HP (Hewlett-Packard) H-150 User Manual

Data Explorer™ Software

Version 4 Series Software

User Guide

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 docume nt . T hi s do cument is believed to be com pl et e a nd accurate at the time of publica ti on. 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.

Applied Biosystems is a registered trade m ark of Applera Corporation or its subsidiaries in the U.S. and certain other countries. AB (Design), Applera, Biospectrometry, CombiSolv, Data Explorer, Mariner, and Voyager are trademarks of Applera Corporation

or its subsidiaries in the U.S. and cer tain other co untries. HP and Laserjet ar e registered tradem arks of Hewlett-Packard Co. Microsoft, PowerPoint, Visual Basic, and Windows NT are registered trade ma rks of Mic rosoft Corporation. All other tradem arks are the sole property of their res p ective owners.

Printed in the USA, 7/2001 Part Number 4317717 Rev. C

Table of Contents

How to Use This Guide.............................................................. xi

Chapter 1 Data Explorer™ Basics

1.1 Overview .............................................................................. 1-2

1.2 File Formats and Types

1.2.1 Software Applications Compatibility ....................................... 1-5

1.2.2 Data (.DAT) File Format ......................................................... 1-5

1.3 Parts of the Data Explorer Window

1.4 Customizing the Data Explorer Window

1.4.1 Setting Default Values ...........................................................1-17

1.4.2 Customizing Processing and Graphic Settings (.SET) ...........1-17

1.4.3 Customizing Toolbars ............................................................1-21

1.5 Setting Graphic Options

1.5.1 Changing Background Color .................................................1-23

............................................................ 1-5

............................................. 1-11

....................................... 1-17

.......................................................... 1-23

1.5.2 Customizing Graphic Options ................................................1-24

1.5.3 Reverting to Previous Graphic Options .................................1-29

1.6 Managing Files

1.6.1 Converting .SPC File Format to .DAT File Format

(Mariner Data Only) ..............................................................1-30

1.6.2 Converting Data from Profile to Centroid

(Mariner Data Only) ..............................................................1-33

