TotalChrom Tutorial

for Version 6.3

Part Number
N515-6021

Release
B

Publication Date
November 2004

Any comments about the documentation for this product should be addressed to:
User Assistance
PerkinElmer
710 Bridgeport Avenue
Shelton, CT 06484-4794
Or emailed to: [email protected]
Notices
The information contained in this document is subject to change without notice.
Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes
no warranty of any kind with regard to this document, including, but not limited to,
the implied warranties of merchantability and fitness for a particular purpose.
PerkinElmer shall not be liable for errors contained herein for incidental consequential
damages in connection with furnishing, performance or use of this material.

NOTE: TotalChrom is the updated version of the software previously marketed as

Turbochrom.
Copyright Information
This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form
whatsoever or translated into any language without the prior, written permission of
PerkinElmer, Inc.
Copyright 2004 PerkinElmer, Inc.
Produced in the U.S.A.
Trademarks
Registered names, trademarks, etc. used in this document, even when not specifically
marked as such, are protected by law.
PerkinElmer is a registered trademark of PerkinElmer, Inc.
600 Series LINK, TotalChrom, TotalChrom Client/Server, and TotalChrom Workstation
are trademarks of PerkinElmer Inc.
Turbochrom is a trademark of Applera Corporation.

Table of Contents

Welcome
Welcome to PerkinElmer's Line of Chromatography Software Products................................... 1

Where Do I Begin?
Register with Software Support.................................................................................................. 2
Users New to Computers ............................................................................................................ 2
Users New to Microsoft Windows.............................................................................................. 3

About Installation
How to Prepare for Installation................................................................................................... 5
What If I Install TotalChrom Myself and Need Help ................................................................. 6

How Can I Be Productive Quickly?

Users New to a Chromatography Data System........................................................................... 7
Make the Most of Your Optional Service Install ........................................................................ 7
Get Acquainted without Pressure................................................................................................ 7
Use the TotalChrom Users Tutorial........................................................................................... 8
Learn the Basics First ................................................................................................................. 8
Collect Practice Runs.................................................................................................................. 9
Register for a Users Class........................................................................................................ 10
PerkinElmer Product Specialists............................................................................................... 10

What If I Have Problems?

Try This First ............................................................................................................................ 11
Internet Support Help ............................................................................................................... 14
When All Else Fails and You Need Help ................................................................................. 14
Placing the Call . . .................................................................................................................... 14
Contacting PerkinElmer .................................................................................................... 15
What Happens to My Problem or Suggestion? ......................................................................... 16
What If My Problem Cant Be Resolved Immediately? ........................................................... 16

Upgrades and Updates?

What Is an Upgrade? ................................................................................................................ 17
How Is This Different from a Software Update? ...................................................................... 18
What Is PerkinElmers Policy Regarding Software Upgrades and Updates? ........................... 18
What Is a Maintenance Release? .............................................................................................. 18
Supplemental Maintenance Releases ........................................................................................ 19
Summary................................................................................................................................... 19

Table of Contents

Tutorial Introduction
About the TotalChrom Tutorial.................................................................................................21
Before You Begin......................................................................................................................22
Checklist.............................................................................................................................22
Other Helpful Hints............................................................................................................23

Tutorial Part 1
The TotalChrom Navigator .......................................................................................................24
Collecting Your First Data File .................................................................................................26
Building a Quick Method ...................................................................................................30
Building a Vial List ............................................................................................................35
Injecting your Standard and Acquiring Data ......................................................................38
Viewing the Real-Time Plot...............................................................................................39
Zooming In on the Real-Time Plot..............................................................................40
Rescaling a Plot...........................................................................................................41
The Default Report and Plot........................................................................................42

Tutorial Part 2
Optimizing a Method Using Graphic Editing............................................................................43
Opening the Graphic Method Editor ..................................................................................44
Changing the Plot Display..................................................................................................47
Fine Tuning Peak Detection ...............................................................................................50
Creating a Component List.................................................................................................55
Using the Method Editor ...........................................................................................................59
Setting Calibration Parameters ...........................................................................................59
Performing a Manual Calibration.......................................................................................63
Saving a Method.................................................................................................................68
Building a Report Format ..........................................................................................................69
Building a Sequence ..................................................................................................................72
Using the Sequence Template ............................................................................................72
Using the Sequence Spreadsheet ........................................................................................75
Batch Reprocessing a Sequence File .........................................................................................80
Viewing Results using Reprocess Results.................................................................................82
Congratulations! You have successfully completed the TotalChrom Tutorial...................90

ii

Welcome

Welcome to PerkinElmers Line of Chromatography Software

Products
Your Global TotalChrom Support team would like to do everything possible to help
you become quickly productive with this product. Before running the software, please
take a few moments to review this tutorial. It is intended to provide you with an
overview of how to get the most out of your investment and our software support organization. These are some of the most important pages you will have to read over the
next few days, so please share this information with all users of this product.
Topics include:

Where Do I Begin?

About Installation

How Can I Be Productive Quickly?

What If I Have Problems?

What About Software Updates and Upgrades?

Where Do I Begin?

Register with Software Support

You must be registered with PerkinElmer Software Support so that you can qualify
for a support program and be notified of software enhancements as well as any
problems.

TotalChrom Client/Server customers: Your signed Software License Agreement

fulfills this requirement.

TotalChrom Workstation customers: You must fill out your permanent License
PAK application and send it to PerkinElmer by following the directions on the
form. If you do not currently have your permanent License PAKs from the
TotalChrom PAK Administrator, you are probably not registered with us.

TotalChrom Turnkey customers: Turnkey systems are shipped with the software
and permanent PAK installed on the hard drive.
Note: Turnkey customers should only follow the installation instruction card
provided with their system and skip all sections in this tutorial that are related
to installation.

Users New to Computers

If this is your first experience with computers, we suggest that you become familiar
with your system and with Microsoft Windows before proceeding. You do not need
to be an expert to run a computer, but at least one person at your facility needs to be
comfortable with the operating system. The best place to start is with the Windows
documentation supplied with your computer. We highly recommend purchasing third
party tutorials and quick reference programs available at your local software store.
These are economical, fun, and have the advantage of letting you work on your
system at your convenience. You can also attend introductory computer courses that

Where Do I Begin?

are available at local community colleges, technical schools, and even local software
stores.

Users New to Microsoft Windows

TotalChrom performance, functionality, and ease of use are dependent on the correct
installation, configuration, and an understanding of basic Windows operation. Before
you begin to operate TotalChrom (or any Windows application), we strongly suggest
spending some time getting comfortable with this new environment. If you follow the
routine below, your chromatography processing will be enjoyable and productive.
1.

If you did not purchase a computer from PerkinElmer, make sure the
computer used for TotalChrom is configured according to the minimum
TotalChrom requirements (refer to the product release notes). We
cannot support our products on any system configuration that does not meet
these requirements.

2.

Do not attempt to operate Windows applications without first

understanding how to operate Windows. Windows, not TotalChrom,
controls basic operations such as file opening, closing, saving, and printing.
It is much easier to learn how these operations function in a basic application
distributed with the Windows program (such as Write and Paint) before
continuing. The first few sections of the Windows Users Guide provide
excellent startup tutorials for your personnel. Spending some time with these
will greatly enhance your implementation efforts.

3.

Make sure the operating system is operating smoothly on your

workstation before you proceed to TotalChrom. If the basic Windows
applications such as Write or Paint cannot print or are too slow, TotalChrom
or any other application will behave the same.

About Installation
Note: Turnkey systems are shipped with the software installed on the hard drive. Turnkey
customers should only follow the installation instruction card provided with their system
and skip all sections in this tutorial that are related to installation.
Before your computer can collect data, you need to do the following:
1.

Install and configure the computer hardware components.

2.

Install and configure the operating system software.

3.

Install and configure the communication and data collection hardware.

a)

IEEE, serial, or terminal server

b) 900/NCI Interfaces, 600 Series LINK, or SoftLINK Interfaces and their

cables
c)
4.

Analog signal cables

Install and configure the TotalChrom software.

LINK instrument control users may have additional installation steps to prepare third
party analytical instrumentation for LINK instrument control. In some cases involving
non-PerkinElmer instruments, you may have to order and install additional boards.
Make certain you have consulted with your PerkinElmer sales/service representative
regarding connections to third party vendor instruments so these pre-installation
requirements can be met.
If you would like to schedule a service representative to perform this installation,
contact your local PerkinElmer Service Center for instructions. In the U.S., contact
the PerkinElmer Customer Support Center at 1-800-762-4000.

About Installation

How to Prepare for Installation

The time required for installation varies considerably. It depends on whether the
computer system was purchased from PerkinElmer or someone else and the number
of instruments you want to connect to the system.
Note: If you arranged for a PerkinElmer service representative to come on-site to
install TotalChrom, please remember that they have dedicated this day to getting your
new system up and running. If they spend time rearranging the lab, searching for
boxes, or performing other odd jobs that should have been done prior to the visit just
means less time spent doing what you really need done.
To get the most out of your day, please complete the following steps in preparation
for the arrival of our service staff. Check each step as you complete it. Your service
engineer may review this with you prior to the installation and perhaps have a few
more suggestions based on your exact purchase.

Unpack all equipment, both hardware and software. Compare the items that
arrived against your sales order to make sure you received all items.

Cables that need to be routed through walls, ceilings, etc. should be in place by
the time of installation.

Provide the required bench space for the data system. Make certain there is
adequate electrical power and that the space is clean, clear, and safe.




Place the A/D interfaces and/or LINK modules in the desired locations.

The detector leads and remote-start leads for your PerkinElmer instruments are
connected by the PerkinElmer service engineer. For non-PerkinElmer
instruments, please have these signals connected with twisted pair cabling for
connection to the 900 series interface. We cannot open up other vendors
equipment.

Have available a copy of your computer and/or operating system manuals. Also,
have the manuals and disks for third party software, detectors, computer,
expansion cards, and peripheral equipment.

Make sure you have the required cables. These include analog lead lines, printer
cables, IEEE/serial cables, remote lead lines, etc.

About Installation

If you purchased LINK instrument control for analytical instruments other than
PerkinElmer, you may need to make changes to this equipment in advance of
your installation visit. Your service engineer or sales representative will have
details on these changes.

