Thermo Fisher Scientific ImageQuest 1.0.1 User guide

Thermo ImageQuest

Version 1.0.1

User Guide

XCALI-97200 Revision B May 2009

Xcalibur is a registered trademark of Thermo Fisher Scientific Inc. in the United States.

Microsoft and Windows are registered trademarks of Microsoft Corporation in the United States and other

countries.

LTQ XL, LTQ-Orbitrap, and ImageQuest are trademarks of Thermo Fisher Scientific.

All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.

Samples courtesy of Roswell Park Cancer Institute, Buffalo, NY.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the

product operation. This document is copyright protected and any reproduction of the whole or any part of this

document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this

document is for reference purposes only. System configurations and specifications in this document supersede

all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-

free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might

result from any use of this document, even if the information in the document is followed properly.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This

document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of

Sale shall govern all conflicting information between the two documents.

Release history: ImageQuest 1.0.1

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

Thermo Scientific ImageQuest User Guide iii

C

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v

Chapter 1 Overview of ImageQuest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

The ImageQuest Main Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Using ImageQuest Views. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Optical View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Ion Chromatogram View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Two Dimension View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Three Dimension View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Spectrum View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Averaging Spectra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Data Set Tree View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Sky View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Using the Cursor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Chapter 2 Using ImageQuest to Process Images. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Changing the Spectra View Range. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Changing an Optical Image View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Changing the 2D Setup View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

2D View Impact on Other Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Changing the 3D View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Changing a Combo File View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Chapter 3 Working with MALDI Files and Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Working with Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Viewing Data from a Raw File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Opening a Raw File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Working with Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Creating a New Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Editing a Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Overlaying Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Animating Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Printing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Saving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Opening a Previously Extracted Data File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Contents

iv ImageQuest User Guide Thermo Scientific

Appendix A ImageQuest Reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35

Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Toolbar Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

File Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

View Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Spectrum View buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Spectrum Rescaling Buttons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Data Set Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

ImageQuest Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Scale Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

2D View Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

3D View Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Dialog Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Create New Data Set Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

ImageQuest Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Spectrum Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Mass Tolerance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Information View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Data Set View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Raw File View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Position File View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Tune Method View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Instrument Method View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Scan Header View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Spectrum List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Status Log View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Error Log View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Thermo Scientific ImageQuest User Guide v

P

Preface

This guide describes how to use ImageQuest™ to process and analyze tissue imaging data from

a MALDI instrument on LTQ XL and LTQ-Orbitrap mass spectrometers.

To provide us with comments about this document, please click the link below. Thank you in

advance for your help.

Contents

•Related Documentation

•Product Requirements

•Contacting Us

Preface

vi ImageQuest User Guide Thermo Scientific

Related Documentation

Thermo ImageQuest includes Help and these manuals as PDF files:

• Thermo ImageQuest Help

• Thermo ImageQuest User Guide

YTo view product manuals

Go to Start > All Programs > Thermo ImageQuest > ImageQuest Manual. After

installation, the manual can be located at

C:\Program Files\Thermo\ImageQuest\Manual\ImageQuest.pdf.

YTo open Help

• From the Thermo ImageQuest window, choose Help > ImageQuest Help.

• If available for a specific window or dialog box, click Help or press F1 for

information about setting parameters.

For more information, including upcoming application notes, visit www.thermo.com.

Product Requirements

You can run ImageQuest on a computer connected to a Thermo Scientific instrument or on a

separate workstation computer. To run ImageQuest, you must meet these minimum

requirements:

System Requirements

PC • 2 GHz processor with 2GB RAM

•CD-ROM drive

• Video card and monitor capable of 1280x1024 resolution (XGA)

• 75 GB or greater available on the C: drive

•NTFS format

Instrument

(supported or

required)

• MALDI on LTQ XL™

• MALDI on LTQ-Orbitrap™

Software • Microsoft® Windows® XP Professional with Service Pack 2

• Xcalibur™ 2.0.5 or higher

•LTQ 2.5

Preface

Thermo Scientific ImageQuest User Guide vii

Contacting Us

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

YTo contact Technical Support

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

YTo contact Customer Service for ordering information

YTo copy manuals from the Internet

Go to mssupport.thermo.com and click Customer Manuals in the left margin of the

window.