1.6.3 Converting to and Exporting ASCII Data ..............................1-34

1.6.4 Importing a Trace in ASCII Format ........................................ 1-35

1.6.5 Extracting and Saving Information

from .DAT, .RSD, and .RCD Files ..........................................1-36

1.6.6 Copying from Data Files ........................................................1-38

...................................................................... 1-30

™

Data Explorer

Software User’s Guide iii

Table of Contents

Chapter 2 Using Chromatog ram and S pectrum Windows

2.1 Opening and Closing Data Files ................................................. 2-2

2.1.1 Opening Data Files ................................................................ 2-2

2.1.2 Displaying Mariner DAD Traces ............................................. 2-6

2.1.3 Displaying Voyager Chromatograms ...................................... 2-7

2.1.4 Viewing Read-Only Files ........................................................ 2-7

2.1.5 Moving Between Open Files .................................................. 2-8

2.1.6 Closing Data Files .................................................................2-10

2.2 Adjusting the Display Range

2.3 Organizing Windows

2.4 Manipulating Traces

2.4.1 Zooming, Centering, and Customizing a Trace ......................2-14

2.4.2 Duplicating a Trace ...............................................................2-15

2.4.3 Dividing the Active Trace ......................................................2-15

2.4.4 Adding Traces from

the Same Data File to a Window ...........................................2-16

2.4.5 Removing Traces ..................................................................2-21

2.4.6 Expanding and Linking Traces ..............................................2-21

2.4.7 Recalling and Rearranging Traces (Processing History) ........2-22

2.4.8 Overlaying Traces .................................................................2-24

2.4.9 Annotating Traces .................................................................2-28

2.4.10 Viewing Trace Labels ............................................................2-30

2.4.11 Printing Traces ......................................................................2-33

2.5 Working with Multiple Data Files

2.5.1 Working with Separate Data Files .........................................2-36

2.5.2 Copying Traces from Multiple Data Files to a Window ...........2-37

2.6 Saving, Opening, and Deleting .DAT Results

2.7 Exporting, Opening, and Deleting .RCD and .RSD Results Files (Mariner Data Only)

2.8 Saving, Opening, and Deleting .SPC Results Files (Mariner Data Only)

............................................................... 2-13

............................................................... 2-14

................................................................ 2-39

................................................................ 2-40

..................................................... 2-11

................................................ 2-36

................................ 2-38

iv Applied Biosystems

Table of Contents

Chapter 3 Peak Detection and Labeling

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

3.1.1 Default Peak Detection .......................................................... 3-2

3.1.2 The Resolution-Based Peak Detection Routine ...................... 3-3

3.2 Peak Detection

3.2.1 Strategy for Mariner Peak Detection ....................................... 3-6

3.2.2 Strategy for Voyager Peak Detection ...................................... 3-8

3.2.3 Setting Peak Detection Parameters ...................................... 3-11

3.2.4 Peak Detection Parameter Descriptions ................................3-19

3.2.5 Charge State

3.3 Peak List

3.3.1 Displaying the Peak List ........................................................3-37

3.3.2 Inserting Peaks in the Peak List ............................................3-39

3.3.3 Saving the Peak List .............................................................3-40

3.3.4 Sorting, Filtering, and Printing the Peak List .........................3-42

3.4 Deisotoping a Spectrum

3.5 Peak Labeling

3.5.1 Charge State Labels .............................................................3-53

3.5.2 Setting Chromatogram and Spectrum Peak Labels ...............3-54

3.5.3 Setting Custom Peak Labels .................................................3-61

3.6 Process that Occurs During Peak Detection, Centroiding, and Integration

3.7 Default Peak Detection Settings

....................................................................... 3-6

Determination and Examples ................................................3-32

............................................................................. 3-37

.......................................................... 3-45

....................................................................... 3-52

..................................................... 3-67

................................................ 3-71

Data Explorer

™

Software User’s Guide v

Table of Contents

Chapter 4 Examining Chromatogram Data

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

4.2 Creating an Extracted Ion Chromatogram

4.2.1 Creating an Extracted Ion Chromatogram (XIC) ..................... 4-5

4.2.2 Creating a Constant Neutral Loss (CNL) Chromatogram ........ 4-9

4.3 Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)

4.4 Noise Filtering/Smoothing

4.5 Adding and Subtracting Raw Spectra Within a Data File

4.6 Displaying MS Method Data (Mariner Data Only)

4.7 Adjusting the Baseline

4.7.1 Using Baseline Offset ...........................................................4-27

4.7.2 Using Baseline Correction .....................................................4-29

................................................................ 4-13

........................................................ 4-17

............................................................ 4-27

..................................... 4-5

.................. 4-20

........................... 4-23

4.8 Using UV Trace Offset (Mariner Data Only)

.................................. 4-30

Chapter 5 Examining Spe ctrum Da ta

5.1 Overview .............................................................................. 5-2

5.2 Creating a Combined Spectrum

5.3 Manual Calibration

5.3.1 Overview of Manual Calibration ............................................. 5-5

5.3.2 Manually Calibrating .............................................................. 5-7

5.3.3 Creating or Modifying a Calibration Reference File (.REF) ....5-17

5.3.4 Reverting to Instrument Calibration .......................................5-22

5.3.5 Hints for Calibrating Mariner Data .........................................5-24

5.3.6 Hints for Calibrating Voyager Data ........................................5-25

5.4 Automatic Calibration

5.4.1 Overview of Automatic Calibration ........................................ 5-26

5.4.2 Importing and Specifying Automatic Calibration Settings .......5-29

5.4.3 Automatically Calibrating (Mariner Data Only) .......................5-34

.................................................................. 5-5

.............................................................. 5-26

................................................. 5-4

vi Applied Biosystems

Table of Contents

5.5 Centroiding .......................................................................... 5-36

5.6 Mass Deconvolution (Mariner Data Only)

5.7 Noise Filtering/Smoothing

5.8 Adjusting the Baseline

5.8.1 Using Baseline Offset ...........................................................5-45

5.8.2 Using Baseline Correction .....................................................5-47

5.8.3 Using Advanced Baseline Correction ....................................5-48

........................................................ 5-42

............................................................ 5-45

..................................... 5-37

5.9 Truncating a Spectrum

5.10 Converting to a Singly Charged Spectrum (Mariner Data Only)

5.11 AutoSaturation Correction (Mariner Data Only)

5.12 Adding and Subtracting Raw or Processed Spectra from the Same or Different Data Files (Dual Spectral Trace Arithmetic)