Backup any unsaved data to a network or backup drive prior to installation.

What If I Install TotalChrom Myself and Need Help

Your TotalChrom Application Managers Guide contains complete installation and
configuration instructions. In addition, TotalChrom has contact-sensitive Help files
(pressing the F1 key) right at your fingertips, as well as Release Notes and Known
Bugs. These files contain last minute information that we received from our beta
testers after manuals were printed. Your question and its resolution may be addressed
in these files so please consult these files first when you have a problem.
On a properly configured computer system with Microsoft Windows already
installed, it takes only a few minutes to install the TotalChrom software. If you are
having problems, chances are they have to do with improper configuration of the
system before you installed TotalChrom.
If you have problems that are not addressed in the documentation or Release Notes,
call the TotalChrom Support Specialists in your area (for U.S. and Canada call
1-800-762-4000). Phone assistance can generally handle most of these situations, but
you may want to make sure someone familiar with the computer setup is around if
computer configuration issues are new to you. Have all the information about your
system at hand for the support specialist.
If you would rather have on-site evaluation of any problem, either now or in the
future, PerkinElmer has a field service organization prepared to provide on-site
service for any TotalChrom need.

How Can I Be Productive Quickly?

There is no magic in becoming proficient with pipettes, pH meters, and precision
balances. It took practice and training for these tools to become valuable aids in your
daily life. TotalChrom is your data-handling tool, and like any other tool in your lab,
the time spent learning and practicing will make your experience much more
productive and satisfying.

Users New to a Chromatography Data System

If this is your first step up from chart recorders or integrators, take some time to
understand the concepts of how your new system collects and stores data, how it defines
a method, and how it permits access to these files for reprocessing data. The
TotalChrom Users Guide provides an overview of these subjects. Please, review these
sections before you start to use TotalChrom. Your job will be much easier when you
understand what you are trying to accomplish as you go through the keystrokes.

Make the Most of Your Optional Service Install

To get the most out of this day, review all of the information in the introductory
chapters of your TotalChrom Users Guide BEFORE the PerkinElmer service
representative installs the system. Before your service representative leaves, you
should understand the basics of creating a method, configuring an instrument, and
collecting data from a run.

Get Acquainted without Pressure

It can be frustrating to try to learn a new system while faced with the pressures of
completing your daily assignments. Take the time now to schedule an adequate
phasing in period for new users of your system to get acquainted with the variety of
ways your data can be collected, integrated, processed, and retrieved. We think the
average new user should need at least three days without interruption to become
familiar with the system. This includes one full day with Windows, one with
TotalChrom, and one for making practice injections to reinforce the newly learned
information.
7

How Can I Be Productive Quickly?

Use the TotalChrom Users Tutorial

This manual contains a TotalChrom Users Tutorial. Make sure each user completes
the tutorial exercises before they begin to collect data or process data with the
software. The tutorial only takes a few hours and provides a quick overview of basic
elements of the software.
Also, DO NOT delete the example files shipped with TotalChrom when you are done
with the tutorial. These are helpful for use as troubleshooting aids if needed in the future.

Learn the Basics First

TotalChrom has features and flexibility that many labs never realized existed. We know
you are anxious to see how TotalChrom integrates that 200-component capillary run and
whether it can really calibrate on so many levels. Hold off on this for now. Concentrate
on the BASICS of the chromatography software before you try the power features.

Know where instant HELP is available

TotalChrom has extensive on-line Help files (F1) for each of the software
modules. As soon as your software is installed, familiarize yourself with the
help topics, how to search for help information, and how to look up definitions. These can be printed out for reference. In addition, the user manuals
provide another source of helpful information. Most operational questions
can be addressed by using these aids.

Method Creation
Know how to create a basic method and how to use the naming convention
for files created by your system. Make sure you understand how to adjust
the parameters in each method, and what the consequence of that adjustment
is, without trying to apply those to your application. All parameters are
defined in the users guide, and we provide example method files with the
software.

Sequences
Make sure you understand the concept behind sequences for TotalChrom.
Practice by making and using several sequences with the supplied data files
to analyze the effect of changing parameters. The sequence is the main
blueprint for TotalChrom. It tells the system what to do next, with what
method, where the method is located, and what adjustments, if any, are
necessary to arrive at the final result. The sequence does exactly what you
tell it to do, whether it is what you intended or not. If you are not sure of an
entry, check the help files or users guide rather then making a guess.

How Can I Be Productive Quickly?

Graphics
TotalChrom graphics routines provide countless ways to view, edit, and
manipulate data. The ability to view raw data down to a single sampled data
point, or to select a small portion of the entire chromatogram for expansion,
is probably foreign to former users of chart recorders or simple integrators.
Use the sample data files with this tutorial to practice the variety of graphics
options your package allows. These files can be restored from your
TotalChrom CD so you can experiment with them to your hearts content. It
is best to try all those features now and become proficient with the test data,
so when the real data comes along, you will be prepared to work with it
quickly. It is a good idea to copy these over after each practice session so
the next user has fresh files when they start learning.

Collect Practice Runs

Prepare several identical standards to use to learn the data acquisition portion of your
software package. Do not be concerned at this point with internal or external quantitation or calibration. Set up your method for a simple area percent analysis, and get
comfortable with the process of downloading to the interface, integration, optimizing
for noise and area thresholds, and the effects of varying sampling rates. This is a
good time to practice setting up Baseline Timed Events to see how each event affects
integration on a known sample. Make sure you are comfortable with your
understanding of how data, method, and sequence files are edited, saved, and named
before moving on.
Now prepare a rack of samples for external standard analysis. After making your
standard injection(s), set up your method for external standard analysis, name your
components, and calibrate your method following the instructions in the users guide.
Inject controls until you are comfortable with your results. Repeat the process with
an internal standard run.
When you are comfortable making practice runs and manipulating data, you are ready
to move on to your specific application. Print out the method and sequence files from
a successful practice run to serve as hard copy templates. Mark the changes you need
to make for your application on the printouts. You will find that the screen edits
proceed more quickly, and you are not likely to forget anything. Clear any unwanted
data and method files from the system so it is not cluttered with unnecessary files.
(You might like to save some of those practice files on disk to serve as default files
for your application.)

How Can I Be Productive Quickly?

Register for a Users Class

Most labs will have a few users that will quickly understand TotalChrom. As the first
month of TotalChrom implementation nears completion, arrange to have one or more
users participate in a product-training course. Do not sign up for the class before you
have at least 30 days on the system. Our technical trainers have seen new users take
the class before the installation of TotalChrom, and they just do not have the
experience with the software to get everything out of the class they would have if they
had waited.
In the U.S., you can request a Technical Training brochure, current schedule, or class
registration by calling the PerkinElmer Technical Training Center at 1-800-762-4000.
Outside the U.S., contact your PerkinElmer representative for local information.

PerkinElmer Product Specialists

The PerkinElmer field organization has a staff of highly skilled local specialists in
GC, LC, and data handling products who are available for on-site assistance with any
application need your lab might have. These specialists draw on many years of
experience in laboratory environments just like yours. If you would like to use these
resources, feel free to contact your PerkinElmer sales staff. In the U.S., call the Sales
Administration staff at 1-800-762-4000.

10

What If I Have Problems?

Try This First

Troubleshooting system and software problems can be a real challenge to users who
have extensive experience in computer systems, networks, and communications. For
those of us who have much less experience, and just want to get our samples out the
door, the complexity and proliferation of computerized data handling systems and
software may seem a bit overwhelming.
Whether you have a single, stand-alone TotalChrom Workstation, or a powerful
network composed of 30 licenses of TotalChrom Client/Server sharing data with a
LIMS system, the basics of what to do when a problem occurs are pretty much the
same. Approaching a system problem methodically BEFORE contacting software
support or service personnel can save you time and money. For example, start by
answering the following questions:

Does your system at least meet the MINIMUM requirements as stated in the
TotalChrom Release Notes?
If it does not, you WILL have problems. These truly are the basic
requirements for the version of software.

Did you check the documentation?

Check the section of your documentation that explains the commands and
procedures you are using to make sure you are operating the software
correctly. It may be that what you are trying to do simply cannot be done, or
perhaps the feature you are thinking of is actually located in another module
of the software.
Do not forget the HELP files (by pressing the F1 key) right at your
fingertips, as well as the Release Notes and Known Bugs files available from
your TotalChrom program group. These files contain last minute information we received from our beta testers after manuals were printed. Your
question and its resolution may be right here.

11

What If I Have Problems?

Have you performed good housekeeping procedures on your system?

Users with MIS staffs overseeing their system needs probably have
established system housekeeping procedures. However, if you also pull
double duty as the keeper of your computer, you will need to perform
weekly maintenance. This includes disk defragmentation, file backup, and
removal of any files you no longer need (for example; error log files). Data
acquisition systems such as TotalChrom are incredibly disk intensive, so the
cleaner your hard drive, the faster your system.
Also check your systems TEMP directory to make sure its not cluttered
with .TMP files you no longer need. Use a general diagnostics utility once
each month to check all other components of the system for signs of failure.
Do not forget to check those cables as well to make sure they are seated
correctly and are not worn from moving equipment around. A little
preventative action now will help ensure that your system is in top shape.

Are you encountering specific error messages?

I think it said something like . . . may not be much help to people trying to
identify what is wrong. Determine whether those errors are coming from
your computer, DOS, Windows, or the chromatography software, and write
down or make a screen print of exactly what the message says. Each of
these error messages should be described in the appropriate manuals
supplied with your system or software; this description will help direct you
to the problem.
TotalChrom has a log directory that stores error messages encountered by
TotalChrom. Your TotalChrom Support Specialists may request that you
send these log files for further analysis. We recommend that you keep at
least a weeks worth of these files on hand. This will help us to determine if
the system has a history of repeated error messages.

Note: LINK customers should be aware that any instrument control errors displayed
in TotalChrom are actually returned from the analytical instrument. They are usually
explained in the manual that comes with your instrument (GC or LC) and not in the
TotalChrom or LINK documentation.

Is the problem repeatable, or can it be duplicated on another system?

Fundamental to solving software and hardware mysteries is knowing exactly
when they occur and what the conditions are that lead to their occurrence.
a)

12

If you have multiple TotalChrom systems available, check whether the

problem occurs on other systems as well. If it does not, this may point to a
system problem and will help focus the troubleshooting effort.

