parameters. This option must be enabled and a mass
entered on the LoginPC, or in the Sample List, for the Browser to identify target
peaks.

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OpenLynx Setup

Mass Find Mode Select Nearest or Most Intense from the drop down list box, to
select the peak nearest the mass of interest or the most intense peak within the Mass
Window.

Mass Window Enter the size of the window to search the combined spectrum for
the entered mass and any adducts. E.g. a mass window of 2 is 1 Dalton around the
mass entered.

Primary Threshold Check this box, enter a threshold above which peaks must be
to be considered as ’Found’ and select PPM or mDa from the drop down list box.
These peaks will be displayed in the found colour in the OpenLynx Browser.

Secondary Threshold Check this box, enter a threshold above which peaks must
be to be considered as ’Found Tentative’ and select PPM or mDa from the drop
down list box. Peaks above this threshold but below the Primary Threshold will be
displayed in the found tentative color in the OpenLynx Browser.

Threshold Mode Select Relative or Absolute from the drop down list box.

Threshold (MS+) Enter a minimum threshold for positive spectra, above which
peaks must be to be included. For example, if a threshold of 20 is entered, the peak
must be at least 20% of the base peak intensity.

Confirmation Threshold (MS+) Enter a threshold for positive spectra, above

which peaks must be to be considered a good match. These peaks will be displayed
in the found color in the OpenLynx Browser. Peaks which fall between the
Threshold and Confirmation Threshold will be displayed in the found tentative color
in the OpenLynx Browser.

Threshold (MS-) Enter a minimum threshold for negative spectra, above which
peaks must be to be included. For example, if a threshold of 20 is entered, the peak
must be at least 20% of the base peak intensity.

Confirmation Threshold (MS-) Enter a threshold for negative spectra, above

Page 36
OpenLynx Setup

Chromatogram Test Page

The Chromatogram Test page allows an area threshold to be defined. The area of a
chromatogram peak must be above this threshold to be displayed as found in the
OpenLynx Browser. This means that the intensity of the peak is being tested in
addition to the presence of the compound.

The threshold can be applied to specified types of chromatogram.

Figure 2.17 The Chromatogram Test page

Enable Chromatogram Test Check this box to enable chromatogram threshold

testing.

Threshold (%) Enter a percentage area of the chromatogram, which the peak must
be above, in order to be displayed as ’Found’ on the OpenLynx Browser.

Chromatograms to test Check the box for each type of chromatogram that the
thresholding test should be applied to. Note: Only chromatograms where the
Report Chromatogram checkboxes have been selected on the MS Data, DAD
Data and Analog Data pages will be available.

Page 37
OpenLynx Setup

Quality Control Page

Quality Control checking is used to check that the mass spectrometer and HPLC
system are working correctly and to ensure the consistency of data acquired. A QC
sample with a known retention time and peak intensity is acquired and the results
compared to the values entered on this page.

To use the Quality Control options in OpenLynx Login the QC On box on the QC
Options dialog in OpenLynx Login must be selected.

Figure 2.18 The Quality Control page

QC Required Check this box if QC checking is required.

Multi-probe Capability Check this box if a MUX system is to be used.

Probes Enter the number of probes on the MUX system. The corresponding
number of Stream buttons will be enabled.

Trace From the drop down list box, select the type of chromatogram trace against
which to compare the QC Samples.

+/- RT (mins) Enter the retention time tolerance, this will be used with the
Retention Time(s) defined on the Stream Parameters dialog (see below) to decide if
the peak has passed the QC test. A peak found at the Retention Time ± the RT
(mins) will be considered as passing the test.

Page 38
OpenLynx Setup

+/- Peak Area Enter the peak area tolerance, this will be used with the % Total
Area(s) defined on the Stream Parameters dialog (see below) to decide if the peak
has passed the QC test. A peak found with the % Total Area ± the Peak Area will be
considered as passing the test.

QC Failure E-Mail Enables you to specify a text message to be sent automatically

by E-Mail if a QC sample fails. The subject of the e-mail will be "QC Failure".

E-Mail Address Enter the e-mail address to which you want the QC Failure
e-mail to be sent.

E-Mail Text Enter the message that you want the QC Failure e-mail to contain.

Stream n To define the parameters of a particular probe, press the relevant Stream
button. The Stream Parameters dialog is displayed.

Figure 2.19 The Stream Parameters dialog

Retention Time Enter the expected retention time of the peak in the QC sample.

% Total Area Enter the area of the chosen peak, as a percentage of the total area
of all the peaks. If the peak area is not equal to the value specified, ± Peak Area
(defined on the Quality Control page), then the QC will fail.

Peak 2 and Peak 3 Check these boxes and enter the Retention Time and %
Total Area for additional peaks.

Mode Select Relative % or Absolute from the drop down list box. Relative % is
the specified Min Intensity as a percentage relative to the base peak. Absolute is
the absolute intensity specified in the Min Intensity field.

Min Intensity Enter the intensity (Relative % or Absolute), which the specified
peaks must be above in order for the QC Sample to be passed.

Page 39
OpenLynx Setup

Quantify Page

Figure 2.20 The Quantify page

This page allows the parameters to be defined so that OpenLynx can calculate the
concentration and amount of sample based on the areas of peaks detected. These
values will be displayed in the Concentration and Amount columns on the
OpenLynx Browser. For more information see "The MassLynx User’s Guide,
Quantify chapter".

The amount is calculated as Concentration x Factor 1.

Disable Select this option if quantification is not required.

Use calibration coefficients Select this option for values calculated externally
and enter the coefficients of the calibration curve in the C0, C1 and C2 fields.

Use MassLynx Quantify calibration file (*.cbd) Select this option to use a
calibration file created in MassLynx. Note: Only the first calibration in the file will
be used.

Chromatogram Trace Select the type of chromatograms to be quantified from

the drop down list box.

Page 40
OpenLynx Setup

User Factor Select this option and enter the number of nitrogens to use as the
division factor for adjusting the concentration of the data obtained.

Number of Nitrogens in Formula Select this option to use the number of

nitrogens in the input formula as the division factor for adjusting the concentration
of the data obtained.

Library Page

Figure 2.21 The Library page

Use this page to define a library that will be used to search for results and to append
any acquired spectra to. For more information on library searching see the Library
chapter in the MassLynx User’s Guide.

Select Library

Name Enter the name of the required library or select one from the dropdown list
box.

Advanced Press this button to display the Library selection dialog.

Page 41
OpenLynx Setup

Figure 2.22 The Library Selection dialog

Library location (directory) Enter the name of the directory in which the
libraries are located.

A library can be created containing all spectra or spectra can be split into MS
positive, MS negative Diode array categories. E.g. Lib1 can be created with all
spectra or can be created as three libraries lib1(MS+), lib1(MS-) and lib1(UV).

Append data type postscript to library names Check this box to allow the
different data types to be Searched/Stored in separate libraries.

MS positive spectra (MS+), MS negative spectra (MS-) and Diode array

spectra (UV) Check the boxes for the different data type libraries to be searched
for or saved.

Search Library

Perform library search on spectra Check this box to perform a library search,
using the results acquired.

Settings Press this button to display the Library Search Settings dialog.

Page 42
OpenLynx Setup

Figure 2.23 The Library Search Settings dialog

Number of library hits to report The result of a Library search is a list of

library compounds or "hits" whose spectra give the best match with the unknown
spectrum. Enter the number of hits to be reported.

Rank library hits by Select one of Forward Fit or Reverse Fit. The Forward
fit value shows how likely it is that the search spectrum is a pure sample of the
Library entry. The Reverse fit value shows how likely it is that the search spectrum
contains the Library entry, in this case the search spectrum may be a mixture of
compounds.

Search n largest peaks in spectrum Enter the number of spectral peaks to be

compared during the search.

Minimum Search Fit Specify a Minimum Forward and/or a Minimum Reverse

fit value, which a Library entry must have before it will appear in the Hit list. To
make the filter active the user should type a value between 0 and 1000 into the edit
control.

Library Presearch Use these options define the speed and accuracy of a search.
The library presearch file contains a spectrum, for each library entry, which has been
reduced to the 8 most intense mass-weighted peaks. The unknown spectrum is
reduced to its 8 most intense mass-weighted peaks and then compared to the library
presearch file.

No presearch All peaks will be compared to all library entries. This is the most
accurate method of searching, but will also take the most time.

Main search top n presearch matches Takes the top n matches from the
presearch and compares the unknown with them.

Page 43
OpenLynx Setup

Main search entries with n% presearch fit Takes all entries with an n% fit
or above from the presearch and compares the unknown with them.

To refine a search further the user can specify the Retention time with window
(min +/–) and Retention index with window (+/–) filters. Check the relevant box
and enter the time or retention index windows within which the library entry must
be. Note: For the retention index search both the library entry and the unknown
must have had a retention index calibration performed on it.

Build Library

Automatically append spectra to library Check this box to append acquired

spectra to the library named above.

Settings Press this button to display the Library selection dialog.