............................................................ 5-56

......... 5-59

............................. 5-62

................... 5-64

Chapter 6 Using Tools and Applications

6.1 Using the Elemental Composition Calcul ator ................................. 6-2

6.1.1 Determining Elemental Composition ...................................... 6-2

6.1.2 Setting Limits ......................................................................... 6-7

6.2 Using the Isotope Calculator

6.3 Using the Mass Resolution Calculator

6.4 Using the Signal-to-Noise Ratio Calculator

6.5 Using the Ion Fragmentation Calculator

6.6 Using the Elemental Targeting Application

6.7 Using the Macro Recorder

6.7.1 Before Using the Macro Recorder .........................................6-34

6.7.2 Recording a Macro ................................................................6-37

6.7.3 Assigning Macros to Buttons .................................................6-38

6.7.4 Running a Macro ..................................................................6-39

..................................................... 6-13

......................................... 6-20

................................... 6-23

....................................... 6-25

................................... 6-31

....................................................... 6-34

6.7.5 Deleting a Macro ...................................................................6-41

6.7.6 Advanced Macro Editing .......................................................6-42

6.7.7 Importing or Exporting Macros in DATAEXPLORER.VB6 ......6-43

6.7.8 Running Macros Automatically

When Opening and Closing Files ..........................................6-45

™

Data Explorer

Software User’s Guide vii

Table of Contents

Chapter 7 Data Explorer Examples

7.1 Mariner Data Examples............................................................ 7-2

7.1.1 Improving Signal-To-Noise Ratio ............................................ 7-2

7.1.2 Deconvoluting and Evaluating

Unresolved Chromatographic Peaks .......................................7-4

7.1.3 Determining if a Peak is Background Noise ............................ 7-8

7.2 Voyager Data Examples

7.2.1 Detecting and Labeling Partially Resolved Peaks ..................7-11

7.2.2 Processing Before Calibrating to Optimize Mass Accuracy ...7-14

7.2.3 Detecting Peaks from Complex Digests ................................7-18

.......................................................... 7-11

Chapter 8 Viewing Voyager PSD D ata

8.1 Displaying PSD Data ............................................................... 8-2

8.2 Applying Fragment Labels

8.3 Calibrating a PSD Spectrum

8.3.1 Checking Peak Detection ......................................................8-11

8.3.2 Calibrating ............................................................................8-12

8.3.3 Creating PSD Calibration (.CAL) Files and

Applying to Other Data Files .................................................8-20

8.3.4 Creating PSD Calibration Reference (.REF) Files .................8-21

8.3.5 Changing the Precursor Mass ...............................................8-23

......................................................... 8-8

..................................................... 8-10

Chapter 9 Troubleshooting

9.1 Overview .............................................................................. 9-2

9.2 General Troubleshooting

9.3 Processing, Tools, and Applications Troubleshooting

9.4 Calibration Troubleshooting

9.5 Printing Troubleshooting

9.6 Peak Detection and Labeling Troubleshooting

.......................................................... 9-3

....................... 9-6

...................................................... 9-10

.......................................................... 9-14

............................... 9-15

viii Applied Biosystems

Table of Contents

Appendix A Warranty Information ........................................ A-1

Appendix B Overview of Isotopes........................................ B-1

Appendix C Data Explorer Toolbox

(Visual Basic Macros)

......................................................... C-1

C.1 Overview C.2 Preparing Data Before Accessing Macros C.3 Accessing the Macros C.4 Using the Ladder S equencing Toolbox C.5 Using the Peptide Fragmentation Toolbox C.6 Using the Polymer Analysis Toolbox C.7 Using MS Fit/MS Tag Toolbox

.............................................................................. C-2

.............................................................. C-4

.................................................. C-18

Index

..................................... C-3

......................................... C-5

..................................... C-9

.......................................... C-15

Data Explorer

™

Software User’s Guide ix

Table of Contents

x Applied Biosystems

How to Use This Guide

Purpose of

this guide

The Applied Biosystems Data Explorer ™ Software User’s Guide describes processing and analyzing data with the

Data Explorer software. You can use the Data Explorer software to analyze data collected on:

• Mariner

software

• Voyager Version 5.0 and later software

™

Workstations with Version 3.0 and later

™

-DE Biospectrometry™ Workstations with

Audience This guide is intended for novice and experienced Mariner

or Voyager workstation users who are analyzing biomolecules.

