Thermo Fisher Scientific Data Analysis Software Owner's manual

Brand: Thermo Fisher Scientific

Model: Data Analysis Software

Category: Software manuals

Type: Owner's manual

DRAFT August 10, 2001 2:47 pm

DASgsg_Title.fm

Data Analysis Software

for VISION™, BioCAD® 700E, SPRINT™, and INTEGRAL®

Workstations

Version 3 Series Software

Getting Started Guide

DRAFT August 10, 2001 2:47 pm

DASgsg_Title.fm

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

Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that

may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall

Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use

of this document.

ABI PRISM, Applied Biosystems, BioCAD, CytoFluor, GeneScan, INTEGRAL, POROS, Procise, and Tropix are registered

trademarks of Applera Corporation or its subsidiaries in the U.S. and certain other countries.

AB (Design), Applera, Data Explorer, Expedite, FMAT, Mariner, PEG-PS, Pioneer, Proteomics Solution 1, SPRINT, VISION, and

Voyager are trademarks of Applera Corporation or its subsidiaries in the U.S. and certain other countries.

ICAT is a trademark of the University of Washington in the U.S. and certain other countries, exclusively licensed to Applied

Biosystems Group of Applera Corporation.

MDS is a registered trademark, and SCIEX is a trademark of MDS, Inc.

TaqMan is a registered trademark of Roche Molecular Systems, Inc.

Microsoft, MS, MS-DOS, and Windows are registered trademarks of Microsoft Corporation.

Pentium is a registered trademark of Intel Corporation.

All other trademarks are the sole property of their respective owners.

Printed in the USA, 06/2001

Part Number 602309-01 Rev. A

Table of Contents

Data Analysis Software Getting Started Guide iii

Table of Contents

Chapter 1 Before You Begin

1.1 What You Will Learn ..................................................................................... 1-2

1.2 Data Analysis Software Overview ................................................................. 1-3

1.3 Guidelines for Accessing Files in the Data Analysis Module ........................ 1-6

1.4 Changes to Version 3.0 Software ................................................................. 1-8

1.5 Using the Sample Files Provided .................................................................. 1-9

Chapter 2 Analyzing Data

2.1 Overview ....................................................................................................... 2-2

2.2 Analyzing Using Default Analysis Parameters .............................................. 2-3

2.3 Adjusting Analysis Parameters ..................................................................... 2-8

2.4 Background Analyzing ................................................................................ 2-19

Chapter 3 Reporting Results

3.1 Overview ....................................................................................................... 3-2

3.2 Generating a Report with Default Report Format Parameters ...................... 3-3

3.3 Customizing Report Format Parameters .......................................................3-4

3.4 Printing a Customized Report ....................................................................... 3-9

Chapter 4 Generating Calibration Curves and

Quantitating Unknowns

4.1 Overview ....................................................................................................... 4-2

4.2 Opening the Sample Data Files ....................................................................4-4

4.3 Adjusting Processing Parameters ................................................................. 4-5

4.4 Entering Component Information .................................................................. 4-7

4.5 Generating Result Files ................................................................................. 4-9

Table of Contents

iv Applied Biosystems

4.6 Entering Calibration Levels and Component Amounts ............................... 4-10

4.7 Associating Areas With Levels and Generating Calibration Curves ........... 4-14

4.8 Adjusting the Report Format ....................................................................... 4-18

4.9 Creating a Method File for Unknowns ......................................................... 4-20

4.10 Quantitating Unknowns ...............................................................................4-21

Appendix A Technical Support and Training

A.1 Contacting Technical Support ..................................................................A-2

A.2 Obtaining Technical Documents ..............................................................A-8

A.3 Obtaining Customer Training Information ............................................... A-10

Index

Data Analysis Software Getting Started Guide 1-1

1 Before You Begin

This chapter includes the following sections:

1.1 What You Will Learn .................................. 1-2

1.2 Data Analysis Software Overview .............. 1-3

1.3 Guidelines for Accessing Files

in the Data Analysis Module ...................... 1-6

1.4 Changes to Version 3.0 Software............... 1-7

1.5 Using the Sample Data Files Provided....... 1-8

Chapter 1 Before You Begin

1-2 Applied Biosystems

11.1 What You Will Learn

The following table explains what you will learn in each chapter

of the Data Analysis Getting Started Guide:

NOTE: This guide contains brief procedures. For more

detailed procedures and reference information, refer to the

Data Analysis Software User’s Guide.