YTo suggest changes to documentation or to Help

• Fill out a reader survey online at www.thermo.com/lcms-techpubs.

• Send an e-mail message to the Technical Publications Editor at

techpubs-lcms@thermofisher.com.

Phone 800-532-4752

Fax 561-688-8736

E-mail us.techsupport.analyze@thermofisher.com

Knowledge base www.thermokb.com

Phone 800-532-4752

Fax 561-688-8731

E-mail us.customer-support.analyze@thermofisher.com

Web site www.thermo.com/ms

Thermo Scientific ImageQuest User Guide 1

1

Overview of ImageQuest

The Thermo™ ImageQuest software supports MALDI tissue imaging on LTQ XL and

Orbitrap mass spectrometers, providing the ability to analyze, manipulate, and process tissue

imaging data in a targeted analytical procedure that makes it easier to identify the intensity

and location of an analyte. ImageQuest does the following:

• Displays MALDI images in two- and three-dimensional figures

• Displays the tissue optical image and supports image manipulation including overlap of

images

• Provides ion chromatogram and MSn spectra visualizations of the 2D-image

• Saves extracted data

• Prints files

• Exports figures to the clipboard

This chapter provides information about the ImageQuest main window, its views, functions,

and features:

Contents

•The ImageQuest Main Window

•Using ImageQuest Views

•Using the Cursor

1 Overview of ImageQuest

The ImageQuest Main Window

2ImageQuest User Guide Thermo Scientific

The ImageQuest Main Window

The ImageQuest main window (see Figure 1) consists of the following:

• A title bar containing the sample name and the application name

•A menu bar

• A toolbar

• The selected view - Tool buttons provide access to specific views or view all options.

For example, click to display the 2D view.

Figure 1. ImageQuest main window

Title bar

Menu bar

Main toolbar

View pages

Status bar

Sky view

Data set area

Histogram

1 Overview of ImageQuest

Using ImageQuest Views

Thermo Scientific ImageQuest User Guide 3

Using ImageQuest Views

The Main screen also displays the following views:

•Optical View

•Ion Chromatogram View

•Two Dimension View

•Three Dimension View

•Spectrum View

•Data Set Tree View

•Sky View

Figure 2 displays the location of views on the main screen.

Figure 2. ImageQuest views

Two dimension view Three dimension view

Optical view

Ion chromatogram

view

Spectra

view

1 Overview of ImageQuest

Using ImageQuest Views

4ImageQuest User Guide Thermo Scientific

Optical View

In the optical image view, the software displays the scanned positions as blue dots. The

information in this image is contained in the MALDI position file prior to data acquisition.

The software can display the scan dots on top of the optical image depending on the density

of the array.

Figure 3. Optical View

Ion Chromatogram View

The Ion chromatogram view displays intensity in relation to the scan number. Each scan is a

specific location (pixel) on the tissue. Use this view to see where the most intense scans are.

You can select a point in the 1D view to display a spectrum at that point (see Figure 4). The

software also displays the correspondent points in the 2D and optical images.

You can also select a range to average all the spectra at that range. See “Averaging Spectra” on

page 8 for more information. The software also displays the correspondent rectangle over the

selected range in 2D and optical images.