Structure of

this guide

Chapter/Append ix Content

Chapter 1, Data Explorer™ Basics Describes file formats, file management, the

The Applied Biosystems Data Explorer ™ Software User’s Guide is organized into chapters and appendixes. Each chapter page is marked with a tab and a header to help you find information.

The table below describes the material covered in each chapter and appendix.

parts of the Data Explorer window, and how to customize the Data Explorer software.

Chapter 2, Using Chromatogram and Spectrum Windows

Chapter 3, Peak Detection and Labeling

Chapter 4, Examining Chromatogram Data

Describes window and trace handling. Also describes saving results.

Provides background information on peak detection, centroiding, and integration. Describes peak detection, peak labeling, and peak deisotoping.

Describes processing and analyzing chromatographic data.

™

Data Explorer

Software User’s Guide xi

How to Use This Gu ide

Chapter/Append ix Content

Chapter 5, Examining Spectrum Data

Chapter 6, Using Tools and Applications

Chapter 7, Data Explorer Examples Includes specific examples for Mariner data

Chapter 8, Viewing Voyager PSD Data

Chapter 9, Troubleshooting Includes symptoms and possible causes of,

Describes processing and analyzing mass spectral data.

Describes how to generate results using several tools and applications: the Centroid calculator, Elemental Composition calculator, Isotope calculator, Mass Resolution calculator, Ion Fragmentation calculator and Signal-to-Noise calculator. Also describes using the Macro Recorder and the Elemental Targeting Application.

and Voyager data. Examples include how to improve the signal-to-noise ratio for reserpine, deconvolute unresolved peaks in cyctochrome c (Mariner data), and label partially resolved peaks (Voyager data).

Describes how to view, label, and calibrate PSD data.

and corrective actions for potential system

problems. Appendix A, Warranty Provides warranty and service information. Appendix B, Overview of Isotopes Includes background information you need

for understanding isotopes.

Appendix C, Data Explorer Toolbox (Visual Basic Macros)

xii Applied Biosystems

Describes loading Visual Basic

preparing data, and running the macros.

macros,

How to Use This Guide

Conventions This guide uses the following conventions to make text

easier to understand.

• Bold indicates user action. For example: Type 0 and press Enter for the remaining

fields.

• Italic text denotes new or important words, and is also

used for emphasis. For example:

Before analyzing, always prepare fresh matrix.

Notes, Cautions,

Warnings, and

Hints

A note provides important information to the operator. For example:

NOTE: If you are prompted to insert the boot diskette into the drive, insert it, then press any key.

A caution provides information to avoid damage to the system or loss of data. For example:

CAUTION

Do not touch the lamp. This may damage the lamp.

A warning provides information essential to the safety of the operator. For example:

WARNING

CHEMICAL HAZARD. Wear appropriate personal

protection and always observe safe laboratory practices when operating your system.

A hint provides helpful suggestions not essential to the use of the system. For example:

Hint: To avoid complicated file naming, use Save First to Pass or Save Best Only modes.

™

Data Explorer

Software User’s Guide xiii

How to Use This Gu ide

documentation

The related documents shipped with your system include:

• Mariner

document to learn detailed information about the Mariner Workstation.

• Voyager User’s Guide—Use this document to learn detailed

information about the Voyager-DE Workstation.

• Printer documentation (depends on the printer you purchase)—Use this documentation to set up and service your printer.

• Microsoft

related documents—Use this guide to learn detailed information about the Microsoft Windows NT user interface.

™

Workstation User’s Guide—Use this

™

-DE Biospectrometry Workstation

Windows NT® User’s Guide and

Send us your

comments

We welcome your comments and suggestions for improving our manuals. You can send us your comments in two ways.