Figure 2.24 The Library Build Settings dialog

Create library if doesn’t already exit Check this box if the library named in
the Library Search section does not exist and the Automatically append spectra to
library box has been checked. A new library will be created when processing is
complete.

Maximum number of peaks in entry Enter the maximum number of peaks to

be saved with an entry.

Page 44
OpenLynx Setup

Elemental Page

Figure 2.25 The Elemental page

This page allows users to perform Elemental Composition calculations. For more
information on elemental composition see the Spectrum chapter in the MassLynx
User’s Guide.

Perform Elemental Composition Check this box to perform elemental

composition calculations.

Browse Press this button and select an elemental composition settings file (*.els)
from the browser displayed. These files are created in the elemental composition
program and contain the parameters to be used to search with.

Perform Restricted Search Check this box to restrict the search to those
elements defined in the Formula entered in the Sample List. The limit on the
elements is set in the *.els file selected.

E.g. sample list contains the formula C23H45N7O6F2

*.els file has From 0 To 30 for H (on the Symbol Parameters page)

The search will only be for the elements C, H, N, O and F and a composition
containing a maximum of 30 Hyrdrogens.

Page 45
OpenLynx Setup

Perform Full Spectrum Scan If this box is not checked, then the elemental
calculations are performed for peaks found at the masses entered on the Login
screen. If this box is checked and a value entered in the Number of Peaks box, and
if peaks are not found at the masses entered on the Login screen, the software will
search the spectrum and perform elemental calculations on the largest peaks above
the threshold.

Threshold (abs) and Threshold (%) Select one of these options and enter a
value above which peaks must be to be included in the elemental calculations.

Page 46
OpenLynx Setup

Acquisition Process Page

Figure 2.26 The Acquisition Parameters page

This page allows users to define extra processing which will be performed on the
files at the time of acquisition. E.g. ChroSplit.exe for splitting Batch data files
acquired using the Gilson Multi-Injector. If files are reprocessed this processing
will not be performed.

Acquisition Process Press the Browse button and select the required *.exe file
from the dialog displayed.

Acquisition Parameter File Press the Browse button and select the required file
from the dialog displayed.

Acquisition Process Options Enter the string of characters which define the
required process options.

Page 47
OpenLynx Setup

Page 48
OpenLynx Setup

Notes
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OpenLynx Setup

Notes
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Page 50
OpenLynx Browser

OpenLynx Browser
Chapter 3
Overview
The OpenLynx Browser is used to view OpenLynx Report files, print results or
export results to other applications (such as LIMS systems or Excel) via the
clipboard or TAB delimited text files.

The OpenLynx Browser can be installed as a standalone to MassLynx to allow

viewing of results on remote computers.

Creating Report Files

An OpenLynx Browser report file (*.rpt) is created when a job submitted from the
LoginPC is processed. Report files can be created from another PC by specifying
OpenLynx.exe in the Process column of a Sample List and the OpenLynx
Parameters file (*.olp) in the Process Parameter column.

If compound targeting is required, then a mass to search for must be entered via the
LoginPC or in the Sample List.

The OpenLynx Browser Screen

Figure 3.1 The OpenLynx Browser

The screen is split into 7 panes although some may not be displayed depending on
the processing selected in the OpenLynx method.

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OpenLynx Browser

• The Plate pane showing the plate layout and compounds found.

• The Sample Description pane showing sample information and whether the
compound, being searched for, has been found or not.

• The Fraction Results List pane showing fraction collection information. This
pane will not be displayed if fraction collection has not been performed.

• The Results Table pane showing a list of detected compounds.

• The Spectrum pane showing the spectrum for the well highlighted and the
retention time selected.

• The Elemental Composition/Library Search Results pane showing the results of

any Elemental Composition and/or Library searching for the peak selected in
the Results Table pane. This pane will not be displayed if both Elemental
Composition and Library searching have not been performed.

• The Chromatogram pane showing the integrated chromatogram for the well
highlighted.

Accessing OpenLynx Browser

To access the OpenLynx Browser select OpenLynx Browser from the OpenLynx
menu on the top level MassLynx Screen.

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OpenLynx Browser

The OpenLynx Browser Toolbar

Toolbar Menu equivalent Purpose
button

File… Open Open an existing OpenLynx Browser report

Edit… Copy Copy the selection and put it on the

clipboard

File… Print Print an OpenLynx Browser file

OpenLynx Browser go to first Well

OpenLynx Browser go to previous Well

OpenLynx Browser go to next Well

OpenLynx Browser go to last Well

Display previous plate

Display next plate

Display default range

View… Swap List View Swaps between the Elemental Composition

and the Library Search Results view.

Help… About Display program information, version

OpenLynx Results number and copyright
Browser

Page 53
OpenLynx Browser

Getting Started
n To Open an Existing OpenLynx Browser File

1. Press the Toolbar button, or select Open from the File menu.

2. Select the required OpenLynx Browser results file (*.rpt) and press Open.

n To Copy an OpenLynx Browser File

Plate, Sample Summary and Spectrum List information can be copied to the
clipboard and pasted into other Windows applications. See "Copy Control Page" on
page 68 for more details.

1. Press the Toolbar button, or select Copy from the Edit menu.

n To Print an OpenLynx Browser File

1. Press the Toolbar button, or select Print from the File menu. The Print
Control dialog is displayed.

Figure 3.2 The Print Control dialog

2. Select Print Current Sample to print information for the currently selected
well.

3. Select Print All to print information for all wells on all plates.

4. Select Print Selection and select a From and To well number from the drop
down list boxes.

5. Select Print All Colours Black to print all of the coloured data in black.

6. To change the margin settings for the printed report, press the Margins button.
The Set Margins dialog is displayed.

Page 54
OpenLynx Browser

Figure 3.3 The Set Margins dialog

7. Enter the required width in centimetres for the Top, Bottom, Left and Right
margins and press OK.

8. From the Print Control Dialog, press OK to print the report.

Reports can also be printed from Windows NT Explorer. Select the required files
and choose Print from the File menu. Note: This method will not allow the user to
select which samples are printed.

Page 55
OpenLynx Browser

Report Schemes
n To Open a Report Scheme

1. Select Report Scheme Open from the File menu.

2. Select the required *.ors file from the dialog displayed.

3. Press Open.

n To Save a Report Scheme

1. Select Report Scheme Save As from the File menu.

2. Select the required location and enter a *.ors filename in the dialog displayed.

3. Press Save.

Report Scheme Settings

The information on printed reports can be defined via the Report Scheme Settings
dialog. To access the dialog select Report Scheme Settings from the OpenLynx
Browser File menu.

Print Control Page

Figure 3.4 The Edit Report Settings dialog, Print Control page

Page 56
OpenLynx Browser

Plate Summary Check this box to produce a Plate report. This is a picture of the
plate showing:

• 1 for found compounds.

• ? for found tentative compounds.

• 0 for compounds not found.

• + if no compound was searched for.

• - for unused wells.

Sample Summary Check this box to produce a summary report for a Sample.
Note: The number of samples printed is controlled from the Print Control dialog.
See To Print an OpenLynx Browser File, on page 54.

Sample Report Check this box to produce a more detailed report for a sample.

Sample on New Page Check this box to start each sample of the Sample Report
on a new page.

Peak Information Tables To display peak information tables below a

chromatogram, check the box relevant to the type of information required.

Spectra height (mm) Check this box and enter the required height, to print the
spectra associated with a sample.

Chromatogram height (mm) Check this box and enter the required height, to
print the chromatograms associated with a sample.

All Chromatograms On One Axis Check this box to use one axis for all
chromatograms.

Mass Chromatograms/Axis Check this box and enter the number of

chromatograms to display on each axis. This is used to make overlaid mass
chromatograms easier to view. The default of 1 will display each chromatogram on
a different axis.

Maximum Spectra Displayed To limit the number of spectra printed on a page,

check this box and specify the maximum number of spectra to print.

Side by Side Chromatograms Check this box to print two chromatograms per
line. Note: The Peak information table will not be displayed if this option is
chosen.

Side by Side Spectra Check this box to print two spectra per line. Library
search results and Elemental calculations will not be displayed if this option is
chosen.

Chromatogram Print Order The order in which chromatograms and spectra are
printed can be defined by selecting one of MS First, Analog First or DAD First for
chromatograms, and Time Order or Chromatogram Order for spectra

Page Orientation Select Portrait or Landscape to print the report with the
required page orientation.

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OpenLynx Browser

Report Column Selection Pages

The basic format of the Report Column Selection pages is the same, each has a list
of fields which can appear as column headings on the type of report selected. Click
on the corresponding tab for the type of report required. The Report Column
Selection pages are:

• Fraction Results Summary page

• Spectrum Report page

• Spectrum Search Report page

• Sample Header page

• Chromatogram Report page

• Sample Summary page

• Results Summary page

• Report Header page

• Elemental Report page.