In … You will learn how to …

Chapter 2, Analyzing

Data • Analyze using default analysis parameters

• Adjust and save analysis parameters

• Background analyze

Chapter 3, Reporting

Results • Generate a report with default report format

parameters

• Adjust report format parameters

• Print a customized report

Chapter 4,

Generating

Calibration Curves

and Quantitating

Unknowns

• Adjust processing parameters

• Enter component information

• Generate result files

• Enter calibration levels and component amounts

• Associate areas with levels and generate calibration

curves

• Adjust the report format

• Create a method file for unknowns

• Quantitate unknowns

Data Analysis Software Overview

Data Analysis Software Getting Started Guide 1-3

1.2 Data Analysis

Software Overview

Overview Applied Biosystems Data Analysis software is part of your

BioCAD®, VISION™, or INTEGRAL® software version 3.0 or

later.

Applied Biosystems Data Analysis software includes two

modules:

•Group Analysis—Allows you to view, compare, and

export chromatograms.

•Data Analysis—Allows you to process, calibrate, and

report data that you acquire on your SPRINT™,

BioCAD 700E, VISION, or INTEGRAL 100Q Workstation.

For information on Group Analysis and Data Analysis functions

not described in this guide, see the Data Analysis User’s Guide.

Analysis and

report

parameters

The Data Analysis module allows you to adjust the following

parameters in a BioCAD, VISION, or INTEGRAL method file

(.MET):

•Analysis parameters (.MTH)—Include:

•Processing parameters—Control peak detection,

integration, and report/replot printing

•Calibration parameters—Identify and calibrate

components analyzed

•Report format parameters (.RPT)—Determine

parameters included in a printed report

Chapter 1 Before You Begin

1-4 Applied Biosystems

1Analysis (.MTH) and report format (.RPT) parameters are

embedded in each method (.MET), data (.B*), and group

(.GRO) file. Each of these files contains default analysis and

report format parameters that you can use as is, or customize.

Figure 1-1 Analysis and Report Format Parameters

within a Method File (.MET)

For more information, refer to the Data Analysis User’s Guide.

Assumption Each BioCAD® SPRINT, BioCAD 700E, VISION™, or

INTEGRAL® workstation comes with a Getting Started Guide for

the workstation. This Data Analysis Software Getting Started

Guide assumes you have already performed the procedures in

the Getting Started Guide provided with your workstation.

Windows® 95 The Data Analysis software is a Windows® 95 application and

this guide assumes familiarity with Windows 95 conventions.

See the Introducing Microsoft® Windows® 95 manual provided

with the Windows 95 software, for more information.

.MTH

.RPT

*.MET System Configuration

Instrument Control

UV #1

.MTH

.RPT

UV #2

.MTH

.RPT

AUX

Data Analysis Software Overview

Data Analysis Software Getting Started Guide 1-5

Data Analysis

editors and

windows

The Data Analysis module includes:

•Text Method Editor—Allows you to create or change

analysis parameters (processing and calibration). Changes

are saved to the analysis section of a method file (.MET),

data file (.B*), or group file (.GRO).

•Report Format Editor—Allows you to create or change

reporting parameters. Changes are saved to the report

format section of a method file (.MET), data file (.B*), or

group file (.GRO).

•Graphic Method Editor—Allows you to analyze a data file

and view its chromatogram and allows you to change the

analysis parameters (processing and calibration) by

graphically manipulating a chromatogram. Changes are

saved to the analysis section of a method file (.MET), data

file (.B*), or group file (.GRO).

•Fit Analysis Window—Allows you to plot the calibration

curve for any component that has amount and response

data in the analysis section of the associated method file.

Chapter 1 Before You Begin

1-6 Applied Biosystems

11.3 Guidelines for Accessing Files

in the Data Analysis Module

Before using the Data Analysis module, note the following:

• You always open or select either a method file (.MET), data

file (.B*), or group file (.GRO) in the Method Editor, Group

Analysis window, or Control Panel before accessing the

Data Analysis module.

• You cannot open method files (.MET), data files (.B*), or

group files (.GRO) directly within the Data Analysis module.

• To access a different method file or data file, you must

return to the Group Analysis window or the Method Editor,

then select another file and data channel to re-access the

Data Analysis module.

• You can view only one data channel (UV #1, UV #2, or

Auxiliary) at a time in the Data Analysis module. You select

the data channel to view when you open a file.

• You can access analysis parameters (.MTH), report format

parameters (.RPT), raw data (.RAW), or results (.RST)

sections of a selected method file (.MET), data file (.B*), or

group file (.GRO) from within the Data Analysis module.

• Once in the Data Analysis module, do not save files as

separate .MTH, .RPT, or .RST files. These file types cannot

be used by the BioCAD, VISION, or INTEGRAL software.