• On the web at:

www.appliedbiosystems.com/about/contact.html

• By e-mail at:

T echPubs@appliedbiosystems.com

xiv Applied Biosystems

1 Data Explorer™

Basics

This chapter contains the following sections:

1.1 Overview................................................... 1-2

1.2 File Formats and Types ............................. 1-5

1.3 Parts of the Data Explorer Window.......... 1-11

1.4 Customizing the Data Explorer Window... 1-17

1.5 Setting Graphic Options .......................... 1-23

1.6 Managing Files........................................ 1-30

Chapter

Data Explorer™ Software User’s Guide 1-1

Chapter 1 Data Explorer™ Basics

1.1 Overview

Description The Data Explorer

graphical software that you use to analyze, calibrate, and report data. You can use the Data Explorer software to analyze data collected on:

• Mariner

• Voyager

Features Data Explorer software includes a suite of tools and

processing options to allow you to graphically and interactively manipulate chromatogra phi c and mas s spec tr al data. For example, you can:

• Smooth and noise-filter data.

™

Version 4.0 processing software is

™

Workstations

™

-DE Biospectrometry™ Workstations

NOTE: Application systems that automatically acquire and process data, such as Mariner High Throughput Analysis Option (CombiSolve Solution 1 Explorer software.

™

Option, require specific versions of Data

™

) and Proteomics

1-2 Applied Biosystems

• Automatically and manually calibrate spectral data.

• Set peak detection parameters and custom labels for

regions of the trace. Detected peaks can be evaluated for charge-state determination according to user-defined parameters.

• Determine elemental composition, theoretical isotope distributions, resolution, signal-to-noise ratio, and fragment ions.

• Perform target compound analysis (elemental targeting).

• Customize windows, toolbars, and traces.

• Create scripts and macros to automate your work using

the Macro Recorder and Visual Basic

Editor.

Overview

Starting and

exiting the

software

To start the Data Explorer software from the Windows NT desktop, double-click the Data Explorer icon on the desktop. The Data Explorer window opens.

The Data Explorer window is blank with only a few menus displayed until you open a data file.

Figure 1-1 shows the Data Explorer main window with a Mariner data file open. Figure 1-2 shows the Data Explorer main window with a Voyager data file open.

To exit th e so ftw are, se lect Exit from the File menu in the Data Explorer window. The Data Explorer software closes.

Figure 1-1 Data Explorer Window with Mariner Data

™

Data Explorer

Software User’s Guide 1-3

Chapter 1 Data Explorer™ Basics

Figure 1-2 Data Explorer Window with Voyager Data

Default colors The default colors are different for Mariner and Voyager:

• Mariner—Black background, yellow traces, and green labels

• Voyager—White background, blue traces, and red labels

You can customize the default colors as needed. See Section 1.5.1, Changing Background Color.

NOTE: For consistency, all Mariner and Voyager screen examples in the following sections of this User’s Guide are shown with a white background.

1-4 Applied Biosystems

File Formats and Types

1.2 File Formats and Types

This section describes:

• Software applications compati bility

• Data (.DAT) file format

1.2.1 Software Applications Compatibility

You can use the Data Explorer Macro Recorder function to create Visual Basic scripts to automate tasks. You can also use the Visual Basic Editor directly to create more complex programs customized to suit your needs. For more information, see Section 6.7, Using the Macro Recorder.

Additionally, you can convert data to ASCII format for import into other software applications or import ASCII results. For more information, see Section 1.6.3, Converting to and Exporting ASCII Data, and Section 1.6.4, Importing a Trace in ASCII Format.

1.2.2 Data (.DAT) File Format

.DAT file format Data generated by Mariner and Voyager systems is stored in

.DAT file format. The .DAT file format incorporates all information about how a data file was acquired and processed into a single file. This format improves data processing and data storage efficiency.

Data files can contain spectra from a single acquisition or from multiple acquisitions (for example, multiple spectral data from a Voyager acquisition or multiple injection results from a Mariner CombiSolv run).

™

Data Explorer

Software User’s Guide 1-5

Chapter 1 Data Explorer™ Basics

Mariner .SPC file

format

Voyager .MS file

format

Extracting

information from

.DAT files

Table 1-1 Information Stored In a .DAT File

In Mariner software versions earlier than version 3.0, data files are stored in .SPC format. You can view and process .SPC files in Data Explorer, or you can convert these files to .DAT format. For information about the differences between the .DAT and the .SPC formats, see the Mariner User’s Guide.