What If I Have Problems?

b) Can the problem be duplicated with the test data files that came with the
system? If not, this may point to a problem with the new files you created.
c)

Are you on a network? See if the problem still exists when you are
disconnected from the network to rule out a network problem.
Remember that system operation is dependent on everything communicating
in harmony. In the case of data acquisition software, the timing and number
of these communications are incredibly complex and demanding on the
system, involving both internal (computer, disk drive, printer) and external
(instrument control, IEEE and serial communications) devices.
Occasionally, something interferes with this communication and simply
cannot be traced. Perhaps it is the result of electrical disturbances in your
lines from voltage brownouts or surges; a strong magnetic field created by
equipment in the next lab; a loose connection; a failing piece of hardware; or
just the night cleaning crew plugging their vacuum cleaners into the same
circuit as the system analyzing your overnight run. If the problem seems to
have disappeared, make a note of it just in case, but you can generally
proceed without concern.

What has changed since the problem started?

It was working fine yesterday. No one touched anything...really!
Software doesnt just break. Ask everyone who uses or maintains your
system whether anything has been done to it that you do not know about.

Has someone installed a new software package or driver that might be

interfering?

Has someone on the night shift altered the TotalChrom or Windows

configuration file since you last operated the system?

Has someone changed my directory permissions?

Have my user and/or TotalChrom process account passwords expired?

It is not impossible that a software file gets corrupted somehow, but before
you reinstall the software, check out the obvious culprits first. These can
often be diagnosed quickly by rebooting your system with a blank system
disk containing basic autoexec and config files. If the problem disappears
with the use of this system disk, look to the startup files for a potential
conflict.
Hardware on the other hand does break. Even worse, it can break with an
insidious style that drives users and support specialists crazy. It can work
fine one day and create havoc the next. Often we cannot catch this until it
finally breaks for good. Every system should have a good diagnostic
software tool that puts its hardware through the paces so hardware faults can

13

What If I Have Problems?

be determined or ruled out. Do not forget the obvious here, or maybe not so
obvious, too.

Did someone move equipment? If so are the cables seated properly?

Is your hard disk full?

Is your printer connected and turned on?

Did someone wrap that extra length of cable around the base of an old
centrifuge to clean up the lab counter top?

More than half of all the calls to Software Support have nothing to do with
the actual TotalChrom software, but are the result of problems with the
operating system (DOS), Windows, network configuration, hardware system
configuration, or device drivers for printers and other devices.

Internet Support Help

Additional support information is provided on the PerkinElmer web site:
http://las.perkinelmer.com/content/onesource/index.html
This service provides an economical vehicle for users to get the latest information
regarding product support issues.

When All Else Fails and You Need Help

If you tried all of the above and still need help or advice, it is time to contact us.
PerkinElmer has several options in place for assistance with PerkinElmer software
and hardware. Your local sales or service representative will provide you with
information regarding how to access providers of assistance in your particular
country.
If your shipment contains a companion pamphlet covering software support options in
your country, review that pamphlet to see what options are available to you BEFORE
that first question or problem comes up. Keep this information along with user
manuals, software media, and the license agreement in a safe, accessible location.

Placing the Call . . .

When you need to talk to a technical representative, the following list can help you
get the most from that conversation. Like you, we want to resolve your call as quickly
as possible.

Have the phone within reach of the system.

We may have you try several things on your system to determine the source
of your problem. Or, we may have you go over the steps you are having

14

What If I Have Problems?

problems with, keystroke by keystroke, as we duplicate them on the other

side.

Have your Serial Number, Software Licenses and/or your original software
media available.
You will need these to access most centralized phone support programs and
services.

Have your computer hardware, Windows, and software manuals available.

We may need to refer you to these for additional information.

Know the version and service packs of all relevant software packages.

Record any error messages exactly as they appear on the system.

Make sure you can state exactly where errors occurred and what steps are
required to reproduce them.

Have available the make and model numbers of your computer and
associated hardware.

Have the end user make the call.

Note: DO NOT make calls on behalf of the end user having the problem unless you
fully understand both the problem and the system. These calls are seldom resolved
quickly because of the unfamiliarity of the caller with the situation.

Contacting PerkinElmer

Customer Support

US & Canada Customers

Outside the US

Phone: (800) 762-4000

Local PerkinElmer Sales Office

15

What If I Have Problems?

What Happens to My Problem or Suggestion?

As problems and suggestions regarding software operation, functionality, features, or
documentation are reported by registered users, Software Support begins a software
investigation. This investigation starts with a search for whether the issue has been
previously reported. If it has, you will be notified of the resolution. If a problem has
not been reported, Software Support will attempt to duplicate your experience on
standard supported computer systems sold by PerkinElmer.
If the problem can be duplicated by Software Support, and it resides in our software, a
Software Investigation Report (SIR) will be prepared and forwarded to the PerkinElmer
Product Department, as well as, Software Development for further action.

What If My Problem Cant Be Resolved Immediately?

Occasionally, everything we do in a remote troubleshooting process comes up empty,
and we need to do some research with the product, your system and data, our
engineering staff, or a third party. If we cannot reproduce the problem, we will assist
you with as much user education, system configuration troubleshooting, and hardware
troubleshooting as is possible from a remote location. We will continue until the
problem is resolved or until we can advise you what we think is necessary for it to be
resolved.
In cases where we cannot make the symptoms appear as described, we may need to
get additional information from you regarding the system you are working on and its
setup and configuration. We may also need verification that the software is installed
according to product documentation. This process may require eliminating
potentially interfering third party software or hardware in an effort to return the
product to a functioning state. Sometimes this can be a tedious process over the
phone, and as Murphys Law dictates, this always seems to occur when you have to
get those 200 samples out the door. Please be patient. You are our eyes, ears, and
hands in these situations, and we need you.
If the problem requires on-site assistance, or is the result of operation of the software
on non-standard or non-supported hardware or system configurations, Software
Support may make several suggestions. One may be to request you involve the local
PerkinElmer Service office and get a service engineer on site who can help us evaluate the situation first hand. Software Support will work with the local office to assist
in the effort.

16

Upgrades and Updates?

Your PerkinElmer purchase grants the right to use the software version that was
shipped to you. Like a book, audiotape, or videotape of your favorite movie, the
media is yours, but the content remains the property of PerkinElmer. In the software
business, vendors convey this right to use with a software license.
The analogy stops here. Where the development costs of a good book or movie end
with its release, the development costs of good software continue as the product
expands to new operating systems, new applications, and incorporates new ideas from
users. If existing license holders want to take advantage of the new features and
fixes, they can do so economically by using the vendors software update and upgrade
program. In essence, these programs re-license the existing product users, giving them
the right to use the new version.
The terms Upgrade and Update are often used interchangeably. In reality they
represent distinct classes of software offerings to existing users of the product.

What Is an Upgrade?
There are two types of upgrades Product Upgrades and Software Upgrades.
Product Upgrades exist so customers have an option to buy into the PerkinElmer line
of products with minimal features, then migrate up to more feature-packed products at
a reduced price as conditions permit. Upgrading is usually associated with the
strategic needs of a growing lab as determined by the lab manager in consultation
with a PerkinElmer sales engineer.
For example, you may have bought a Product Upgrade to TotalChrom from our
Turbochrom Professional chromatography software. We only mention product
upgrades here to help distinguish them from software upgrades.
Software Upgrades are major releases of an established product that incorporate
significant enhancements to the software, or take advantage of a major new platform,
operating system, or user interface. TotalChrom v6.2 is a Software Upgrade from the
Turbochrom Professional v4 revision.

17

Upgrades and Updates?

How Is This Different from a Software Update?

Minor enhancements, feature changes, and/or problem fixes that come about as a
result of users interacting with the software are periodically made to the product code.
As these enhancements and fixes accumulate and pass testing protocol, we may issue
a Software Update.
An update does not have the major feature enhancements usually associated with an
upgrade, but usually has a host of improvements and fixes that help make your life
easier. An update revision is reflected by a change in the second digit of the version
code (for example; TotalChrom v6.2 to TotalChrom v6.x).

What Is PerkinElmers Policy Regarding Software Upgrades

and Updates?
Software Upgrades and Updates will be announced in a letter to registered end users.
This letter will advise you of the procedure to follow and what costs are involved to
get the new license. If you are not registered, you will not receive notice of these
new products.
As a general rule, it is beneficial for users to move to the current shipping release of
the software. Aside from the fact that the current release always contains the latest in
enhancements and fixes requested from users, old releases become harder and harder
to support as they are replaced. In general, centralized phone support resources
support the LAST TWO minor revision series. Assistance on versions more than two
revisions old is generally confined to existing information in our database.

What Is a Maintenance Release?

As you may know, software development is a dynamic process. While you may be
using v1.1.1, Software Support may be testing v1.1.2, while Software Quality
Assurance may be testing v1.1.3, while Software Development may be coding v1.1.4.
If Software Support does not release v1.1.2, or if v1.1.3 never makes it past SQA
testing, you may never see these versions. You may think we skipped a version or at
least skipped telling you about it, but actually it may have never have made it to
release.
However, if v1.1.2 was approved for release, we may have issued a Maintenance
Release (MR). A MR is identified by a change in the third digit of the software
revision code (for example; v6.1.0 to v6.1.2). MRs generally contain fixes only. No
documentation changes are made.
MR availability and ordering information can be located in the software support area
of our web site ( http://las.perkinelmer.com/ ). You can also get this information from
your local software support representative. Support will only ship MRs to users
who are registered for the version of the product for which the MR was created.
18

Upgrades and Updates?

Supplemental Maintenance Releases

Occasionally, software engineering may release a maintenance disk containing a few
fixes to a specific program module that has limited value to the entire user base.
Supplemental maintenance releases (SMRs) are only released when a few problems
can be fixed without affecting other modules in the software. SMR code will be made
available on the PerkinElmer web site for direct access by users.

Summary
We hope this introduction has been helpful. All of us in Software Support want your
experiences with our products and the entire PerkinElmer team to be successful for
many years. Please let us know how we can be of more help, whether it is a feature
you would like to see in the software, or a support program you would like to see us
implement in the future.

19

Upgrades and Updates?