Figure 3.5 The Spectrum Report page

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OpenLynx Browser

n To Add a Field

Click, with the left mouse button, on a field in the Available Fields box and press
the button. The new field is added to the bottom of the Reported Fields list.

n To Remove a Field

Click with the left mouse button, on the field to remove, in the Available Fields box
and press the button. The field will be removed from the Reported Fields list.

n To Change the Order of Fields

Click with the left mouse button, on the field move, in the Available Fields box and
press the or button until the field is in the required position.

n Field Alias

If the field name in the Available Fields list does not correspond to a description the
user will recognise, enter a different name in the Alias box. E.g. State could be
displayed on the report as Pass/Fail. This field may also be used to display field
names in another language.

n To Change the Field Width

Enter a new value in the Width box. Note: This option is not available on the
Sample Header and Report Header pages.

Results Summary Page

The Results Summary page has three extra options, Nominated Results Trace,
Largest Peak Only and All Found Peaks.

Select one of the options from the Nominated Results Trace dropdown list box to
define which type of trace is used for the calculation of the Area % Total.

If a chromatogram has more than one found peak, you can choose to include the
Largest Peak Only or All Found Peaks in the report.

Report Header Page

The Report Header page has four extra fields, Report Header Text, Display report
name, Display submitter name and Display date and time.

Enter text to appear at the top of a report in the Report Header Text field. This text
will be displayed between the Report name and Submitter name, if selected, see
below.

Check the Display report name box to print “OpenLynx Report” at the top of the
report. If this text is not required, make sure the box is unchecked and enter your
own text in the Report Header Text field as described above.

Check the Display Submitter name box to print the name of the submitter as
defined in the OpenLynx Login program (User name).

Check the Display date and time box to print the date and time of printing.

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OpenLynx Browser

Sample Header Page

The Sample Header page has two extra fields, Print "Sample Report" Title and
Print Sample Header.

Check the Print "Sample Report" Title box to print “Sample Report” at the top of
each page of the report.

Check the Print Sample Header box to print the sample header for each sample.

Chromatogram Report Page

The Chromatogram Report page has one extra field, Current Trace. Each type of
trace can have a different set of fields associated with it, select each option from the
dropdown list box and select the fields you wish to report for this type of
chromatogram.

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OpenLynx Browser

View Options
A number of options are available to change the appearance of the Browser screen,
to access them select Options from the View menu.

Spectrum Page

Figure 3.6 The Spectrum page

Peak Annotation Decimal Places Change this value, by pressing the arrows, to
change the number of decimal places displayed on peak annotation. Range 0 to 4
decimal places.

Select one of Threshold (abs) or Threshold (%) and enter a value above which
peaks must be to be displayed on the Spectrum.

Accurate Mass Error Reporting Check this box to display the difference
between the observed mass and the expected mass. Check the PPM or mDa box to
display the results in parts per million or millidaltons.

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OpenLynx Browser

Horizontal Axis Decimal Places Change this value, by pressing the arrows, to
change the number of decimal places displayed on the horizontal axis. Range 0 to 4
decimal places.

Wavelength Label Enter the text to appear as the label on the horizontal axis for
diode array data.

Daltons Label Enter the text to appear as the label on the horizontal axis for mass
spectral data.

Peak Number Check this box to display the Peak number before the retention
time in the Spectrum header.

Retention Time Check this box to display the Retention Time in the Spectrum
header.

Process Description Check this box to display the Process Description in the
Spectrum Header.

Select all Spectra Check this box to display all spectra for the selected well.

Default range to data When checked, the default mass display range of a
spectrum will be based upon the peaks the spectrum contains, only the mass range
which actually contains data will be displayed.

If unchecked the default display range will be the actual mass range the spectrum
was originally acquired over.

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OpenLynx Browser

Chromatogram Page

Figure 3.7 The Chromatogram page

Peak Integration Check this box to display the baselines for the results of the
chromatogram trace.

Chromatogram Purity Check this box to display the chromatogram peak purity
on the chromatogram peak tops.

Peak Numbers Check this box to display the peak number above a peak on the
chromatogram peak tops.

Found Mass Check this box to display the mass of a found peak. When checked,
the Spectrum Purity and Decimal Places options become available, press the
arrows or enter a value for the number of decimal places to display for the found
peak.

Spectrum Purity Check this box to display the spectrum purity on the
chromatogram peak top of a found peak.

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OpenLynx Browser

Base Peak Mass Check this box to display the base peak mass values on the
chromatogram peak tops. When checked, the Decimal Places option becomes
available, press the arrows or enter a value for the number of decimal places to
display.

Retention Time Check this box to display the retention time values on the
chromatogram peak tops. When checked, the Decimal Places option becomes
available, press the arrows or enter a value for the number of decimal places to
display.

Threshold (%) Enter a value which peaks must be above in order to be displayed
on the Chromatogram.

Horizontal Axis Decimal Places Change this value, by pressing the arrows,
to change the number of decimal places displayed on the horizontal axis.

Label Enter the text to appear as the label on the horizontal axis.

Fill Peaks Check this box to fill integrated peaks in green if found (or found
tentative) and red if not found. This option uses colours from the Colors page.

Fill Background Check this box to fill the area under integrated peaks in the
Unused color, specified on the Colors page.

Process Description Check this box to display the process description on the
chromatogram.

Replace DAD Check this box and enter the text to use in the process description
displayed on the chromatogram, this will replace the text DAD which would
normally be displayed.

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OpenLynx Browser

Default Plate Page

Figure 3.8 The Default Plate page

For autosamplers controlled by the MassLynx software a plate layout will have been
defined (see the MassLynx Guide to Data Acquisition). This cannot be changed.

For autosamplers not controlled by the MassLynx software, this page is used to
organise the data acquired so that it can be displayed in plate format.

Rows Enter the number of rows on the plate to be used.

Columns Enter the number of columns on the plate to be used.

Origin This is the corner of the rack that the vial grid referencing starts from.
Select one of Top Right, Top Left, Bottom Right or Bottom Left from the drop
down list box.

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OpenLynx Browser

Method This is the method of numbering the wells on a plate. There are three
options:

• XY which references the vials A1, B1 etc.

• Sequential Discontinuous which numbers the vials 1, 2, 3 across a row, left to

right if origin is top left, and then starts the next row from the left again.

• Sequential Continuous which numbers the vials 1, 2, 3 across a row, left to

right if origin is top left, then continues number the next row, right to left etc.

If a Gilson autosampler or a Waters 2700 autosampler is used with OpenLynx then

the vial referencing must be set to either sequential continuous or sequential
discontinuous.

Horizontal If the method chosen is X,Y then this box becomes enabled. It allows
horizontal referencing of the plate to be a number or a letter.

Vertical If the method chosen is X,Y then this box becomes enabled. It allows
vertical referencing of the plate to be a number or a letter.

Horizontal Priority Check this box if samples are to be acquired horizontally

across the plate.

If Referencing = X,Y, Horizontal = Letter, Vertical = Number and

Horizontal Priority is checked, this will result in samples being acquired in the order
A1, A2, A3. If the Horizontal Priority box is not checked samples will be acquired
in the order 1A, 1B, 1C etc.

If Referencing = sequential continuous or discontinuous and Horizontal Priority is

checked, this will result in samples being acquired from row 1 then row 2. If the
Horizontal Priority box is not checked samples will be acquired from column 1, then
column 2 etc.

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OpenLynx Browser

Colors Page

Figure 3.9 The Colors page

This page allows the user to define the colors used on the Plate pane and the
Chromatogram pane.

Select a color from the drop down list box.

The mass to be searched for is entered in the MassLynx Sample List or the
OpenLynx Login PC.

Threshold values are on the Spectrum Test Page of the OpenLynx setup.

Found The intensity of the peaks is above all threshold values.

Found (Tentative) The intensity of the peaks is above the primary threshold but
below the Confirmation threshold. For more details see the Spectrum Test page in
the OpenLynx Setup chapter.

Not Found There were no peaks for the mass entered.

Not Searched No mass was entered.

Unused There was no sample defined for this position on the plate.

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OpenLynx Browser

Copy Control Page

Figure 3.10 The Copy Control page

This page allows the user to define which information is copied to the clipboard, for
use in other Windows applications.

Plate Check this box to copy Plate information for all plates in the run. This
copies a series of rows containing:

• 1 for found compounds.

• ? for found tentative compounds.

• 0 for compounds not found.

• + if no compound was searched for.

• - for unused wells.

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OpenLynx Browser

Sample Summary Check this box to copy summary information for each
Sample. The Sample Summary information is written to the clipboard using the
settings for the Sample Summary and Results Summary in the current Report
Scheme.

Spectrum List Check this box to copy details of each peak for each Sample.

Column Pages
These pages have a similar format and allow the user to define which information is
displayed in the Results Table, Fraction Results List, Elemental Composition
Results List and Library Search Results List Panes. The Column Pages are:

• List Columns page

• Elemental Columns page

• Fraction Columns page

• Library Columns page.

Figure 3.11 The List Columns page

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OpenLynx Browser

Check the boxes next to the fields required.

Columns can be removed from the Results Table pane by clicking, with the right
mouse button, on a column and selecting the Remove Column pop up menu that
appears. Columns can only be restored by selecting them again on these pages.