In Voyager software versions earlier than version 5.0, data files are stored in .MS, .MSF, .MSA, and .MSB format. You can view and process .MS, .MSF, .MSA, and .MSB files in Data Explorer. You cannot convert them to .DAT format.

NOTE: Voyager .SPC format files are not s upported in the Data Explorer software.

You can also store parameter settings in separate files by extracting information from a .DAT file as needed for use with other files. For more information, see Section 1.6.5, Extracting and Saving Information from .DAT, .RSD, and .RCD Files.

The types of information stored in a .DAT file are described below.

™

Workstation

Category File Type File Content

Settings .BIC Instrument settings for controlling the operation of the

mass analyzer. For more information, see the:

• Mariner Workstation User’s Guide

• Voyager Biospectrometry Workstation User’s

Guide

1-6 Applied Biosystems

Table 1-1 Information Stored In a .DAT File (Continued)

Category File Type File Content

File Formats and Types

Settings

(continued)

Display .LBC Chromatogram label information. See Section 3.5.3,

Process .CAL Calibration constants generated by mass calibration.

.MSM (Mariner only)

.SET Graphic and processing settings. See Section 1.4.2,

.LBS Spectrum label information. See Section 3.5.3, Setting

MS Method settings, if data was acquired using an .MSM file.

NOTE: To access the instrument settings used to acquire each spectrum in an MS Method, you must first extract the .MSM file from the data file, then export the .BIC files from the .MSM file using the Export button in the MS Method editor. For more information on exporting a .BIC file from an .MSM file, see the Mariner Workstation User’s Guide.

Customizing Processing and Graphic Settings (.SET).

Setting Custom Peak Labels.

Custom Peak Labels.

For more information, see “Exporting .BIC, .MSM, and .CAL files” on page 1-36, and “Applying new constants to additional files” on page 5-16.

.CTS Processed trace that you access by selecting

Processing History from the Display menu. For information, see Section 2.4.7, Recalling and Rearranging Traces (Processing History).

NOTE: You select the name of the trace from the Processing History menu. You do not directly select a .CTS file. To purge or disable .CTS files, see “Setting Processing History options” on page 2-23.

™

Data Explorer

Software User’s Guide 1-7

Chapter 1 Data Explorer™ Basics

Additional files

types

Category File Type File Content

Data .PKT Text file containing a chromatogram or a spectrum peak

.TXT Data file exported to an ASCII text file. See

Data .SPC

(Mariner only)

.MS (Voyager only)

Additional file types you may see on your system are described below.

Table 1-2 Additional File Types

list that you can save from the Output window. See “Output window” on page 1-15.

Section 1.6.3, Converting to and Exporting ASCII Data. Data file format for files acquired before Version 3.0 of

the Mariner Instrument Control Panel.

NOTE: Voyager data files in .SPC format have a file structure different from Mariner data files in .SPC format, and are not supported in the Data Explorer software.

Data file format for files acquired before Version 5.0 of the Voyager Instrument Control Panel.

.MSA and .MSF (Voyager only)

.MSB (Voyager only)

Procedure .TUN

(Mariner only)

1-8 Applied Biosystems

PSD data file format for composite and fragment files acquired before Version 5.0 of the Voyager Instrument Control Panel.

NOTE: The Data Explorer software cannot generate composite spectra from .MSF fragment files.

Baseline-corrected data file format for composite and fragment files acquired before Version 5.0 of the Voyager Instrument Control Panel.

AutoTune method. See the Mariner Workstation User’s

Guide.

File Formats and Types

Table 1-2 Additional File Types (Continued)

Category File Type File Content

Reference .REF List of masses to select from during calibration. See

“Creating and saving a calibration reference file” on page 5-18.

Process .RCT

(Mariner only)

.RST Results file saved from:

Results file saved from:

• Mariner .SPC format data file (versions earlier than 3.0) in the Data Explorer software after a chromatogram is manually processed.