20

Tutorial Introduction

About the TotalChrom Tutorial

The TotalChrom Tutorial is designed for your interactive use with TotalChrom to
help you get started by performing basic tasks. To familiarize you with this process,
the tutorial leads you through the following series of procedures that are organized to
illustrate your typical workflow:

Creating a quick method

A method is a collection of parameters that determine how TotalChrom
acquires and analyzes data.
A quick method is a method that defines only those parameters that are
essential for acquiring data.

Acquiring data with that method

Optimizing the method

Optimizing means adjusting method parameters to provide the best analysis
of the raw data.

Creating a report format file for printing the results of the analysis
A report format file contains the specifications for the analysis report and
some of the reports formatting characteristics.

Building a sequence that utilizes the optimized method

A sequence is a collection of one or more rows of information that defines
analysis cycles. The sequence that you create controls how data is acquired,
analyzed, and/or reprocessed.

Reprocessing stored data with that sequence

Reprocessing is the reanalysis of stored data.

This tutorial does not cover every feature in TotalChrom. It follows a specific path,
while TotalChroms flexibility and the variety of instruments it supports offer many
paths.
For a complete description of all TotalChrom functions and operations, see the
TotalChrom Users Guide.

21

Tutorial Introduction

For electronic information, TotalChrom has online help that you can access at any
time. For information about online help, see The Help System in Chapter 1 of the
TotalChrom Users Guide.

Before You Begin

It may take between 1 and 1-1/4 hours to complete the entire tutorial. If necessary,
you can break it into two sessions: Part 1 will take between 20 and 30 minutes, and
Part 2 will take between 35 and 45 minutes.
The tutorial assumes that TotalChrom has been installed as described in the
Application Managers Guide. It also assumes that you know how to operate your
chromatograph and that you know the basics of using Microsoft Windows.
For an explanation of the features in Microsoft Windows that you need to know in
order to run TotalChrom, see Chapter 2 in the Application Managers Guide.

Checklist
Complete the following preparations before you start the tutorial:

22

Make sure that at least one interface (Model 900, Model 600 LINK, SoftLINK or
NCI) is connected to a chromatograph.






Prepare a single, known standard with a relatively short run time.

Ensure that the above directory has RWXD privileges for both the TCProcess
account as well as the users logon account.

Copy the Examples directory (located in C:\PenExe\TcWS\Ver6.3.0 or a similar

directory) to the above training directory. These files will be used throughout the
training exercise.

Turn on your printer and check the paper supply.

Ensure that Windows is running.
In the Windows Explorer, you may want to create a training directory on your
local drive. For example, C:\PenExe\TcWS\Ver6.3.0\tutorial.

Tutorial Introduction

Other Helpful Hints

Follow the directory and file name instructions carefully. You will save everything
in the C:\PenExe\...\tutorial directory then delete all the files after you have
completed the tutorial.

When you collect data in Part 1 of the tutorial, you must provide values that are
appropriate for the analysis that you are performing and for the equipment you
are using.

The defaults on your system may be different from what the tutorial describes or
illustrates. The tutorial may direct you to enter or select something that is already
present or selected, or where your instruments do not provide a choice.

If there are no directions for a parameter, just leave it as is.

When there are multiple ways to do something, the choices are listed and
separated by OR.

We are ready to begin the interactive part of the tutorial.

23

Tutorial Part 1

The TotalChrom Navigator

You access the various functions in TotalChrom from the Navigator window. The
most convenient way to start the Navigator is from the TCWS_Links windows (or
TCCS_Links for TotalChrom Client/Server), which is created during installation.

To open the Navigator window:

1.

Click the Start button and point to Programs, then click TotalChrom
Workstation Ver6.3 to display the Links window. Double-click on the
TCNav icon in this window.

The Logon dialog box appears:

Note: You must logon to a user account that has manager permissions enabled. If you
have any questions, consult your system manager.

24

Tutorial Part 1

2.

Enter your Logon User Name and your Password. Then choose OK.
The Navigator window appears:

Title Bar
Menu Bar

Instrument
Selection
Panel

Status Bar

The Navigator window is a graphical representation of the major functions in

TotalChrom. The Navigator has four main areas:

Title Bar and Menu Bar on the top.

Instrument Selection Panel on the left.

Function Buttons in the central part of the screen.

Note: This screen shows that the TCPublisher reporting option was selected. To
change to Review and Approve, select TotalChrom Review & Approve in the
Reporting Options dialog. This is displayed by selecting Reporting from the
Build>Configuration>User> menu.

Status Bar at the bottom of the window.

We will use the instrument selection panel and several function buttons in the tutorial.

25

Tutorial Part 1

Collecting Your First Data File

In this part of the tutorial you will:

Use Quick Start

Build a quick method by designating instrument parameters

Build a vial list

Acquire data

Adjust the real-time plot of the data points as they are acquired

Review the printed output

Using Quick Start to Acquire Data

The Quick Start option allows you to collect data without developing a comprehensive method. With Quick Start, you enter only the parameters that are essential for
performing a run.
Quick Start is helpful when you are first starting to use TotalChrom, if you are
performing a survey run on a type of sample that you have not analyzed before, or
when you are developing instrument settings for an analysis.

To begin the setup procedure to acquire data:

1.

26

Select the instrument you want to use for data collection from the instrument
selection panel in the Navigator (you will use this instrument throughout the
entire tutorial).

Tutorial Part 1

2.

Click on the Setup button in the Navigator.

The Setup Instrument dialog box appears.

3.

In the Setup Instrument dialog box, select Quick start as the Setup Type.

4.

Click the folder icon next to the Raw File Path text box as shown above.

27

Tutorial Part 1

The TotalChrom Path-Select dialog box appears:

5.

In the TotalChrom Path-Select dialog box, select the full-path

C:\penexe\..\examples directory by double-clicking until the complete
Path is displayed above the list of directories. Choose OK.

6.

Perform the same procedure for the Result File Path text box.

7.

To enter a Base File Name, click on the button to the right of the text box.

The Default Base Names dialog box appears.

28

Tutorial Part 1

8.

In the Default Base Names dialog box, select NONE for the Separator and
type TEST into the Base File Name field.

This dialog discusses Tokenized filenames (a new feature to version 6.2). Please
consult your Users Guide for a more detailed description about this option.
All files related to this quick method that we are creating raw, result,
method, and sequence files will use this base file name.
TotalChrom will append a three-digit run or cycle number to this name
(based on the number of digits specified for the suffix under the Default
Base Names dialog) when it creates the raw and result file names.
9.

Click OK to close Default Base Names dialog box.

10. Leave the Suppress processing and Suppress reports/plots check boxes
unchecked as shown in the above screen.
We want to process the data file immediately after it is collected, and we
want a printed report and plot at the end of the run.
11. Do not click the OK button yet.

You have completed the entries in the Setup dialog box. The next
step is to build a quick method.
For additional information on the Setup dialog box, see Acquiring and Viewing
Data in Chapter 12 of the TotalChrom Users Guide.

29

Tutorial Part 1

Building a Quick Method

The Quick Method button in the Setup dialog box opens the Quick Method Editor,
which is a limited version of the Method Editor. You can access the instrument and
processing parameters in the Quick Method Editor.
The Quick Method button also opens a series of dialog boxes in which you set the
instrument parameters. In each of these dialog boxes you will select options and enter
values that are appropriate for the analysis you are performing and for the instrument
you selected.

To build a quick method:

1.

In the Setup Instrument dialog box, click on the button to the left of Quick
method.

The Quick Method Editor window opens, with the Documentation dialog box.
This is the first in the series of dialog boxes that will be displayed
automatically.
2.

You may enter any descriptive information about the method in this window
or click on NEXT to leave it blank. Do Not Select Audit Trail.
The next window to appear is the Instrument Notes dialog box.

30

Tutorial Part 1

3.

You may enter any instrument specific information into this dialog or choose
from the template drop-down menu for one of the pre-designed instrument
templates. You may also choose to leave it blank, if so, click NEXT to display
the Data Acquisition dialog box.
The information displayed on the Data Channels tab varies depending on the
instrument you selected at the beginning of this procedure. This is shown in
the following two figures:

Data Channels tab for a 900/NCI Series Interface

Data Channels tab for a LINK-controlled instrument

31

Tutorial Part 1

4.

Under Data Channel, select the channel (A, B, or Dual) that matches the way
your detector output is connected to the interface.

5.

For a LINK-controlled instrument, select a data source from the drop-down

list (some instruments do not provide a choice).
OR
For a 900/NCI Series Interface, select the required voltage range that
corresponds to the output from your detector.

6.

Select a Set Data Rate option.

If you know how wide your narrowest peak is at its baseline, select By peak
width at Base and enter the number of seconds in the text box. TotalChrom
will use this to calculate the optimum sampling rate for that peak.
OR
Select By sampling rate and select or enter a rate (depending on the
instrument).
Suggested sampling rates are:
Capillary GC
=
HPLC or IC
=
Packed column GC =

32

20 pts/sec
5 pts/sec
2 pts/sec

Tutorial Part 1

7.

We want to save the complete run rather than using delay and run times to
store only a part of it.
For a LINK-controlled instrument, select Store all data from run.
OR
For a 900/NCI Series Interface, leave Delay time set to 0, and enter a
Run time that corresponds to the length of your run.

8.

Choose NEXT to display the first in a series of dialog boxes for the
instrument you selected.

9.

Complete each series of dialog boxes using the appropriate values for your
sample and equipment. (Since the people following this tutorial will be using
a variety of equipment, we cannot anticipate the specific entries.)

Note: Press F1 when a dialog box is open to display the online Help for that box.
The dialog boxes displayed in the rest of this series depend on the instrument
you selected and on the instrument modules you configured. We will not
enter any processing parameters for this quick method. It is often easier to
set these parameters after the fact using the Graphic Method Editor. We will
use that function in Part 2 of the tutorial.
When you reach the Components dialog box, which is the last screen in the
series for all instrument types, click on Finish.

33

Tutorial Part 1

When you complete Quick Method dialog boxes, the Method Summary,
Component List, or a combination of the two screens will be displayed
showing the initial parameters you have set.

To save the Quick Method:

1.

Choose Save from the File menu to save the method.

The quick method is saved using the base file name that you entered in the
Setup dialog box, plus the .MTH extension (for example, TEST.MTH in this
tutorial).