List Columns Page

The List Columns page also shows the number of decimal places to display for the
relevant fields. These can be changed by clicking, with the right mouse button, on
the field and selecting the number of decimal places from the pop up menu
displayed.

Fraction Display Page

The Fraction Display page allows the fraction collection regions on the
chromatogram to be highlighted.

Figure 3.12 The Fraction Display page

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OpenLynx Browser

Show Fractions Check this box to display the Lines and Fill Colours on the
chromatogram pane.

Show on all Chromatograms If this box is checked, the fraction collection

regions are shown on all chromatograms. If this box is not checked, only the
chromatograms relating to the fraction display fraction regions.

Lines There are three sets of lines that can be displayed on the chromatogram.

• The Start Line shown at the start of each fraction.

• The End Line shown at the end of each fraction.

• Current a set of lines displayed at each end of the fraction selected in the
Fraction Results List pane.

For each line required.

1. Click on the line type.

2. Select the Colour from the drop down list box.

3. Select the Width from the drop down list box.

4. Click on Solid, Dotted or Dashed to display the line. Click on None to

hide the line.

Fill Fraction Display Check this box to display the region of the chromatogram
that the fraction was collected from, using the fill colours described below.

First Colour Select the required colour from the drop down list box. The area of
the chromatogram that the first fraction was collected will be displayed in this
colour. If there are more than two fractions collected from a chromatogram, this
colour will also be used to show the 1st, 3rd, 5th, 7th etc. fractions.

Second Colour Select the required colour from the drop down list box. The area
of the chromatogram that the second fraction was collected will be displayed in this
colour. If there are more than three fractions collected from a chromatogram, this
colour will also be used to show the 2nd, 4th, 6th, 8th etc. fractions.

Current Colour Select the required colour from the drop down list box. The area
of the chromatogram for the fraction selected in the Fraction Results List pane will
be displayed in this colour.

Double clicking, with the right mouse button, on a fraction area of the
chromatogram will make the fraction the current fraction. The fraction will be
selected in the Fraction Results List pane and the Current colours and lines will be
used in the chromatogram pane.

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OpenLynx Browser

Other Display Options

n To display two documents simultaneously

1. Select Open from the File menu. This will display a new window over the
top of the previous one.

2. Select Tile or Cascade from the window menu. This will display the two
child windows in the style chosen.

3. Repeat the above steps as often as required.

n To display two different views of the same document

Select New Window from the Window menu. A copy of the current window
created, named “filename:2”. Select Cascade, Tile Horizontally or Tile Vertically
from the Window menu to display this new window along side the existing
document to compare results of similar searches.

n To change the size of a pane

To change the size of the panes on display, position the mouse pointer on the line

between the two panes until the symbol appears, or select Split from the
Window menu. Hold down the left mouse button and drag until the pane is the
required size.

n To change the size of the display

On a standard screen set to 800 by 600 pixels there may not be enough room to
display all the information in all of the panes. Changing the desktop settings will
display more information.

1. Press the Start button, select Settings and then Control Panel.

2. From the Control Panel select Display.

3. On the Settings page change the Desktop Area to 1024 by 768 pixels or
above.

4. Press the Test button and if the test page displays correctly press the OK
button.

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OpenLynx Browser

Other Menu Options

File Menu

Load on startup If this option is selected from the File menu, the next time the
Browser is opened, the last Browser file viewed is automatically loaded. A tick
mark appears next to the item when selected, selecting the option again will turn it
off.

Send To If this option is selected, an e-mail message is created with the currently
selected report attached to it. Enter the address to send it to and press the send
button.

Note: To view the report the recipient of the e-mail must have the MassLynx (with
the OpenLynx option) or OpenLynx Browser software installed. The attachment
can then be saved as normal and opened in MassLynx or the OpenLynx Browser. It
can also be opened by double clicking on the report in the e-mail message. If the
OpenLynx Browser software is not installed as a stand-alone program the following
dialog will be displayed.

Figure 3.13 The Program Not Found dialog

Press the Locate button and select the MassLynx directory, or type in the location
of the MassLynx directory and then press the OK button.

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OpenLynx Browser

Failed Samples Options

Select Failed Samples Options from the File menu. The Failed Samples Options
dialog allows you to define the parameters used when you select the Create List of
Failed Samples option, described below.

Figure 3.14 The Failed Samples Options dialog

Enable E-Mailing of Report File Check this box to e-mail the *.rpt file (formed
when the *.olb file is processed), to the recipient specified in the E-Mail Address
field. The *.olb file is processed when the user submits it to the MassLynx queue.

Create File In Enter the location to which you want the failed samples *.olb file to
be saved.

Create List of Failed Samples

Select this option to create a *.olb file, containing all of the samples that were
marked as Not Found. The *.olb file can then be submitted to the MassLynx queue
and analysed, using a different ion mode or ionisation method.

This procedure must be carried out in the following order:

1. Analyse the original sample list in electrospray positive mode.

2. Select Create List of Failed Samples from the File menu to collect the Not
Found samples into a *.olb file.

3. Analyse the samples in the *.olb file in electrospray negative mode.

If necessary, repeat this procedure using APCI positive mode and APCI negative
mode.

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OpenLynx Browser

View Menu

Refresh This option rereads the current Browser Report and updates the display
information. This command should be used if the content of the Browser Report has
changed as a result of processing further samples.

Swap List View This option allows the user to swap between the Elemental
Composition Results List view and the Library Search Results List view, if both lists
have been generated.

Toolbar If this option is selected from the View menu, then the Toolbar will be
visible. A tick mark appears next to the item when selected, selecting the option
again will turn it off.

Status Bar If this option is selected from the View menu, then the Status Bar will
be visible. A tick mark appears next to the item when selected, selecting the option
again will turn it off.

Window Menu

New Window Selecting this item will create a copy of the current window. This
is useful for displaying different views of the same document. The second
document will have a ’:2’ after the name. To change between documents, select the
document required from the documents listed at the bottom of the Window menu. A
tick will appear next to the document that is currently active.

Cascade Select this option to arrange document windows so that the title bar of
each window is visible.

Tile Select this option to arrange open windows side by side on the screen, dividing
the available space equally between the open windows so that they are all visible.

Arrange icons Select this option to arrange all iconised windows into rows.

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OpenLynx Browser

The Plate Pane

Figure 3.15 The Plate pane

The Plate Pane displays information about all the samples from the currently
selected plate. The vials are color coded to indicate whether they contained a
sample in which compounds were:

• Found — Light green

• Found (Tentative) — Olive green

• Not found — Red

• Not Searched — Blue

• Contained no sample — Grey.

The default colors can be changed see "Colors Page" on page 67.

The currently selected vial is indicated by being shown recessed. Change the
current vial by clicking on a new vial, using the vial selection toolbar buttons ( ,
, and ) or the arrow keys.

Clicking on a well, with the left mouse button, will display detailed information
about that well in the other panes of the screen.

The current plate number can be changed by using the previous plate and next

plate toolbar buttons.

The appearance of a plate can be modified using the View Options command. This
enables the number of rows and columns, reference labels and vial colors to be set.
See View Options, on page 61 for more details.

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OpenLynx Browser

The Sample Description Pane

Figure 3.16 The Sample Description pane

This pane shows a list and description of the masses found in the selected well.

Submitter The username entered on the first page of the OpenLynx Login
program.

Sample The filename of the sample, as entered in the Login dialog or Sample List.

Vial The plate number followed by the well column and row references.

ID The sample id as entered in the Login dialog or Sample List.

Description The file description, as entered in the Login dialog or Sample List.

The Fraction Results List Pane

Figure 3.17 The Fraction Collection Results pane

This pane shows a list of fractions collected and will not be displayed if fraction
collection was not performed.

Trigger The mass on which the fraction collection was triggered.

Original Target The mass minus any adducts.

Ion Mode The ion mode of the collected fraction.

Start Time The retention time at the beginning of the fraction collection.

End Time The retention time at the end of the fraction collection.

Collection Site Where the fraction was collected.

No. Of Tubes The number of tubes the fraction collection required.

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OpenLynx Browser

n To change the width of a column

The width of the columns can be changed, by positioning the mouse pointer on the
heading between two columns until the symbol appears, and then clicking the
left mouse button and dragging the column separators in the list header.

The Results Table Pane

Figure 3.18 The Results Table pane

For the analysis of complex libraries where on-line chromatography is used, the
yes/no answer is supplemented with a results table. This table is split into the
following columns:

Peak Number This lists the number of compounds that have been detected using
the parameters specified in the OpenLynx Setup. Each detected compound has its
own peak number.

Compound If an entered mass is detected in a particular Peak Number then this

column will display ’Found’.

Mass If an entered mass is detected in a particular spectrum then this column will
display the mass followed by the % Purity. If no compounds were found this will be
blank.

Function This column states the MS function and ionisation technique in which
the chromatographic peak was detected.

Time The retention time of the spectrum in decimal minutes.