See Section 2.8, Saving, Opening, and Deleting .SPC Results Files (Mariner Data Only).

• Mariner .DAT format data file (version 3.0 and later) in the Mariner Instrument Control Panel for a snapshot of chromatogram data.

NOTE: Results for a .DAT file are stored within the .DAT file, not as a separate file.

• Mariner .SPC format data file (versions earlier than 3.0) in the Data Explorer software after a spectrum is manually processed.

See Section 2.8, Saving, Opening, and Deleting .SPC Results Files (Mariner Data Only).

• Voyager .MS format data file in the Data Explorer software after a spectrum is manually processed.

• Mariner .DAT format data file (version 3.0 and later) in the Mariner Instrument Control Panel for a snapshot of spectrum data.

NOTE: Results for a .DAT file are stored within the .DAT file, not as a separate file.

Data Explorer

™

Software User’s Guide 1-9

Chapter 1 Data Explorer™ Basics

Table 1-2 Additional File Types (Continued)

Category File Type File Content

Process

(continued)

.RCD Chromatogram results file exported from .DAT files. See

Section 2.7, Exporting, Opening, and Deleting .RCD and .RSD Results Files (Mariner Data Only).

.RSD Spectr um results file exported from .DAT files. See

Section 2.7, Exporting, Opening, and Deleting .RCD and .RSD Results Files (Mariner Data Only).

1-10 Applied Biosystems

1.3 Parts of the Data Explorer Window

This section describes:

• Overview

• Toolbar

• Chromatogr am and Spe ctru m windows

• Tabs for data files

• Data file names

• Output window

Overview Figure 1-3 shows the Data Explorer window with Mariner data.

Toolbar

Chromatogram

window

Parts of the Data E xplorer Window

Data file name

Spectrum

window

Tabs for

open data files

Output

window

Figure 1-3 Parts of the Data Explorer Window

™

Data Explorer

Software User’s Guide 1-11

Chapter 1 Data Explorer™ Basics

Toolbar The toolbar contains buttons that access Data Explorer

functions. For a description of a toolbar button, place the cursor on the

button. A brief description of the button (ToolTip) is displayed below the button.

For information on adding or removing toolbar buttons, see “Customizing toolbars” on page 1-21.

Chromatogram

and Spectrum

windows

Table 1-3 Mariner Data Displayed in Chromatogram and Spectrum Windows

Window Mariner Data

CHRO Displays:

• Total Ion Chromatogram—Includes the entire mass range saved in the data file.

• Extracted Ion Chromatogram (XIC) (optional)—Includes only the signal response from a mass window or range

• Constant Neutral Loss Chromatogram (CNL) (optional)—Extr a c ts only the response from peaks that are separated by a selected mass difference.

Optionally displays the following from Diode Array data (DAD):

• Total Absorbance Chromatogram (TAC)

• Channel (Ch)

• Extracted Absorbance Chromatogram (XAC)

Can be displayed as % Intensity versus Retention Time or Spectrum number by selecting Traces from the Display menu, then selecting X Axis In, then selecting Spectrum Number or Time.

Refer to the following tables for descriptions of the types of data that you can display in the Chromatogram (CHRO) and Spectrum (SPEC) windows:

• Mariner data—Table 1-3

• Voyager data—Table 1-4

1-12 Applied Biosystems

Parts of the Data E xplorer Window

Table 1-3 Mariner Data Displayed in Chromatogram and Spectrum Windows

(Continued)

Window Marin er D ata

SPEC Displays the spectrum for the selected time in the TIC or TAC trace. By

default, displays spectrum #1. The trace label includes “DAD” for spectra selected from TAC.

Indicates Base Peak (BP) mass and intensity for the tallest peak in the spectrum. Displayed as % Intensity versus Mass-to-Charge (m/z). The right axis is scaled to the intensity of the base peak.

Table 1-4 Voyager Data Displayed in Chromatogram and Spectrum Windows

Window Voyager Data

CHRO Window is not displayed by default.

Optionally displays Total Ion Current (TIC) for multiple spectra .DA T files if you select Restore Chromatogram from the View menu.

NOTE: DAD functions are not supported for Voyager data.

SPEC Depends on the type of data file you open:

• Single spectrum files—Displays the spectrum and labels the plot as spectrum #1.