2.

Choose Exit from the File menu to return to the Setup Instrument dialog box.

For more information on instrument parameters, see Chapter 6,

Developing Instrument Parameters in the Method, in the TotalChrom
Users Guide.

For more information about quick methods, see Using Quick Method
in Chapter 12 of the TotalChrom Users Guide.

Although it is not required for all instrument configurations, the next task we
will perform in this tutorial is building a vial list to specify the samples to be
injected.

34

Tutorial Part 1

Building a Vial List

You can build a vial list for any instrument, but it is only required if you are using a
LINK-controlled autosampler. We will build a vial list in order to become familiar
with that part of TotalChrom.
The Vial List button in the Setup Instrument dialog box opens a limited version of the
Sequence Editor. In addition to entering vial numbers, you can also enter the sample
name, number, rack number (if applicable), and injection site (if you are using a
LINK-controlled GC). There are other columns that are not used in a normal Quick
Start setup.

To build a vial list:

1.

In the Setup Instrument dialog box, click on the Vial list button.

This opens the Vial List window with the Sequence Information window:

35

Tutorial Part 1

2.

If you are using a LINK-controlled LC autosampler, you must indicate the

tray type.
a.

Choose Global Parameters from the Change menu to display the Global
Parameters dialog box.

b.

Select the type of tray installed in your autosampler from the Tray dropdown list.

c.

Click on OK.

3.

In the Sequence Information window, select the first cell in the Vial column
by clicking in it.

4.

For a LINK-controlled autosampler, enter the vial number where your

sample is located.
For all other instrument configurations, leave the default entry.

5.
36

Do not enter any more vials. Instead, delete the remaining rows, 2 through 5.

Tutorial Part 1

6.

Highlight row 2 then Display the Edit menu.

Notice that you have several choices for manipulating rows in the
spreadsheet and that each has a keyboard shortcut.

7.

Choose Delete from the Edit menu. Row 2 is deleted and rows 3-5 move up
in the spreadsheet.

8.

Delete the remaining 3 rows in the same manner.

You have completed the vial list and are ready to save it and start the run.

To save the vial list:

1.

Choose Save from the File menu.

The vial list is saved as a sequence (of 1 cycle in this case), using the base
file name you entered in the Setup dialog box, plus the .SEQ extension
(TEST.SEQ in this tutorial).

2.

Choose Exit from the File menu to close the vial list window and return to
the Setup Instrument dialog box.

3.

Choose OK in the Setup Instrument dialog box to initialize the instrument

and return to the Navigator.
For more information, see Building a Vial List in Chapter 12 of the
TotalChrom Users Guide.

You have now completed everything you need to acquire data.

You are ready to inject your standard and acquire data.

37

Tutorial Part 1

Injecting your Standard and Acquiring Data

Now that you have completed the Setup procedure and the instrument is initialized, the
text in the Status box in the Navigator indicates that the instrument is Ready. (The other
items displayed in the Status box depend on the type of instrument that you are using.)

To start data acquisition:

The way you start the run depends on your instruments and how they are connected.

For a LINK-controlled autosampler, click on the Run button in the Navigator

then choose Start Run from the menu.

OR

For an A/D connected to a chromatograph with an autosampler, the A/D

may be wired to start sampling when the autosampler injects. In this case,
simply start your instrument.
OR

For an instrument without an autosampler, inject your standard into the

chromatograph. If your chromatograph is connected to a LINK, press start
on the chromatograph. If your chromatograph is connected to an A/D, you
may have to press the start button on its front panel.
When the run begins, the Status box indicates that the instrument is active
and sampling.

For more information, see Controlling Data Acquisition in Chapter 12 of

the TotalChrom Users Guide.
38

Tutorial Part 1

Viewing the Real-Time Plot

The Real-Time Plot button lets you display a plot of the data as it is being acquired by
an interface.

To open the Real-Time Plot window:

In the Navigator, click on the Real-Time Plot button to open the Real-Time
Plot window.

The parameters for the initial display come from the Real-Time Plot Scale
dialog box that you completed in the quick method by accepting its defaults.
There are a number of things that you can do from the Real-Time Plot
window. We will experiment with changing the display from the Options
menu. Display changes are temporary, affecting the current display only;
they do not change the settings in the method and they do not affect data
acquisition.

39

Tutorial Part 1

Zooming In on the Real-Time Plot

The Zoom In and Zoom Out commands in the Options menu of the Real-Time Plot
window let you enlarge and reduce your view of the real-time plot as the data points
are being collected.
Zoom In halves the value of the voltage axis, thereby enlarging the plotted peaks and
revealing more detail about the incoming data. Zoom Out doubles that value, reducing
the size of the plotted peaks.

To zoom in and out of the real-time plot:

1.

In the Real-Time Plot window, display the Options menu.

2.

Choose Zoom In (for the channel you want to view) to enlarge the plot.

3.

Choose Zoom In again until the view is as large as you want it to be.

4.

Choose Zoom Out until the plot view is restored to its original size.

Note: You can zoom in and out without displaying the Options menu by using the
keyboard shortcuts F5 and F6 while the real-time plot is displayed.
Zoom In and Zoom Out act on the full-scale value for the voltage axis,
halving and doubling it respectively. Our next step is to change the voltage
axis value explicitly from the Rescale dialog box.

40

Tutorial Part 1

Rescaling a Plot
The Rescale command in the Options menu lets you change the scaling parameters of
the plot while data are being collected.

To change the scaling parameters in the real-time plot:

1.

In the Real-Time Plot window, choose Rescale from the Options menu to
open the Rescale dialog box.

Under Voltage Axis, the value for Full Scale is the value that is currently
being used for the display. That value may be (a) from the method, (b) as
altered by zooming, or (c) as you specifically changed it in this dialog box.
2.

Double the value for Full Scale, then choose OK.

The plot is redisplayed with a new Y-axis scale that reduces the displayed
peak size by one half (the same effect as zooming out).
You can continue to experiment with the Real-Time Plot display while the
run is finishing.

3.

Allow the run to finish and the data to be processed.

OR
If the run is not yet complete and you are ready to continue with the tutorial,
you can stop the run by selecting Stop Run from the Run menu. It would be
helpful if at least one peak has been detected.

4.

To close the Real-Time Plot window, choose Exit from the Instrument menu
to return to the Navigator.
When the run is completed (or stopped), the default report and annotated
replot will be printed.

For more information, see Viewing Real-Time Plots in Chapter 12 of the

TotalChrom Users Guide.

41

Tutorial Part 1

Once you have acquired a data file, you can use the stored data file to set up better
processing parameters. You do this by using the Graphic Method Editor. We will use
this function in Part 2 of the tutorial.
First, lets look at the printed output from our data analysis.
The Default Report and Plot
If your printer was attached and turned on, a report and plot were printed after data
analysis. Lets take a quick look at these printouts. Both were formatted using default
settings.
The top part of the report contains information from the method, such as data channel
and run time. These items, and the information on the report itself, are configurable.
We will customize a report in Part 2 of the tutorial.
The plot is also headed by identifying information. The way the plot is printed is also
configurable in the method (it has no relationship to the scale of the real-time plot.)
Note: We will not reuse any of the files created in this part of the tutorial. In Part 2
we will use sample files that are shipped with TotalChrom.

You have completed Part 1 of the TotalChrom tutorial.

You need another 35 to 45 minutes to go through Part 2, which you

should complete in one session.

If necessary, you can stop here and continue at another time.

Note: Every step in the rest of the tutorial is built on, and is a continuation of, the
previous step. Therefore, you need to complete it as a whole.

42

Tutorial Part 2

Optimizing a Method Using Graphic Editing

In this part of the tutorial you will use some of the basic features of the Graphic
Method Editor to:

Change the plot display

Adjust peak detection parameters

Create a component list

A method contains the parameters that determine how TotalChrom analyzes raw data.
With the Graphic Method Editor, you can adjust those method parameters and see the
effects of the change immediately.
Viewing the data in graphic form helps you determine if peaks are being detected
correctly, if baselines are being placed properly, and if expected retention times and
search windows for components are identifying peaks accurately.
To edit a method in the Graphic Method Editor, you specify a raw data file that
represents a chromatogram of the analysis that you want to optimize. TotalChrom
processes the raw data with the method that is referenced in the raw file header and
then displays the chromatogram, showing the resulting integration and peak
identification.
For more information about the Graphic Method Editor, see Chapter 10 in the
TotalChrom Users Guide.

43

Tutorial Part 2

Opening the Graphic Method Editor

We will start by opening the Graphic Method Editor and displaying a chromatogram
that has already been optimized.
Note: Since we need to work with something known in this part of the tutorial, we
will not use the quick method and result file from Part 1.

To open the Graphic Method Editor and load a file:

1.

In the Navigator, click on the Graphic Edit button.

The Graphic Method Editor window opens as well as a file selection dialog
box that displays a list of raw data files.

2.

44

Select the Examples directory from the TotalChrom Quick Paths dropdown list or from the list of directories.

Tutorial Part 2

3.

From the list of files in the Examples directory, select halo003.raw.

4.

Choose Open.
The default display shows a working chromatogram in the main work area of
the window and a reference chromatogram above it. The name of the raw
data file appears in the status bar and the name of the method used to process
the data appears in the title bar.

45

Tutorial Part 2

In the following steps, we will explore some of the ways that you can
optimize a method to achieve this kind of result.
Note: For this tutorial, we will create an unsatisfactory method so that we have
something to optimize. The step below is for that purpose; it will most likely not be
your normal procedure.

To reset the method parameters to defaults:

Choose New from the File menu.

The default method parameters are applied to the halo003.raw file.

Before we change any of the method parameters, we will experiment with changing
the way the chromatographic information is displayed.

46

Tutorial Part 2

Changing the Plot Display

There are several ways to change the plot display. We will experiment with two of
them in this part of the tutorial.
You can use the mouse to change the display by highlighting the area of the plot that
you want to expand. We will do this from the reference chromatogram; you can also
do it from the working chromatogram.

To select and manipulate a portion of the reference chromatogram:

1.

Select a part of the reference chromatogram as shown in the example below

by holding down the left mouse button and dragging the mouse to outline the
area.

2.

Release the mouse button.