Trace Description of the chromatogram used to locate this spectrum. This may be
blank if a specific retention time was used to locate spectrum. The information
listed here can be, amongst others, TIC, DAD or a mass chromatogram.

% Total Area The area of a particular peak represented as a percentage of the total
area of all the peaks detected using a particular trace.

Height The height of a particular peak represented as a percentage of the total area
of all the peaks detected using a particular trace.

RT Index The retention index of a particular peak.

RT Log P The measure of the hydrophobicity of a particular peak.

Concentration If quantification was selected this column will display the

concentration of the detected compound. …. will be displayed if the concentration
' '

was not calculated for this peak.

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OpenLynx Browser

Amount This column will display the Concentration, multiplied by a User Factor
defined in the sample list, or the Factor specified on the Quantify page of the
OpenLynx Setup. The Factor can be a user-specified number, or the number of
nitrogens in the chemical formula, depending on the option selected. …. will be
' '

displayed if the amount was not calculated for this peak.

State If a good quality spectrum was found the State field contains the message
OK. If the State was not found to be OK then the State field may contain one or
more of the following messages. Overloaded, Noisy or Too few peaks.

n To change the width of a column

n To remove a column

Columns can be removed from the display. Click with the right mouse button on a
column heading and select Remove Column from the pop up menu displayed.

Note: Columns can only be restored from the List Columns dialog.

n To select a result

The result highlighted will be displayed in the Spectrum, Chromatogram and

Sample Description panes. To select another result to view click, with the left
mouse button, on any part of the row of the result required, or use the arrow keys to
page up and down the list of results.

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OpenLynx Browser

The Spectrum Pane

Figure 3.19 The Spectrum pane

This pane displays the mass Spectra of the index entry highlighted in the Results
Table pane.

When a new sample is selected the first spectrum in each of the acquisition functions
is displayed. Individual spectra can be displayed by selecting the corresponding
Peak Number field in the Results Table pane.

Multiple entries can be displayed by holding down the Ctrl key and clicking on the
required entries or holding down the Shift key and clicking on the last entry in a
block.

The Spectrum Pane will appear blank if no sample is currently selected or if the
current size of the pane is not large enough to show all the spectra currently
required.

The text in red on the left-hand side of the pane is the mass spectrum retention time.

The text on the right hand side of the pane shows the acquisition function type and
ionisation mode followed by the absolute intensity of the largest peak in the
spectrum, on the next line.

n Altering the range of the horizontal axis (zoom) with the mouse

Press the left mouse button at one end of the region of interest, and without releasing
the button, drag the mouse horizontally to the other end. As you drag the mouse you
will see a "rubber band" stretched out to indicate the range you have selected; don’t
go beyond the bounds of the axis. When the mouse button is released the selected
range will be re-displayed to fill the current window.

This operation can be repeated as often as required.

Pressing the toolbar button will restore both the Spectrum and Chromatogram
display to the default range.

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OpenLynx Browser

The Elemental Composition Results List/Library

Search Results List Pane
This pane will display either the Elemental Composition Results List or the Library
Search Results List, depending on the information selected in the OpenLynx Setup
and the view selected. If both Elemental Composition and Library Searching results
have been obtained then press the toolbar button or select Swap List View
from the View menu to switch between the two views.

n To change the width of a column

The Elemental Composition Results List

Figure 3.20 The Elemental Composition Results List

This displays the results of the Elemental Composition processing (defined in the
OpenLynx Setup) for the peak number highlighted in the Results Table pane.

Mass The entered mass.

Calculated Mass The calculated mass for the formula shown in the Formula
column.

mDa The difference between the calculated mass and the entered mass in
milliDaltons.

PPM The difference between the calculated mass and the entered mass in parts per
million.

DBE The double bond equivalent for the formula shown in the Formula column.

Formula A suggested formula for the entered mass.

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OpenLynx Browser

The Library Search Results List

Figure 3.21 The Library Search Results List

This displays the results of the Library Search processing (defined in the OpenLynx
Setup) for the peak number highlighted in the Results Table pane.

Entry The library entry number of the compound.

Name The library entry name of the compound.

Forward The forward search match value.

Reverse The reverse search match value.

Mass The library entry mass of the compound.

Filter 1 If the library searched was user created then this field will display the
retention time which appears in the Value 1 field on the Edit Library dialog,
otherwise this field will display 0.000. See User Libraries in the MassLynx Users
Guide, Library chapter.

Filter 2 If the library searched was user created then this field will display the
retention index which appears in the Value 1 field on the Edit Library dialog,
otherwise this field will display 0.000. See User Libraries in the MassLynx Users
Guide, Library chapter.

Flags If the library searched was user created then this field will display the
information entered in the conditions field on the Login PC, otherwise this field will
be blank.

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OpenLynx Browser

The Chromatogram Pane

Figure 3.22 The Chromatogram pane

This pane displays the processed chromatogram of the Peak Number entry
highlighted in the Results Table pane.

The current chromatogram peak is displayed in a darker color to indicate it is the

current peak.

If a target mass is found within a chromatogram peak the color of that peak is the
found color, in this case green. Found tentative peaks will also be displayed in this
colour. Annotated to this peak is the time, mass found 301, % total purity 37%, and
the retention time in this case 3.05.

The text in red on the left hand side of the pane is the chromatogram description.

The text on the right hand side of the pane is an indication of the maximum intensity
of the chromatogram.

n Altering the range of the horizontal axis (zoom) with the mouse

This operation can be repeated as often as required.

Pressing the toolbar button will restore both the Spectrum and Chromatogram
display to the default range.

n Viewing other chromatograms

Each entry in the results table can have one or more chromatograms associated with
it. To view another chromatogram page down using either the scroll bar or the
arrow keys.

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OpenLynx Browser

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OpenLynx Browser

Notes
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................................................................................................................................................................

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OpenLynx Browser

Notes
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OpenLynx Manager

OpenLynx Manager
Chapter 4
Overview
The OpenLynx Manager allows the user to view batches of samples, delete batches
from the queue and change autosampler bed layouts.

Note: In order to login samples successfully OpenLynx Manager must be open on

the same, or the MSPC, in addition to OpenLynx Login.

The OpenLynx Manager Dialog

To access the OpenLynx Manager dialog select OpenLynx Manager from the
OpenLynx menu on the MassLynx top-level screen.

Figure 4.1 The OpenLynx Manager dialog

Jobs This is a list of jobs submitted to the Mass Spectrometer.

Jobs in Queue This is the number of single or multiple sample jobs in the queue.
One OpenLynx Login is one job.

Current Job This is the name of the job currently being acquired.

Instrument State This is the current state of the mass spectrometer, running,
acquiring etc.

The field at the bottom of the dialog shows the type of login selected. 100 positions
(Single Shot login) is the number of vial positions in the autosampler rack. If plate
login was selected this would show the number of plate positions. See Set Bed
Layout, on page 90 for more details.

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OpenLynx Manager

The File Menu

Report Location

The Report Location dialog allows the manager to define the location to which
report files will be written. To access the dialog select Report Location from the
File menu.

Figure 4.2 The Select OpenLynx Report Destination dialog

Primary Enter the full path of the primary report location.

Secondary Enter the full path of a secondary report location. Reports are written
here if the Primary location is unavailable.

Copy This location could be used for writing an archive copy or writing to A:\

Enable e-mailing of reports Check this box to enable the e-mail option on the
LoginPC. If this box is not checked the e-mail option will not appear on the
LoginPC dialog.

Mail copy of all reports to Enter the e-mail address to which you want to e-mail
a copy of the report. For more information on e-mailing reports, see E-Mail,
on page 92.

Signature to be added to end of reports Enter text to be added to the bottom

of e-mailed reports. E.g. name, job title, and phone number.

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OpenLynx Manager

Generate report summary text files Check this box to copy processed
information to a text file. This will generate a file with the same name as the report,
with a .txt extension, and put it in the same directory as the report. This report will
also be e-mailed if the e-mail option has been selected.

Print Report Format

This allows the manager to define when a report will be printed and which report
format to use. To access the dialog select Print Report Format from the File
menu.

Figure 4.3 The Print Report Format dialog

Print OpenLynx reports upon Job completion Check this box to print the
report as soon as it is complete.

Default report scheme If the report scheme on the Walkup page of the
OpenLynx Setup has been left blank then the report scheme defined here will be
used. Enter a report scheme name, including the full path. For more information on
Report schemes, see the OpenLynx Browser chapter.

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The Administration Menu

Set Bed Layout

The Set Bed Layout dialog allows the user to select the type of bed to use. To
access this dialog select Set Bed Layout from the Administration menu.

Figure 4.4 The Select Bed Layout dialog

Use current MassLynx autosampler bed layout Check this box to use the
current bed layout defined in MassLynx. This option is for Gilson, Waters 2700,
Waters 2790 and PAL CTC autosamplers only.

Use entire bed for plate login For the Gilson, Waters 2700, Waters 2790 and
CTC PAL autosamplers plates can be marked for OpenLynx plate login from the
MassLynx Software, to do this for the Gilson, Waters 2700 and Waters 2790.