Guidelines for Accessing Files in the Data Analysis Module

Data Analysis Software Getting Started Guide 1-7

NOTE: Analysis parameters (.MTH), report format

parameters (.RPT), and raw data (.RAW) are not stored as

separate, permanent files, but as sections of a method or

data file. You can access these sections of a method file or

data file only through the Data Analysis module.

Results (.RST) can be stored as separate files for the

purpose of creating a calibration curve. Report formats

(.RPT) can be stored as separate files for the purpose of

selecting optional reports in analysis parameters.

Chapter 1 Before You Begin

1-8 Applied Biosystems

11.4 Changes to Version 3.0 Software

Version 3.0

changes If you have used earlier versions of Applied Biosystems Data

Analysis software, major changes you need to know about

before using the version 3.0 Data Analysis software are:

•No Analysis Parameters file (.ANP)—The software no

longer uses Analysis Parameter files (.ANP). Instead, each

method file (.MET), data file (.B*), and group file (.GRO)

includes three Analysis sections (.MTH), one for each data

channel. Each analysis section (.MTH) contains processing

(peak detection and integration) and calibration

parameters.

• Data channel references—The data channels are now

referred to as UV #1, UV #2, and Auxiliary, not as channels

A, B, and C.

•Single data channel—You can view and change

parameters for one data channel at a time. You can set

parameters for all three data channels because there are

three analysis sections (.MTH) and three report format

sections (.RPT) within a method file (.MET), data file (.B*),

or group file (.GRO).

•Opening data files—You must open data files from the

Control Panel, Method Editor or Group Analysis module of

the BioCAD, VISION, or INTEGRAL software. Doing so

opens the Data Analysis module. You cannot open data

files directly within the Data Analysis module.

For additional information on changes to version 3.0 software,

see the Data Analysis User’s Guide.

Differences from

Turbochrom

Software

The Data Analysis module incorporates the basic data analysis

features of PE Nelson™ Turbochrom software, but does not

include instrument control features. The differences between

Turbochrom software and Applied Biosystems Data Analysis

software are described in the Data Analysis User’s Guide.

Using the Sample Files Provided

Data Analysis Software Getting Started Guide 1-9

1.5 Using the

Sample Files Provided

Sample files The following sample data files and group files are provided on

your system to use as you perform the procedures in this guide:

•CATMAP.B06

• CALSTD.B00

• CALSTD.B01

• CALSTD.B02

• CALSTD.GRO

• CALUNKNWN.B00

• CALUNKNWN.B01

• CALUNKNWN.GRO

Sample data files are located in the \GETTINGSTARTED

directory for your system. For example, on a VISION system,

data files are located in C:\VISION\GETTINGSTARTED.

CAUTION

The sample files were generated on a VISION Workstation

and may not be compatible with BioCAD 700E, SPRINT, or

INTEGRAL workstations. Do not try to export the sample data

files or open the Method files (.MET): .MET or .CFG from

these files on non-VISION systems.

Resetting the

default analysis

and report

parameters

If the sample files provided on your system have been used to

perform the procedures in this guide, the analysis and report

format sections may have been modified. If they do not contain

the default values, your results will not match the results

presented in this guide. You can reset the default parameters to

ensure the files are the same as when they were used to

generate the examples in this Getting Started Guide.

The following two procedures show you how to reset the default

parameters in the analysis and report format sections of the

sample data files and the sample group file.

Chapter 1 Before You Begin

1-10 Applied Biosystems

1Resetting the data

files To reset the sample data files:

1. Display the Group Analysis window by selecting Group

Analysis from the Window menu in the Control Panel.

2. Select Open Group from the File menu.

3. Select CALSTD.GRO from the \GETTINGSTARTED

directory.

4. Click OK.

The CALSTD.GRO file and its associated data files are

displayed in the Group Analysis window.

5. From the Individual section of the Analysis menu, select

Replace Analysis/Report.

The Replace Analysis/Report Format Sections dialog box

(Figure 1-2) appears.

Figure 1-2 Replace Analysis/Report Format Sections

Dialog Box

Using the Sample Files Provided

Data Analysis Software Getting Started Guide 1-11

6. Select the GETTINGSTARTED directory from the Look in:

drop-down list. If you do not see the directory, click the

button to the right of the drop-down list.

7. Select Data Files from the Files of type: drop-down list.

8. Select as the destination files:

•CATMAP.B06

• CALSTD.B00

• CALSTD.B01

• CALSTD.B02

Hint: You can select multiple files by holding the Control

key and clicking the file names in the list box.

CAUTION

Do not select the CALUNKNWN files. These files should

never be modified from their factory settings.

9. Select UV #1.

10. Select the Analysis source file check box and the

Report format source file check box. The default files

are automatically selected.

11. Click OK.

The default analysis (.MTH) and report format (.RPT)

parameters are copied into the destination files.