The working chromatogram expands to match the highlighted area in the
reference chromatogram.
Notice that the working chromatogram matches the highlighted area exactly,
so that any peak whose full height you do not select is truncated.

3.

Move the cursor (arrow) into the highlighted area in the reference
chromatogram.

47

Tutorial Part 2

The mouse pointer changes to a thick crosshair cursor. This indicates that
you may move the selection rectangle.

4.

Hold down the left mouse button and drag the selection rectangle to another
part of the reference chromatogram.

5.

Release the mouse button.

The working chromatogram is updated to show the new highlighted area in
the reference chromatogram.

6.

48

Position the cursor anywhere in the working chromatogram, then click the
right button to restore the chromatogram to its original scale.

Tutorial Part 2

If you moved the rectangle more than once, click the right mouse button
until the chromatogram returns to its original scale. A message will be
displayed when there are no more expansions.

Next we will change the display by directly altering the values that
define it. We want to see only the area before the first peak to
have a detailed view of the baseline noise so we can begin to
optimize the method.

To rescale the plot to display an area of interest:

1.

With the chromatogram back to its original scale showing the entire run,
choose Rescale Plot from the Display menu.

2.

In the Rescale Plot dialog box, make the following changes:

3.

a.

Change End Time to .55.

b.

Change Offset to 0.

c.

Change Full Scale to 10.

Click on OK to redraw the plot using the new values.

49

Tutorial Part 2

Your screen should look similar to the example below:

For additional information on changing the display, see Changing Display Options
in Chapter 10 of the TotalChrom Users Guide.

Fine Tuning Peak Detection

Since the default peak detection settings are very sensitive, too many peaks were
detected in our sample chromatogram due to baseline noise.
To ensure that TotalChrom detects small peaks but does not interpret baseline noise
as peaks, we must calculate the baseline noise and set noise and area thresholds to
ignore it.

To calculate the optimal noise threshold:

1.

Choose Noise/Area Threshold from the Process menu.

The status bar message tells you to outline the section of baseline that you
want to use for calculating a new threshold level.

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Tutorial Part 2

2.

Select the entire baseline by holding down the left mouse button and
dragging the mouse to outline the area.

3.

Release the mouse button to display the Noise/Area Threshold dialog box.

TotalChrom has calculated the suggested optimum thresholds (these should

be approximately 80 and 400).
4.

Click on OK to reprocess the data and redraw the plot using the suggested
thresholds.

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Tutorial Part 2

As shown in the example below, the new noise and area threshold values
have eliminated the spurious peaks.

6.

Click the right mouse button to return the chromatogram to the previous
level of expansion (full size chromatogram).

The number of data points across a peak influences peak detection. If you have too
many points across the peak, you can either decrease the sampling rate for future runs
(you cannot change the sampling rate for data that is already collected) or increase the
bunching factor to filter out unneeded data from existing files.

The next thing we will do to optimize peak detection is to adjust

the bunching factor.

To set a new bunching factor:

1.

Choose Sampling Rate/Bunching Factor from the Process menu.

The status bar message tells you to outline the narrowest peak to use for
calculation.

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Tutorial Part 2

2.

Outline the width of the first peak (do not select the tailing portion) by
holding down the left mouse button and dragging the mouse.

3.

Release the mouse button to display the Sampling Rate/Bunching Factor

dialog box.

TotalChrom has calculated a recommended bunching factor of 2 in the

example above (compared to the old bunching factor of 1 from the default
method).
4.

With the Bunching Factor option selected, choose OK to reprocess the data
and redraw the chromatogram using the new bunching factor.

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Tutorial Part 2

The change to our chromatogram is subtle. When you optimize a method in

your daily work, the visible changes can be significant.

For more information, see Setting Processing Parameters in Chapter 10 of the

TotalChrom Users Guide.

You have now optimized the method for peak detection and
integration. The next step is to have TotalChrom assign names to
some of the peaks and calculate the amount (or concentration) of
the peaks. To do this you must create a component list.

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Tutorial Part 2

Creating a Component List

During peak detection, TotalChrom assigns a sequential number to each detected
peak. This is referred to as the peak list. The component list, on the other hand, is a
list you create in the method that identifies each peak as a specific component. We
will create three components in this exercise.

To add single peak components:

1.

Choose Edit Components from the Calibration menu.

The plot is narrowed to make room for the Edit Components dialog box:

2.

Click on peak 5 (retention time 2.81) to move the selection rectangle to it

from the first peak.

3.

Select the Ref. check box to have this component act as a reference peak for
other components.
The reference peak is used to adjust the expected retention times during
component identification.

4.

Select the ISTD check box to have this component act as an internal standard
for other components.
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Tutorial Part 2

The internal standard adjusts the responses for any variation in the injection
volume.
5.

For the component name, enter Chlorotoluene.

6.

Change the entries for both Absolute Window and Relative Window to 5.
The total search window is the sum of the absolute and relative windows,
applied to either side of the expected retention time of the component.

7.

Select the Find Tallest Peak in Window check box.

This will identify the tallest peak eluting within the search window as the
designated component.
This completes the entries for this peak. Your dialog box should look like the
example below.

8.

Choose Prev to move the selection rectangle to peak 4 (the peak preceding
peak 5).

Note: To save component information, you MUST choose Next, Prev, or Return. If
you move to another peak by clicking on it instead, your entries are not saved. (This,
however, is a way to discard entries that you do not want to save.)

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Your screen should now look like the example below, with the component
name below peak 5, and with peak 4 selected but not yet defined.

9.

For the component name for peak 4, enter 1,2-Dichloroethene.

10. From both the Reference and ISTD drop-down lists, select Chlorotoluene.
11. Change the Absolute Window entry to 5 (leave Relative Window set to 3).
12. Select the Find Tallest Peak in Window check box.
Your dialog box should look like the following example:

13. Choose Prev to move the selection rectangle to 3 (the peak preceding peak 4).
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Tutorial Part 2

14. For the component name for peak 3, enter Chloroform.

15. From both the Reference and ISTD drop-down lists, select Chlorotoluene.
16. Change the Absolute Window entry to 5 (leave Relative Window set to 3).
17. Select the Find Tallest Peak in Window check box.
18. Choose Return

to close the dialog box.

Your chromatogram is now labeled with the three components you just
created.

For additional information, see Working with Components in Chapter 10

of the TotalChrom Users Guide.

We have finished building the short component list that we need

for the tutorial. The next step is to switch to the Method Editor
and set the calibration parameters for each component.

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Tutorial Part 2

Using the Method Editor

In this part of the tutorial you will:

Set calibration parameters

Perform a manual calibration

You use the Method Editor to develop a complete method. It includes the parameters
that are not available through the Graphic Method Editor or when you develop a
quick method.

Setting Calibration Parameters

Calibration parameters identify and calibrate the components being analyzed by the
method. These parameters include component names, expected retention times, and
calibration data (the responses produced by different component amounts).
You entered the names and expected retention times when you created the component
list in the previous section of the tutorial. In this part of the tutorial, we will set the
remaining calibration parameters in the Method Editor by adding calibration levels
for each component.

To develop calibration parameters in a method:

1.

Choose Method from the Other menu to switch to the Method Editor and
display the summary information for each section of the method.

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2.

Choose Edit Component from the Components menu to open the

Components window.

This window is a secondary level of the Method Editor.

The names of the components that we want to identify in the analysis are on
the left side of the window. Information for the selected component is on the
right side. We will edit this existing information to add a calibration level for
each component.

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3.

Highlight Chloroform, then click on the Calibration tab to open the

calibration information dialog box for that component.

Note: The entries below are TotalChroms initial defaults. The default values may be
different on your system.
4.

Select the Use Curve as the Calibration Type option.

This creates a calibration curve based on the data collected from standard
samples.

5.

Select Area as the Response option.

This tells TotalChrom to calibrate and quantitate using peak area.

6.

Select Point to Point as the Curve Fit Type.

This averages all replicate amount and response data at each calibration level
to derive a point. Each pair of points will be connected by a straight-line
segment to form a calibration curve.

7.

For both Scaling and Weighting, select None.

8.

Under Origin Treatment, select (check) the Include check box.

This will add point (0,0) to the calibration (zero amount to zero response).

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The next part of the procedure describes how to add a new

calibration level in the area at the bottom of the dialog box.

9.

Click in the Level text box and enter Level 1 for the level name.
It is recommended to enter an alphanumeric level name in this box.

10. Click in the Amount text box and enter 30.

The area value will be calculated and filled in when we run a calibration
standard.
11. If there are default entries displayed on your list (anything other than the
Level 1 that you just entered), select each entry and press the Delete key to
delete it. This is the procedure for deleting a calibration level.
Once you click in the Level 2 box, your screen should look like the
following example.

12. Choose Next to display the calibration information for 1,2-Dichloroethene.

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13. Make the same entries for 1,2-Dichloroethene that you made for Chloroform:
Calibration Type = Use Curve
Response = Area
Curve Fit Type = Point to Point
Scaling/Weighting = None
Origin = Include
Calibration level = Level 1
Calibration amount = 30
Delete the default calibration level entries, if any

14. Choose Next to display the calibration information for Chlorotoluene.

15. Make the same entries for Chlorotoluene as you made for the previous
components, except that the calibration amount is 20 instead of 30:
Calibration Type = Use Curve
Response = Area
Curve Fit Type = Point to Point
Scaling/Weighting = None
Origin = Include
Calibration level = Level 1
Calibration amount = 20
Delete the default calibration level entries, if any

16. Choose Apply, then OK to return to the Method Summary window.

Now that we have finished adding a calibration level for each

component, we have everything we need to perform a manual
calibration.

Performing a Manual Calibration

When you manually calibrate a method, you are creating a calibration replicate. A
replicate is an analysis of a calibration standard for a particular calibration level.
Since it is a unique analysis, you can use replicates to average calibrations.
When you perform a manual calibration, you build a list of result files and the
calibration levels that you want to calibrate, and indicate the type of calibration that
you want to perform.

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To perform a manual calibration:

1.

Choose Calibrate from the Components menu to open the Manual

Calibration dialog box.

2.

Browse to the Examples directory, by clicking on the yellow folder icon to

the right of the Selected Files box, and select the result file Halo003.rst from
the File-Select dialog box.

Then click Open. This will be the file that we define as a calibration standard.
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3.