1. For the Gilson autosampler select Bed Layout Editor from the Gilson Tools
menu on the Inlet Editor. (See Gilson Autosamplers — Advanced Options
in the Guide to Data Acquisition).

For the Waters 2700 autosampler select Bed Layout from the Waters2700
menu on the Inlet Editor. (See Waters 2700 Autosampler — Bed Layout in
the Guide to Data Acquisition).

For the Waters 2790 autosampler select Bed Layout from the Waters2790
menu on the Inlet Editor. (See Waters 2790 Autosampler — Bed Layout in
the Guide to Data Acquisition).

2. Click on the Modify Bed Layout tab.

3. Click, with the left mouse button, on the required plate to display the Plate
Position and Type dialog.

4. Check the OpenLynx plate login box to define this plate for plate login.

5. Press OK.

6. Repeat for each plate required.

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OpenLynx Manager

For the CTC PAL autosampler:

1. For the CTC PAL autosampler select OpenLynx Plate Login from the Plate
Login menu on the Inlet Editor. (See CTC PAL Autosampler – Using the
CTC PAL Autosampler with OpenLynx in the Guide to Data Acquisition).

2. If the plate required is labeled Disabled double click on the tray number.
Disabled changes to Enabled, enabled trays can be used for plate login.

Plates defined in this way can only be used for plate login; other plates can be used
for single shot login. Check the Use entire bed for plate login box to override
these settings and use the entire bed for plate login.

Disable Autosampler Pause When a batch is being logged in on the Login PC

the autosampler is paused to prevent injury when putting the plate onto the rack.
Check this box to disable this feature. For safety reasons Micromass recommend
that this option is not used.

Number of available sample positions Enter the number of wells on the plate
being used. Use this option if a Gilson, Waters 2700, Waters 2790 or CTC PAL
autosampler is not being used.

Clear Job Queue

Select this option to delete all batches submitted to the mass spectrometer. A
message will appear asking for confirmation of this action, select Yes to clear the
queue.

Note: This will not delete the job from the queue on the MassLynx screen, you will
have to delete it from there as well.

Reset Bed Status

Select this option to reset communications with the OpenLynx Login program. A
message will appear asking for confirmation of this action, select Yes to reset the
bed status.

Note: Do not use this under normal conditions, as it may produce unexpected
results.

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OpenLynx Manager

E-Mail
Note: To e-mail reports it is recommended that an e-mail account is set up for the
MSPC, from which to send the reports.

If the Enable e-mailing of reports box is checked, on The Select OpenLynx Report
Destination dialog (see page 88), then the MSPC e-mail account must be open to
send the reports.

It is recommended that e-mail is opened before the OpenLynx Manager is started. If

e-mail is not open and the Enable e-mailing of reports box is checked, you will be
prompted to open it. The Choose Profile dialog will be displayed, press OK to
continue.

Figure 4.5 The Choose Profile dialog

The usual e-mail login dialog will then be displayed, enter details as normal and
press OK.

If Cancel is pressed, on either the Choose Profile or Login dialog, then e-mail will
not be opened and no reports will be sent.

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OpenLynx Manager

Notes
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OpenLynx Manager

Notes
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OpenLynx Login

OpenLynx Login
Chapter 5
Overview
The OpenLynx Login program allows users to log in samples for analysis by the
OpenLynx system.

The OpenLynx Login Dialog

Note: The OpenLynx Manager must be running on the MSPC before the OpenLynx
Login program is started.

To start OpenLynx Login, double click on the shortcut to OALogin icon on the
desktop or press the Start button, choose Programs, OpenLynx Login and then
OpenLynx Login. See chapter 1 for information on how to set up a shortcut.

Figure 5.1 The OpenLynx Login dialog

In Administrator mode, all the menu options are enabled, when the method file and
status file directories have been defined the Administrator should Swap to secure
mode.

In Secure mode, the only options available are the Login Samples button, allowing
users to login samples, and the Swap Mode on the Security menu allowing the
Administrator to swap back to administrator mode.

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OpenLynx Login

The Status Bar

The Status bar appears at the bottom of the OpenLynx Login dialog. When the
system is running correctly it will display "Press button to login samples" followed
by the number of Jobs waiting in the queue. If this message does not appear check
the following:

1. The OpenLynx Manager is running.

2. An OpenLynx Status file (*.ols) has been opened.

3. If 1 and 2 are correct select Reset Bed Status from the OpenLynx Manager
File menu.

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OpenLynx Login

QC Setup
QC checking is used to check that the mass spectrometer and HPLC system are
working correctly and to ensure the consistency of data acquired. A QC sample
with a known retention time and peak intensity is acquired and the results compared
to the values entered on the Quality Control page in the Openlynx Setup.

To use the Quality Control options in OpenLynx Login the QC Required box on
the Quality Control Page in OpenLynx Setup must be selected.

To access the QC Options dialog select QC Setup from the OpenLynx Login File
menu.

Note: The MUX facilities in QC Options are not available for OpenLynx 3.5.

Figure 5.2 The QC Options dialog

QC On Check this box to perform QC checking. The other fields in the dialog will
be enabled.

Multi-probe Capability Check this box if a MUX system is being used.

Selecting this checkbox enables the Probe field.

Probes Enter the number of probes on the MUX system. The corresponding
number of Vial Position and Mass fields will be enabled.

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Timed QC Check this box to perform QC checking at a defined time. A timed QC

process will wait on the queue until the Time defined before acquiring data.

The Time field allows the start time for the timed QC acquisition to be defined.
Pressing the buttons will increase or decrease the time by one hour. To change
the minutes click with the left mouse button on the minutes part of the display,
pressing the buttons will now increase or decrease the time by one minute.

QC Sample Every Check this box to perform QC checking after the defined
number of Batches. E.g. if 2 is entered two OpenLynx batches will be acquired
and processed and then the QC sample(s) will be acquired and checked.

OpenLynx Setup File Select the OpenLynx Setup file from the drop down list
box. The file selected should contain the Retention Time and Area (on the Quality
Contol page) of the QC sample. Note: The QC Required box must be checked on
the Quality Control page of the selected OpenLynx Setup file for QC checking to be
performed.

Action on Error The Action on error field allows the users to define what
happens to a batch if an error occurs. Select the required option from the dropdown
list box.

• Ignore Error Ignore the error and continue with the acquisition.
• Suspend This Batch Pauses the current batch and continues with the next
batch in the MassLynx Queue.
• Suspend All Batches Pauses all batches.
• Delete This Batch Deletes the current batch from the queue and continues with
the next one.
If no action is chosen then Ignore Error is used.

User Name Enter your username.

Base File Name Enter the text to use as the Base File Name. When a QC sample
is acquired and processed a *.RAW and a *.rpt file will be produced.

• For non-MUX systems, the name of the files will be the Base File Name
followed by the Job Number.RAW and rpt.
• For MUX systems, the name of the files will be the Base File Name followed
by the Job Number followed by –n where n is the Stream Number.RAW and
rpt.
The Job Number will automatically be incremented by 1 when the QC sample is
next checked.

Job Number This field is display only and shows the current job number.

Reset Job Number Press this button to reset the Job Number to 1.

E-mail User Check this box to automatically e-mail the .rpt file to the address
entered in the E-mail Address box.

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Vial Position For each Vial Position enabled enter the location of the QC Sample.
This must be in the correct format for the plate being used e.g. 1:1,C or 1:21. For
MUX systems all QC samples will be located on one plate, therefore the plate
number must be the same for each Vial Position and the vial numbers must be
sequential. The specified plate/vial will be dedicated to the QC process and the user
will never be prompted to use that plate/vial position during normal sample login.

Mass For each Mass enabled enter the mass to search for. If the specified mass is
not found the QC test will fail. For MUX systems a different mass can be specified
for each Stream.

Reset Login Position

Normally when an OpenLynx batch is entered on the Login PC, the software
indicates where the vials or plates should be placed. This position is immediately
after the previous batch e.g. if the first batch occupies positions 1 to 20 on a plate,
you are prompted to put the first sample of the next batch in position 21. To reset
this position back to 1, select Reset Login Position from the OpenLynx Login File
menu.

Note: If position/plate 1 is defined as the location of the QC sample(s) the software

will use the next available free position.

Sample Login
There are two types of Sample Login:

• Plate Login where data is prepared in spreadsheet or text file form and imported
into the Login program. This option is available for Gilson/Waters 2700, Waters
2790 and CTC PAL autosamplers.

• Single Shot login where data for each sample can be entered manually or
imported from a tab delimted text file.

n Default Data

It is recommended that all data fields are filled with the correct information, but in
some cases fields can be left blank and OpenLynx will fill them with default data.

Well This will default to next available vial position.

Sample ID and MS Data Name These will default to the Job name, plus an
incremental number.

MS Injection Volume This will be taken from the MS Method.

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OpenLynx Login

Plate Login

n To log in samples

Note: The information displayed in the following dialogs may vary according to the
parameters defined in the OpenLynx Setup program.