• Multiple spectrum files—Displays the spectrum for the selected time in the TIC trace (if displayed). By default, displays spectrum #1.

• PSD files—Displays the composite spectrum and labels it as Stitched PSD. You can display segment spectra by clicking

and .

Indicates Base Peak (BP) mass and intensity for the tallest peak in the spectrum. Displayed as % Intensity versus Mass-to-Charge (m/z). The right axis is scaled to the intensity of the base peak.

Data Explorer

™

Software User’s Guide 1-13

Chapter 1 Data Explorer™ Basics

Labels in the chromatogram or spectrum title identify the type of data displayed in the window. For a description of labels, see Section 2.4.10, Viewing Trace Labels.

For more information on Chromatogram and Spectrum windows, see Chapter 2, Using Chromatogram and Spectrum Windows.

Context-sensitive

menus

The commands displayed on the menus in the Data Explorer window depend on the window that is active when you select the menu:

• Only Mariner-related commands are displayed on menus when you open a Mariner .DAT file.

• Only Voyager-related comma nds are displ ay ed on menus when you open a Voyager .DAT file.

• Only spectrum-related commands are displayed if you select menus when the Spectrum window is active.

• Only chromatogram-related commands are displayed if you select menus when the Chromatogram window is active. For Voyager multiple spectra .DAT files, UV functions are disabled.

Tabs for data files Chromatogram and Spectrum windows display a tab at the

bottom (see Figure 1-3 on page 1-11) that allow you to switch between data files, or between Chromatogram and Spectrum windows for a Mariner data file. See “Moving Between Open Files” on page 2-8.

Data file names Data file names are displayed in the:

• Title bar of each window

• Tab for each window

1-14 Applied Biosystems

NOTE: If the full name of the data file does not fit in the tab, part of the name is displayed followed by “...”. To display the full name of the data file, place the cursor on the tab. The full name of the data file is displayed below the tab.

Parts of the Data E xplorer Window

Output window The Output window (see Figure 1-3 on page 1-11) displays

tabs at the bottom that you can click to switch between the types of information displayed:

Output wind ow

tabs

• Result—Displays results generated using commands on the Process, Tools, and Applications menus. For more information on results, see:

• Section 5.3, Manual Calibration, or Section 5.4, Automatic Calibration

• Section 5.6, Mass Deconvolution (Mariner Data Only)

• Section 6.2, Using the Isotope Calculator

• Section 6.3, Using the

Mass Resolution Calculator

• Section 6.4, Using the Signal-to-Noise Ratio Calculator

• Chro Peak List —Displays results of chromatogram peak detection and integration. For more information, see Section 3.3, Peak List.

• Spectrum Peak List—Displays results of spectrum peak detection, integration, and centroiding. For more information, see Section 3.3, Peak List.

• Sample Info—For data files, displays the:

• Software version used for acquisition

• Acquisition time and sample comments entered

when data was acquired

For result files (.RCT, .RST, .RCD, .RSD), displays any processing functions that have been performed and saved in the result file.

™

Data Explorer

Software User’s Guide 1-15

Chapter 1 Data Explorer™ Basics

• Instrument Setting—Displays a list of instrument settings used to obtain the data. The settings are taken from instrument settings pages in the Instrument Control Panel. Also displays segments, event numbers, and event tags from Mariner MS Method acquisitions and LC information if LCMS was acquired using Mariner.

• Elemental Analysis—Displays results for the Elemental Composition calc ula tor. For information, see Section 6.1, Using the Elemental CompositionCalculator.

• Elemental Targeting—Displays results for the Elemental Targeting application. For information, see Section 6.6, Using the Elemental Targeting Application.

Displaying,

clearing, and

closing

The Output window is automatically displayed when you generate results (for example, when you calculate resolution).

To display the Output window manually, select Output Window from the View menu.

To clear the Output window, right-click the Output window, then select Clear Window.

To close the Output window, deselect Output Window from the View menu, or right-click the Output window, then select Hide.

Hint: To maximize the Chromatogram and Spectrum windows after hiding the Output window, click or in the toolbar.

1-16 Applied Biosystems

+ 417 hidden pages