Select Level 1, from the drop-down menu, in the Calibration Parameters Level box.
This is the calibration level of the standard file.

4.

Select Replace as the Type.

If our method had been calibrated, this would replace the existing calibration
replicates with the new replicates.

5.

Choose Add to add the calibration entry to the Filename/Level/Cal Type list
on the bottom of the dialog box.
If you had more levels to calibrate at this time, you would select the next
file, level, and type combination and add it to the list.

6.

Select the Identify peaks before calibrating check box so that the peaks in
the result file will be identified before calibration.
Your screen should look like the example below.

7.

Choose OK to perform the calibration using the information in the

Filename/Level/Cal Type list and return to the Method Summary window.

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8.

To view the updated calibration, return to the Calibration tab by selecting Edit
Component from the Components menu, then click on the Calibration tab.

Notice that the area has been calculated and is displayed at the bottom right
of the window.
9.

Choose OK to return to the Method Summary window.

10. To view the calibration curve, you can Choose Component List from the
Window menu to switch from the Method Summary screen.

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You can also switch between Method Summary and Component List by
minimizing and maximizing the windows in the Method Editor, by clicking
on the appropriate icons in the upper right corner of the window.
11. To return to the Method Summary window, choose Window and select
Method Summary.

For additional information about calibration parameters, see Chapter 8 in

the TotalChrom Users Guide.

Although there are many ways that you can further customize a
method, this completes what we will do in the tutorial. Our next
step is to save what we have done.

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Saving a Method

To save this as a new method:

1.

Choose Save As from the File menu.

2.

When the Description dialog box opens, enter any information that you want
to store with the method file. Do not select Audit trail.

3.

Choose OK.

3.

Name the method by typing practice as the File name.

This saves the method as (C:\penexe\\practice.mth).

5.

Choose Save to save the method.

You have finished optimizing this method and have saved it for
future use.
The next step is to create a format for the report that will be
printed after an analysis that uses this method.

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Building a Report Format

After TotalChrom analyzes a raw data file, it uses a report format file when it prints
the results of the analysis. This file controls which parameters are included in the
printed report and defines how the information appears on the page.
To help you become familiar with this function, we will use the Report Format
Editor to:

Title the report

Add, replace, and delete report columns

Save the report for future use

Creating a new report format:

1.

With the Method Editor window still displayed, choose Report Format
Editor from the Other menu.
Since there is no report format with this name, TotalChrom uses the name of
the method that you have open with default values to set up a new report
format.

The first thing we will do is change the title of the report.

2.

Select Title from the User Notes menu.

3.

In the Title dialog box, change the default title to TUTORIAL REPORT.

4.

Click on OK to redisplay the report with the new title.

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You can display most of the edit dialogs by clicking directly on the desired
area of change (for example, click on TUTORIAL REPORT to display the
Title dialog box).
Next well add a column to the report.
5.

To see a list of all the options for column headings, choose Report to display
the menu.

6.

Select Component Name from the Report menu.

7.

In the Component Name dialog box, change the column number

from 9 (the next available column on the default report) to 3.

8.

Choose Insert/Add.
A column for Component Name is inserted before the Area column. The font
becomes smaller so that the report fits on the screen, and a compressed font
would be used when this report is printed.

Now we will change a column heading by replacing it with a

different selection.

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9.

Select Adjusted Amount from the Report menu.

10. In the Adjusted Amount dialog box, change the column number from 10 to 7.
11. Choose Replace.
Adjusted Amount is added to the report as column 7, in place of Normalized
Area.

The last change we will make before saving the file is to delete a
column from the report.

12. Select Delete Column from the Edit menu.

13. In the Delete Column dialog box, enter 9 for the column to be deleted
(Area/Height).
14. Choose OK.

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Notice that with fewer column headings the font returns to its original size.

15. Choose Save from the File menu.

16. Choose Exit from the File menu to return to the method summary.
Do not close the Method Editor window.
For additional information about report formats, see Chapter 9 in the TotalChrom
Users Guide.

Now that we have optimized and saved the practice method, we

will build a sequence that specifies this optimized method file.

Building a Sequence
Sequences are used to control acquisition and analysis of chromatographic data
produced by a series of injections.
For the purpose of this tutorial, we will build a sequence that we will use to reprocess
stored data. To do this, we will use the sequence template and the sequence spreadsheet.
Note: In most cases, an .idx file would be used for reprocessing data. We will discuss
.idx files, and their use, at the end of this section.

Using the Sequence Template

The sequence template simplifies the process of creating a sequence by letting you
define its essential structure in one dialog box.

To build a sequence using a template:

1.

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With the Method Editor window still displayed, choose Sequence Editor
from the Other menu.

Tutorial Part 2

When the Sequence Editor window opens, the sequence spreadsheet may
also be displayed. We will come back to it later.
2.

In the Sequence Editor window, choose New from the File menu.
This opens the Global Parameters dialog box:

3.

In the Build Parameters tab, select your instrument name from the
Instrument pull down menu.

4.

Select From template as the Build option.

5.

Click on the Configuration tab.

6.

Select Single for Injection Type option.

7.

Select One per row for Methods option.

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8.

Select Same name for Raw data and Result files option.

9.

Choose OK to open the Sequence Template dialog box.

This dialog box is where you enter all the information that you need to create
a basic sequence.
10. In the Study text box, type the name TUTORIAL to identify the analysis
being performed.
11. In the Method text box, browse to the examples directory, by clicking on
the yellow folder icon to the right of the method box, and select
C:\penexe\\practice.mth.
We want to use our newly optimized method to reprocess existing raw data files.
12. Change the Base file name to HALO for Channel A.
Note: HALO is the name of a group of raw files that are supplied with TotalChrom as
examples. We cannot use the raw file that you acquired in Part 1 of the tutorial since
every user has a different one.
This will be the base name of the raw and result files that will be listed in the
sequence spreadsheet.
13. In the Calibration box, deselect Include calibration standards by clicking
on the check box.
We already calibrated the method manually in the Method Editor.
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14. In the Samples box, enter 3 for the Number of samples to be analyzed in
the sequence.
15. In the Samples box, enter 1 in the # Injections per sample.
16. Choose OK to close the Sequence Template dialog box.
When you complete the sequence template, TotalChrom builds the sequence. You
can then view and edit the sequence data in spreadsheet form.

Using the Sequence Spreadsheet

The parameters in a sequence can be displayed in spreadsheet form in the Sequence
Information window. Using the spreadsheet is the easiest way to edit an existing
sequence.

Your sequence spreadsheet should have 3 rows, the number of samples you specified
in the template. Each row contains information about the sample and the values that
will be used when the raw data is reprocessed. To see the following columns and
information you will have to scroll the sequence spreadsheet window to the right:

The Method column shows the name of the method file.

The Report column is the name of the report format file that will be used to
generate the report.

The Data column identifies which files will be reprocessed.

When you build a sequence to acquire a series of injections, this entry will
be the base file name of the raw files that are created.

The parameters that you did not change contain either the default value or no
value.

Note: The columns that are displayed may vary depending on which options were
selected in the Global Parameters, Configuration tab or user defined hidden
columns.

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The Edit menu is the same menu we saw when we developed the vial list in the Part 1
of the tutorial. It offers several choices for manipulating rows in the spreadsheet.
We will use the Change menu to change the paths for the data files so TotalChrom
will know to look for them in the Examples directory rather than the Tutorial
directory.

76

To edit a sequence using the spreadsheet:

1.

Choose Path from the Change menu to open the Change Path dialog box.

2.

Enter 3 for the Ending Row.

3.

Enter an asterisk * in the Path to change text box.

4.

In the New path text box, browse to the Examples directory by clicking on
the yellow file folder to the right of the text box.

Tutorial Part 2

5.

Under Change path for, select Data.

6.

Choose OK.
You will notice that the full path is now displayed in the Data column and
that it now points to the Examples directory.

To change the printer information in the sequence.

1.

Scroll the spreadsheet window horizontally until the printer and plotter
columns are visible. They are at the far right of the spreadsheet.

2.

Select the cell for row 1 of that column by clicking inside it.

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The Default printer is your default Windows printer as shown below.

3.

Click on the Printer pull down menu and select the entry that represents the
printer you want to use.

4.

Do the same for the Plotter column.

5.

Choose Fill Down from the Change menu to copy the entry from row 1 to
every cell in the column.
Right clicking on the cell and selecting Fill Down can also accomplish this.

78

To save this sequence as a new sequence:

1.

Choose Save As from the File menu.

2.

When the Description dialog box opens, enter any information that you want
to store with the sequence file. Do not select Audit trail.

Tutorial Part 2

3.

Choose OK.

4.

In the Save As dialog box, name the sequence practice.

This saves the sequence as C:\penexe\.\practice.seq.

5.

Choose Save to close the dialog box and save the new sequence file.

For more information on sequences, see Chapter 11 in the TotalChrom Users Guide.

Now we are ready to use this sequence with the Batch Reprocessing
function.

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Batch Reprocessing a Sequence File

Once you have acquired data and stored it in a raw data file, you can process that data
repeatedly. The Batch Reprocessing function enables you to reprocess a large number
of files in succession.
One of the purposes of reprocessing data is to re-analyze the raw data files listed in a
sequence. For our last exercise, we will use the sequence file we just created to
reprocess data files with our optimized method.

To reprocess files in a sequence:

1.

Select Batch from the Actions menu.

Because we selected the Batch Reprocessing function when we had a
sequence open, that sequence is supplied as the default.

2.

Choose your Actual data path by clicking on the yellow folder and
browsing to the Examples directory.
The Data Path is the directory where your Raw and Result files are stored. If
you used the full path for your data files in the sequence spreadsheet, which
we did in the previous exercise, you can leave this field blank.

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3.

Click OK.

4.

Choose PEAK DETECTION as the Start analysis and REPLOT

GENERATION as the End analysis.

5.

Choose Local (if you have Client/Server) or Interactive (if you have
Workstation) for the Batch execution.

6.

Select Overwrite existing result files.

7.

Choose OK to accept the rest of the default settings.

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The Batch Reprocessing window opens, listing the raw files that are
scheduled for reprocessing. They are the three files from our sequence.

8.