1. Press the Login Samples button.

Figure 5.3 The OpenLynx Login dialog

2. If the user is a new user, type in your username and press Enter. If user
account creation is enabled a message will appear asking if a new account
should be created, press the Yes button. If user account creation is disabled a
message will appear informing the user that an existing name should be used
or that the Administrator should be contacted to add a new name to the list.
See Options, on page 110 for details.

If the user is not a new user either type in your username and press Enter, or
select your username from the drop down list box.

The Job ID will be assigned by OpenLynx. For more information on setting

up Job Names see Options, on page 110.

If the e-mail option is enabled and you require a report to be sent, check the
E-mail results to address box and enter an e-mail address.

Press the Next button.

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OpenLynx Login

Figure 5.4 The OpenLynx Login dialog

3. The current method description appears in the box on the right of the dialog, if
this is the method you require, press the Next button. If another method is
required, select the required method and press the Next button.

Figure 5.5 The OpenLynx Login dialog

4. Data copied onto the clipboard, from a spreadsheet or a text file, can be pasted
into the dialog by pressing the Paste from Clipboard button.

Data saved in files can be imported into the dialog by pressing the Read from
Delimited File button, and selecting a file from the browser displayed. See
Creating Delimited Files for more information.

To clear all information from the dialog, press the Clear Sample information
button.

When all sample information has been entered, press the Next button.

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OpenLynx Login

5. This page is for HP1100 and Waters 2690 systems and is only displayed if the
HPLC File field has been checked on the Walk-up page (see the OpenLynx
Setup chapter) and User defined HPLC gradient box is checked on the
OpenLynx Login, File, Options page. Normally, LC gradients are defined in
the Inlet Method file defined on the Walk-up page.

This page allows a gradient to be defined for the LC method.

Figure 5.6 The OpenLynx Login dialog

Run Time Set this value to the time in minutes that the method will run
from the point of injection.

Column Heater Enter the temperature in degrees centigrade for the column
heater(s). This will be in the Temperature field for the Waters 2690 and the
Left and/or Right fields for the HP1100.

Injection Volume (µl) Enter the volume of the sample to inject.

If you wish to operate in isocratic mode then you should ensure the timetable
has one entry for time 0.00.

To add a gradient, type in a time, flow and percentage in the relevant boxes
and press the toolbar button. Note: The first entry must have a time
of 0.

To delete a single gradient, click with the left mouse button on a time in the
list and press the toolbar button.

To delete all entries, press the toolbar button. This button is only
available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values
will then be displayed in the edit boxes above the timetable, and can be
altered as appropriate. Once changed, press to re-enter the values into
the timetable. However, if you modify the time value such that it does not
correspond to any existing entry in the timetable pressing will result in a
new entry being created in the timetable.

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OpenLynx Login

The gradient parameters that you can set are:

Time The time at which you wish the following parameters to be attained
during a method run.

Flow Rate Enter the total flow rate of all the solvent channels.

%A This field cannot be changed, it displays the remaining percentage when

the values in the %B, %C and %D fields have been added together.

%B The percentage of solvent B you wish to attain at the given time.

%C The percentage of solvent C you wish to attain at the given time.

%D The percentage of solvent D you wish to attain at the given time.

Acquire Diode Array Data Check this box to acquire diode array data.

When all information has been entered, press the Next button.

Figure 5.7 The OpenLynx Login dialog

6. Place the samples in the position indicated and press the Finish button. The
samples will then be submitted for analysis. OpenLynx will return to the
Login screen with the status bar updated with the number of jobs waiting and
the name of the submitter of the current job.

7. Press the Back button on any screen to go back to the previous screen, if for
example some information needs amending. Press the Cancel button to
cancel the login and return the to the Login screen.

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OpenLynx Login

n Creating Delimited Files

Typically, with Plate Login, large numbers of samples will be processed in one run,
to save typing in information for each sample. Text files are created using
spreadsheets or text editors and imported into the Login program.

These files can be created in Excel and saved as a Text (tab delimited)(*.txt) file, or
in any Windows text editor e.g. Notepad. The following is a list of tips for creating
these files.

Spreadsheets

• Only single pages can be saved as text files, so although workbooks can have
more than one page, each page must be saved as a different text file.

• Save as tab delimited file.

• The spreadsheet must be closed before importing the text file. If the
spreadsheet is not closed previous versions of the file will be imported.

• Define cell format as Text, to prevent the spreadsheet converting numbers with
":" or "/" in them into times and dates.

Text Editor

• Enter field data and Tab to the next field.

Both Spreadsheets and Text Editor

• The files should contain field data only, no column headings.

• The Well numbering should correspond to that defined for your Autosampler,
see the Advanced Options section of the Controlling Inlet Systems and
Autosamplers chapter of the MassLynx NT Guide to Data Acquisition for more
details.

If Well numbers are entered as 1, 2, 3, 4 etc, the first plate will be filled and the
further samples will be placed on the next plate.

If Well numbers are entered as 1:n, 2:n or 1:n,n, 2:n,n etc., samples prefixed
with 1: will be placed on plate 1, samples prefixed with 2: on plate 2 etc.

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OpenLynx Login

Single Shot Login

n To log in samples

Note: The information displayed in the following dialogs may vary according to the
parameters defined in the OpenLynx Setup program.

1. Press the Login Samples button.

Figure 5.8 The OpenLynx Login dialog

If the user is not a new user either type in your username and press Enter, or
select your username from the drop down list box.

The Job ID will be assigned by OpenLynx. For more information on setting

up Job Names see Options, on page 110.

If the e-mail option is enabled and you require a report to be sent, check the
E-mail results to address box and enter an e-mail address.

If the Allow single sample file login box is checked on the Options page (see
Options, on page 110) then an extra field will be displayed, Single Sample
Login Using a File. Check this box if single sample information is to be
supplied from a file. Note: If this box is checked then follow the instructions
for Plate Login from step 3.

Press the Next button.

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OpenLynx Login

Figure 5.9 The OpenLynx Login dialog

3. The current method description appears in the box on the right of the dialog, if
this is the method you require press the Next button. If another method is
required, select the required method and press the Next button.

Figure 5.10 The OpenLynx Login dialog

4. Enter the number of samples and the sample information for the first sample.
If there is more than one sample the screen will change to display
. Pressing the and buttons will page
backward and forwards through the samples, allowing the user to enter the
required sample information for each sample. Pressing the and
buttons takes you to the first and last sample respectively. Note: This option
is only available if the Maximum Samples on the OpenLynx Setup Walk-up
page is greater than 1.

To automatically generate data for samples, enter data for the first sample and
then press the button. Fields such as SampleID and Well will
be incremented on subsequent pages but descriptive fields will only be copied
and may need updating. Note: The Well number does not have to start at 1.
If a well number is not defined the software will automatically generate one
(this is the recommended option).

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OpenLynx Login

Data can also be copied from one page to another. Select the data in a field
and click with the right mouse button to display a pop up menu. Select Copy,
put the cursor in the required field on the page you wish to copy to, click the
right mouse button again and select paste from the menu.

When all sample information has been entered for all samples, press the Next
button.

5. If the HPLC File field has been checked on the Walk Up page (see the
OpenLynx Setup chapter) then a gradient can be defined for the LC method.
See step 5, on page 102 for details on how to set up a gradient.

Figure 5.11 The OpenLynx Login dialog

6. Place the samples in the positions indicated and press the Finish button. The
samples will then be submitted for analysis. OpenLynx will return to the
Login screen with the status bar updated with the number of jobs waiting and
the name of the submitter of the current job.

7. Pressing the Back button on any screen will take you back to the previous
screen, if for example some information needs amending. Pressing the
Cancel button will cancel the login and return the user to the Login screen.

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OpenLynx Login

The File Menu

Methods

This allows the Administrator to define the location of the method files.

Figure 5.12 The Select OpenLynx Method Directory dialog

n To select the method files directory

1. Select Methods from the File menu.

2. Select one of the method files (*.olp) and press the Open button, or double
click on one of the method files.

All method files in the directory will be available to the OpenLynx Login program.

Status

This allows the manager to define which OpenLynx status file will be used.

Figure 5.13 The Select OpenLynx Status Directory dialog

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OpenLynx Login

n To select the OpenLynx Status file

1. Select Status from the File menu.

2. Select the OpenLynx Status file (*.ols) and press the Open button, or double
click on the OpenLynx Status file. There should only be one OpenLynx
Status file.

HLPC File Location

n To select the HPLC file location

1. From the File menu select HPLC File Location. The Select HPLC
Description File Directory dialog is displayed.

Figure 5.14 The Select HPLC Description File Directory dialog

2. Locate the required directory and select an HPLC files and press the Open
button, or double click on one of the files.

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OpenLynx Login

Options

This allows the manager to define Job names and to allow the e-mail option on the
Login dialog.

Figure 5.15 The OpenLynx Login Options dialog

Base Job Name By default, Job names are based on the username with a Job
number appended to it, leave this box blank to continue to name jobs in this way. If
you require Jobs to be named differently, enter the Job Name text in this box.