Chapter 1 Before You Begin

1-12 Applied Biosystems

1Resetting the

group file To reset the sample group file:

1. In the Group Analysis window, select Replace

Analysis/Report from the Group section of the Analysis

menu.

The Replace Analysis/Report Format Sections dialog box

(Figure 1-2) appears.

2. Select the GETTINGSTARTED directory from the Look in:

drop-down list. If you do not see the directory, click the

button to the right of the drop-down list.

3. Select Group Files from the Files of type: drop-down list.

4. Select CALSTD.GRO as the destination file.

CAUTION

Do not select the CALUNKNWN files. These files should

never be modified from their factory settings.

5. Select UV #1.

6. Select the Analysis source file check box and the Report

format source file check box. The default files are

automatically selected.

7. Click OK.

The default analysis (.MTH) and report format (.RPT)

parameters are copied into the destination file.

For more

information For more information on the types of files you can copy

parameters from, see the Data Analysis User’s Guide.

Data Analysis Software Getting Started Guide 2-1

2 Analyzing Data

This chapter includes the following sections:

2.1 Overview........................................................ 2-2

2.2 Analyzing Using

Default Analysis Parameters.......................... 2-3

2.3 Adjusting Analysis Parameters....................... 2-8

2.3.1 Viewing the Peak Report ...................... 2-8

2.3.2 Adjusting Noise and

Area Thresholds ............................... 2-10

2.3.3 Adjusting Bunching Factor ................. 2-12

2.3.4 Setting Baseline Timed Events .......... 2-14

2.3.5 Naming Peaks.................................... 2-16

2.3.6 Saving the Analysis Parameters ........ 2-18

2.3.7 Replacing Analysis Parameters ......... 2-18

2.4 Background Analyzing ................................. 2-19

Chapter 2 Analyzing Data

2-2 Applied Biosystems

2.1 Overview

In this chapter In this chapter, you will learn how to:

• Analyze data, interactively and in the background

• Adjust and save analysis parameters

Peak detection

and integration Peak detection and integration are the processes of extracting

information from raw data.

When you analyze a data file, the Data Analysis software reads

a raw data file and detects peaks and integrates according to

the analysis parameters (.MTH) embedded in the method file

(.MET) used to acquire the data.

The integrated data appears as baseline, peaks, and peak

information in a chromatogram.

Adjusting

integration and

peak detection

(analysis)

parameters

You can change the way the software identifies baseline, peaks,

and peak information by adjusting the analysis parameters in

the Graphic Method Editor.

This chapter introduces the techniques you use to work with the

Graphic Method Editor. After you develop integration

parameters that suit your needs, you can save them as part of

the .MTH section of the data file, and use them for other

analyses.

For more

information For more information on analyzing, adjusting analysis

parameters, and the Graphic Method Editor, see the following

sections of the Data Analysis User’s Guide:

• Chapter 4, Analyzing Data

• Chapter 6, Adjusting Processing Parameters

• Chapter 9, Adjusting Analysis Parameters

Graphically

Analyzing Using Default Analysis Parameters

Data Analysis Software Getting Started Guide 2-3

2.2 Analyzing Using

Default Analysis Parameters

The simplest way to integrate the peaks in a chromatogram is to

analyze the data file using the default analysis parameters.

When you create a method file, it contains a set of default

analysis parameters.

This section includes:

• Resetting default analysis and report parameters

• Analyzing a chromatogram

• Reviewing the chromatogram

• Opening additional files

Resetting

default analysis

and report

parameters

If the sample files provided with your system have been

previously used to perform the procedures in this chapter, they

may not contain default analysis and report format parameters.

To reset the default parameters, see “Resetting the default

analysis and report parameters” on page 1-9.

Chapter 2 Analyzing Data

2-4 Applied Biosystems

Analyzing a

chromatogram To analyze a data file using default analysis parameters:

8. Display the Group Analysis window by selecting Group

Analysis from the Window menu in the Control Panel.

9. Select New Group from the File menu.

10. Select Select Files from the File menu.

The Select Data Files to Analyze dialog box appears.

Loading the

data file 11. From the \GETTINGSTARTED directory, select

CATMAP.B06 and click Add.

12. Click OK.

The chromatogram for CATMAP.B06 is displayed in the

Group Analysis window (Figure 2-3).

Figure 2-3 Chromatogram for CATMAP.B06

13. Deselect the Export and the Print check boxes.

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Thermo Fisher Scientific Data Analysis Software Owner's manual

Brand: Thermo Fisher Scientific

Model: Data Analysis Software

Category: Software manuals

Type: Owner's manual

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Thermo Fisher Scientific Data Analysis Software Owner's manual

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