Choose Start from the Reprocess menu to begin reprocessing the data. You
can also start the Batch process by clicking on the green arrow on the toolbar.
The entries on the list are deleted as they are processed. The report and replot
for each file will be printed once data analysis is complete.

9.

To close the Batch Reprocessing window and return to the Navigator, choose
Exit from the File menu.

For more information on batch reprocessing, see Chapter 15 of the TotalChrom

Users Guide.

Viewing Results using Reprocess Results

Once Reprocessing is complete, you can view the results using Reprocess Results.

To view the result files in Reprocess Results:

1.

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Click on the Results button from Reprocess buttons on the Navigator.

Tutorial Part 2

2.

Select the Halo003.rst file from the Examples directory.

3.

Click Open.

You will notice that the Halo003.rst file now has the method parameters
applied to it that you specified in the practice.mth that you created in the
Graphic Method Editor.
4.

By either using Print Preview, or looking at the printed report, you will
notice that the processing method that was used for this data file is the
practice.mth method that you created.
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Your printed report should resemble the above report.

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Review and Approve Data

This environment will consist of three main windows: one containing a list of sample
information (the file list), another containing a chromatogram plot, or plots, (the
plot window) of the currently selected sample, or samples, from the file list, and the
third containing a report displaying results from those samples (the report window).
These separate windows will be implemented as docking windows, so that the user
may adjust the layout and relative sizes of the windows to his or her liking. This
layout will be saved as part of the environment preferences (in an INI file located in
the individual users subdirectory under the penexe.

The display of any window may be toggled on or off using menu commands or
toolbar buttons. Each window may also be closed using the close button on the
docked window itself. Each window may be toggled between normal size and
maximized in the usual way for docking windows (i.e. the arrow button incorporated
in the frame).
The docking scheme will be implemented such that the open docked windows
completely fill the parent window. While it will be possible to undock a window there
is little point in doing so. Docking will be used here to allow a flexible layout with
easy relative sizing of windows, rather than any other purpose.
When a single file is selected in the file list, the plot window displays the
chromatogram from that file and the report window displays results from that run (if
available). The chromatogram can be annotated with sample information, peak names
and/or other peak information, baselines and labels added by the user. The result data
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Tutorial Part 2

can be displayed in the form of a simple peak table and/or in a specific TotalChrom
report format as defined by a .rpt file.
When more than one file is selected in the file list, the plot window displays all the
chromatograms, in either a stacked or overlay display format and the report window
displays a table containing a summary of results from all the files. There is no
arbitrary limit to the number of chromatograms that can be displayed the stacked
mode is quite valid for any number of plots.
The following example is a scenario of how the Review and Approve process could
be used. This example has been developed to illustrate some key aspects of the
Review and Approve specification; it is neither the simplest nor the most complex
path through the application. While the scenario aims to be accurate in its depiction of
review and approve, it does not attempt to be completely realistic in all matters.

Set Up Conditions
The configuration of the TotalChrom system for this example contains the following
key items:
Review and Approve signature levels:
Review, Final Review, Final Approve and Hold
Review and Approve options:
The same user cannot sign two levels for a report = True. You must enter a comment
for each Hold report = True
Job Types:
Manager, Analyst, Technician
Users:
Susanna (Manager), Michael (Senior Analyst), Vicky (Analyst), and James (Lab
Technician)
Review and Approve permissions:
Susanna Final Approve, Hold
Michael Final Review, Hold
Vicky Review
James no permissions
The sample data set for this example consists of three samples (CK46123, CK46124
and CK46125) each of which has two associated reports (Actives and Impurities).
Processing of these samples yielded three TCR files, each containing two report
definitions.
Vicky has reviewed the results in the Review and Approve environment and signed
each report, such that each now has the status of Reviewed.

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In this Example
1.

Michael logs on to TotalChrom on one of the lab computers and opens the
Review and Approve environment by clicking the
button in the
TotalChrom Navigator. He prefers to be away from his office phone when
reviewing reports.

2.

He selects the three TCR files representing the CK46123, CK46124 and
CK46125 sample reports in the File Open dialog and clicks OK.
The Signature Status column in the file list shows Reviewed for all three TCR
files, as Michael expects (knowing Vicky came in on Sunday to review the
samples after James had finished the chromatographic runs). The chromatogram
and Actives report for the first sample are displayed in the Plot and Report
windows.

3.

He zooms in on the chromatogram to examine the integration and baseline for

each peak of interest in turn.
All look satisfactory. Michael repeats this process for the two remaining TCR
files. The chromatography and integration looks fine for all three samples.

4.

Now he wants to review the reports more closely prior to signing them so he
chooses the All Reports command from the Sign menu.
The Report Review window appears with the Actives report for sample CK46123
displayed. Michael notes that the Review, Final Review and Hold buttons are
enabled on the Sign toolbar, while the Approve and Final Approve buttons are
disabled.

He will not use the Review button since the company SOP only requires two
levels of review. He also hopes he wont be using the Hold button because
rejecting batches of product leads to a lot of paperwork and unwelcome attention
from upper management. Once he has applied a Final Review signature to these
reports they will be ready for Susanna to give Final Approval.
5.

Michael clicks the Zoom In button so that the report text is at a size that is
comfortable for him to read. He then checks the header information carefully to
make sure the correct methods were used. Clicking the scroll bar, he examines
the peak table to ensure the reported amount of each active component is within
limits and that the suitability parameters are within tolerance.

6.

When he is satisfied that all is as it should be Michael clicks the Final Review
button.
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The Impurities report for CK46123 is then displayed. Michael reviews the header
information again and checks the amounts for each impurity, as well as the figure
for total impurities. All these values are well within limits and so Michael clicks
Final Review once again.
7.

Michael repeats his examination on the reports from CK46124. Both of these are
also satisfactory, so he marks both using the Final Review button.

8.

The Actives report for CK46125 also appears acceptable, so he clicks Final
Review once more. This causes the Impurities report for CK46125 to be
displayed. Michael notes that the individual impurities are just within limits but
the total is too high.

9.

He double-checks the addition manually but he knows the TotalChrom custom

expression math is flawless. That process may be getting out of hand he thinks
to himself, as he clicks the Hold button.
The Reason for Hold is displayed and, following the SOP, Michael types in an
explanation of why he is not approving the report.

10. He clicks OK and the notes that the report name in the status bar of the Review
Reports window is now followed by (Hold Unsigned). Since that was the final
report in the set, the Close button has been replaced by Finish, indicating he has
reviewed everything.
11. Michael clicks the Finish button and the Sign reports dialog is displayed. This
shows the three TotalChrom Report files he originally selected as top level nodes
on the tree control. Each top level node has two secondlevel nodes under it,
representing the individual reports. The Status to be Signed column shows three
Reviewed Final and one Hold:
C:\data\september\09\CK46123.tcr
C:\data\september\09\actives_r2.rpt
C:\data\september\09\impurities_r3.rpt

Reviewed Final
Reviewed Final

C:\data\september\09\CK46124.tcr
C:\data\september\09\actives_r2.rpt
C:\data\september\09\impurities_r3.rpt

Reviewed Final
Reviewed Final

C:\data\september\09\CK46124.tcr
C:\data\september\09\actives_r2.rpt
C:\data\september\09\impurities_r3.rpt

Reviewed Final
Hold

12. Michael clicks on the Sign button and the Electronic Signature dialog appears.
13. Michael enters his user name (logon ID) in the first field and his password in the
second field.

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14. When he clicks the OK button the display returns to the main Review and
Approve screen. The file list still contains the three TCR files for samples
CK46123, CK46124 and CK46125. The Status column now displays Reviewed
Final for the first five reports and Hold for the final report.
At that moment Susanna walks into the lab. Debbie said that the analyses that
had to be run again over the weekend. Well, I can tell you that Debbie isn't
going to be happy because one sample is no good. CK46125 has too high a total
level of impurities. We cant let it go. How about the others, asks Susanna.
CK46123 was well within limits and CK46124 was between the two. Well I
suppose we should be grateful that two out of three are OK. Do you want to
look these over, since you are here right now? asks Michael, offering his chair
to Susanna. Sure, she replies, and sits down at the computer.
15. Susanna chooses the All Reports command from the Sign menu and examines
each report in turn in the Review Reports window. The first five reports are all
marked with the Reviewed Final status that Michael signed off.
16. Susanna clicks the Final Approve button for each of these. After the fifth click,
the final report is displayed and Susanna notes the Hold designation in the status
bar.
17. She clicks the Comment button, which is the only button in the Sign toolbar
enabled, since the current unapproved report has a comment attached. A dialog
is displayed showing Michael's reason for holding the report.
You misspelled phenylethyllonamide, Michael, Susanna teases. Thats not
like you.
18. Susanna closes the comment dialog and clicks the Finish button, reviews the
names of the five reports she is signing in the Sign Reports dialog, clicks the Sign
button and finally enters her logon name and password in the Electronic
Signature dialog.
When she accepts that dialog the file list in the main Review and Approve
window is updated to show the following Signature Statuses for the three sample
files:
C:\data\september\09\CK46123.tcr

Reviewed Final

C:\data\september\09\CK46124.tcr

Reviewed Final

C:\data\september\09\CK46124.tcr

Hold

At that moment James rushes into the lab. Good Morning, James says Michael.
Hi Mike, I was hoping Susanna would be with you. Debbie is waiting for you in
your office, Susanna. She asked me to get you right away. OK, I'll go and
break the bad news to her. Call on me if you need support, Michael calls after
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Susanna as she leaves the lab. That's what the PerkinElmer salesperson said,
replies Susanna, but that TotalChrom software is so easy to use I have never had
to..

Congratulations!
You have successfully completed the TotalChrom Tutorial.

This tutorial was designed to give new users a brief overview of how to setup and run
a chromatograph with the TotalChrom software. There are many different features
and options available in TotalChrom that were not discussed in this tutorial. We
strongly recommend that all users read the TotalChrom Users Guide carefully in
order to fully understand this application and how it works.
It is also advised that new users consider attending a TotalChrom training class to
supplement this tutorial. To find out more information about a training class in your
area, please contact 1-800-762-4000.
The global TotalChrom Support Team is readily willing to help you with any
questions or difficulties you might experience while using the TotalChrom software.
To reach your TotalChrom support representatives, call 1-800-762-4000 (U.S. and
Canada). For our international users, please contact your local PerkinElmer office.

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