Next Job Number By default, Job names are based on the username with a Job
number appended to it. When a job has been submitted this number is incremented.
If you require Job numbers to start at a specified number or wish to restart
numbering change the number in this box.

Allow user to change job identifier Check this box to allow the user to change
the automatically generated Job ID on the Login screen.

Default Data File Name By default, the MS Data Name (entered in the Sample
List or on the Login PC) is used as the file name. Alternatively the Sample ID or a
user defined naming system can be used.

Use Sample ID for file name To use the Sample ID, instead of the MS Data
Name, as the file name check this box.

Use Incremental File Naming If you wish to use another file naming system,
instead of the MS Data Name, check this box. The Base File Name and
Increment Number boxes will become enabled. Enter the text to use as the base
file name and the number to start from in the relevant boxes.

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OpenLynx Login

Enable e-mailing of user report To enable the e-mail option on the Login
dialog, check this box. If not checked then the e-mail option does not appear on the
dialog.

Note: The e-mail option must be enabled in the OpenLynx Manager and e-mail
open on the MSPC for reports to be sent.

Title Bar Text Text entered here is displayed on the title bar of the Login dialog.

Batch Identifier Text Text entered here replaces the text ‘Job ID’ displayed on
the Login dialog.

User defined HPLC gradient If users are allowed to define a gradient for the
LC method when logging on a sample, check this box and select the type of HPLC
pump, from the drop down list box.

Allow user to create own user name Check this box to allow users to create
new user accounts on the Please enter your name page. If checked a user can enter
a new name and when the Next button or Return is pressed the Unknown user
name dialog is displayed.

Figure 5.16 The OpenLynx Login Options dialog

If not checked no new user accounts can be created. A message is displayed

informing the user that an existing name should be used or that the Administrator
should be contacted to add a new name to the list. The Administrator must then
check this box, add the user and then uncheck it again to disable user account
creation on the Login PC.

Allow single sample file login Check this box to allow single sample
information to be pasted from the clipboard or read from tab delimited file, as for
plate login.

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OpenLynx Login

The Security Menu

Swap Mode

This allows the administrator to swap between Administrator mode and Secure
mode.

In Administrator mode, all menu options are enabled. In Secure mode, the only
options available are the Login Samples button, allowing users to login samples, and
the Swap Mode on the Security menu allowing the Administrator to swap back to
administrator mode. The user cannot access any options on the Login PC or on the
Desktop.

Selecting Swap Mode from the Security menu will display the Open Access
Security dialog.

Figure 5.17 The OpenLynx Access Security Login dialog

Enter Name and Password and press OK to swap mode.

n The Initial Password

The initial Name is “Admin” and the Password is blank, i.e. enter “Admin” in the
Name field and press OK.

n To change the Password

1. Enter Name and Password.

2. Enter New Password and press the New button.

3. Enter the new password in the Password field and press OK.

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OpenLynx Login

Timeout
To prevent a user from logging on and then leaving the screen partially complete the
Login dialog has a timeout. Data must be entered within 300 seconds (5 mins), if it
is not the Login will be cancelled and the display will return to the Login screen.

n To change the Timeout

1. Press the Start button and select the Run option.

2. Type in regedit and press the OK button.

3. Double click on the HKEY_CURRENT_USER folder.

4. Double click on the Software folder.

5. Double click on the Micromass folder.

6. Double click on the OpenLynx folder.

7. Double click on the Login folder.

8. Double click on the icon to display the Edit Value dialog.

Figure 5.18 The Edit Value dialog

9. Select the Decimal option, enter the required Timeout value ( in seconds) and
press the OK button.

Note: To disable the timeout feature set the value to 0.

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OpenLynx Login

Notes
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OpenLynx Login

Notes
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Registry Settings

Registry Settings
Chapter 6
Introduction
This chapter describes the OpenLynx Registry Settings and how to save, edit and
restore them.

Note: The Registry Settings should only be amended by the System Administrator.

Settings can be saved and restored at any time. It is advisable to take a copy of the
initial settings so that the original setup can be restored without having to re-install
the software.

Initial Settings
OpenLynx Browser

The OpenLynx Browser does not have any initial registry settings, so if the settings
become corrupted you can delete them and start again.

n To delete the Browser Registry Settings

1. Press the Start button and select the Run option.

2. Type in regedit and press the OK button.

3. Double click on the HKEY_CURRENT_USER folder.

4. Double click on the Software folder.

5. Double click on the Micromass folder.

6. Click, with the right mouse button, on the Diversity Browser folder, and
select delete from the pop up menu.

OpenLynx

Appendix A contains the initial registry settings. If problems occur with the
OpenLynx Software check the current settings against these and if they are
corrupted restore the initial ones.

Note: The entire Micromass folder can be saved and restored, but this will delete
settings for other parts of MassLynx system e.g. Inlet configuration.

n To save the initial Registry Settings

1. Put a blank disk in drive a:\

2. Press the Start button and select the Run option.

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Registry Settings

3. Type in regedit and press the OK button.

4. Double click on the HKEY_CURRENT_USER folder.

5. Double click on the Software folder.

6. Double click on the Micromass folder.

7. Click, with the left mouse button, on the OpenLynx folder.

8. Select Export Registry File from the Registry menu.

9. Select Drive A: from the Save in drop down list box, type in the File name
and press the Save button.

n To restore the initial Registry Settings

1. Put the disk with the initial settings in drive a:\

2. Press the Start button and select the Run option.

3. Type in regedit and press the OK button.

4. Double click on the HKEY_CURRENT_USER folder.

5. Double click on the Software folder.

6. Double click on the Micromass folder.

7. Select Import Registry File from the Registry menu.

8. Select Drive A: from the Look in drop down list box, select the required file
and press the Open button.

9. A message will appear informing you that the settings were successfully
entered into the registry.

To Edit a Registry Setting

1. Double click on the or icon, or select the icon and choose Modify
from the Edit menu. This will display the Edit Settings dialog.

Figure 6.1 The Edit String dialog

2. Enter the new value and press OK. Numeric values are displayed as
hexadecimal numbers, click the decimal option to display in decimal format.

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Registry Settings

Appendix A
The Initial Registry Settings

OpenLynx
Batch Manager

AS Layout

Column1

Plate1

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Registry Settings

Administrators

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Registry Settings

Notes
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Registry Settings

Notes
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OpenLynx Users Guide

Index
A L
Acquisition Process Page, 47 Library Columns Page, 69
Adducts, 25 Library Page, 41
Analog Data Page, 23 Library Search Results, 82
Life Cycle of a Sample, 3
B List Columns Page, 69
Load on startup, 73
Browser, 51
M
C
Mass Measure, 31
Chromatogram Page, 63 Modes of Operation, 4
Chromatogram Pane, 83 MS Data Page, 19
Chromatogram Report Page, 58 MS Process Page, 27
Chromatogram Test Page, 37
Clear Job Queue, 91
N
Colors Page, 67
Combine Parameters, 28 Network Connections, 6
Copy Control Page, 68
O
D
OpenLynx Browser, 51
DAD Data Page, 21 File Menu, 73
Default Data, 99 View Menu, 75
Default Plate Page, 65 View Options, 61
OpenLynx Login, 95
E File Menu, 108
Method Files, 108
Elemental Columns Page, 69 Security Menu, 112
Elemental Page, 45 Status Bar, 96
Elemental Report, 58 Status File, 108
E-mailing Reports, 92, 111 OpenLynx Manager, 87
Administration Menu, 90
F File Menu, 88
OpenLynx Setup, 11
Field Alias, 17, 59
Fraction Columns Page, 69
Fraction Display Page, 70 P
Fraction Results List Pane, 77 Plate Login, 90, 100
Fraction Results Summary Page, 58 Plate Pane, 76
Print Control Page, 56
H Print Report Format, 89
Printing Page, 18
HLPC File Location, 109
Q
I
QC Setup, 97
Input Fields, 16 Quality Control Page, 38
Installation, 5 Quantify Page, 40
Installing the Browser, 8
Instrument Page, 25
Isotope Modelling, 30 R
Isotopic Cluster Analysis, 33 Registry Settings, 117

Page 123
OpenLynx Users Guide

Restoring, 118
Report Files, 51
Report Header Page, 58
Report Location, 88
Report Scheme
Settings, 56
Report Schemes, 56
Reprocessing Samples, 3
Reset Login Position, 99
Results Pane, 81
Results Summary Page, 58
Results Table Pane, 78

S
Sample Description Pane, 77
Sample Header Page, 58
Sample Login, 99
Sample Summary Page, 58
Set Bed Layout, 90
Setup, 12
Single Shot Login, 105
Spectrum Page, 61
Spectrum Pane, 80
Spectrum Report Page, 58
Spectrum Search Report Page, 58
Spectrum Test Page, 35
Swap List View, 75
Swap Mode, 112

T
Threshold Spectra, 27
Timeout, 113
Toolbar
OpenLynx Browser, 53
OpenLynx Setup, 12

W
Walk-up Page, 14
Window Menu, 75

Page 124

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