Figure 4. One Dimensional Image

1 Overview of ImageQuest

Using ImageQuest Views

Thermo Scientific ImageQuest User Guide 5

Two Dimension View

Two-dimensional images displays intensity in relation to X and Y axes. In the Rainbow scale,

the intensities are color coded to identify peak intensity: blue and green colors represent a

lower intensity; red and orange colors represent a higher intensity. To change the 2D view, see

“Changing the 2D Setup View” on page 14. Use the two-dimensional image to do these tasks:

• Select any position in the 2D graph and display a spectrum at that point

• Select an area by dragging the cursor over the area to average all the spectra in the area

• Zoom in a selected region, and pan the zoomed region around by dragging the mouse

• Measure a distance between two points

• Get intensity and X and Y coordinates by placing the cursor on the 2D image at a specific

location

Figure 5. Two-dimensional Image

1 Overview of ImageQuest

Using ImageQuest Views

6ImageQuest User Guide Thermo Scientific

Three Dimension View

Three-dimensional images display intensity in relation to the X and Y positions. The

intensities are color coded and presented on the Z-axis. Use this view to see where peaks exist

in a multi-dimensional field or rotate the view to find peaks for further study. Control display

parameters of the three-dimensional object by using the 3D setting tab. See “Changing the

3D View” on page 18. Use the three-dimensional image to rotate the 3D object by quickly

dragging and releasing the mouse. The image rotates in the direction of the mouse movement.

Double-click the object to stop the auto-rotation mode. To make it easier to locate relevant

peaks when examining a new image, rotate the three dimension view to match the two

dimension view.

Figure 6. Three-dimensional Image

1 Overview of ImageQuest

Using ImageQuest Views

Thermo Scientific ImageQuest User Guide 7

Spectrum View

The spectrum view displays mass spectra, making it easy to see the location of peaks. If you

select an area to average spectra, the view displays in red; if you select a single point, the view

displays in black. You can zoom into or out of an area using the toolbar buttons (see

“Changing the Spectra View Range” on page 12).

Figure 7. Spectrum View

1 Overview of ImageQuest

Using ImageQuest Views

8ImageQuest User Guide Thermo Scientific

Averaging Spectra

To find areas of higher general intensity, average spectra within a selected area.

YTo average a spectra

1. Click on the toolbar.

2. In the two dimension view, select the area to average by dragging the cursor diagonally.

ImageQuest outlines the area in the two dimension view.

The Spectrum view shows the averages in red. The Ion Chromatogram view shows the

averages at any one point.

1 Overview of ImageQuest

Using ImageQuest Views

Thermo Scientific ImageQuest User Guide 9

Data Set Tree View

The Data Set view always displays information about the current data sets in the upper left

corner of the main screen. Data sets are files that store specific information, including the

changes you make to raw files. The current data set is highlighted. Use this view to see which

views are available and to determine the composition of combo data sets. It displays the

following information for all current data sets (TIC, mass range, base peak, mass range / TIC)

and displays different ions for different data set types and plot types. Use the toolbar below

the view to create a new data set, edit duplicate sets, or delete a data set. You can only edit

single data sets.

Figure 8. Data Set Tree view

Sky View

ImageQuest displays a two-dimensional image of the current data set with the colors inverted

in the lower left corner of the application. This view helps you to keep track of the high level

view of the image. When you zoom into a specific area, this view always displays the entire

image. Inside the Sky View image, the zoom area appears as a square that you can use to orient

yourself in the zoomed image. To return the two-dimensional view to a full view, double-click

the sky view.

Figure 9. Sky view

Data set toolbar

1 Overview of ImageQuest

Using the Cursor

10 ImageQuest User Guide Thermo Scientific

Using the Cursor

Within the Ion Chromatogram and Spectrum previews, use the cursor in three ways to scale

the display:

• Click in the cell to select a point.

• Drag a line parallel to any axis to select a range.

• Drag a line in any diagonal direction to select an area.

Tabl e 1 describes the effects.

Table 1. Effect of cursor action in an active cell

Cursor Action Effect

Drag parallel to X-axis Rescale a graph showing selected X range only,

retain the same Y range.

Drag parallel to Y-axis Rescale a graph showing selected Y range only,

retain the same X range.

Drag diagonally Rescale a graph showing both the selected X and

Y ranges.

Double-click Close cursor action and return to the original

view.

Thermo Scientific ImageQuest User Guide 11

2

Using ImageQuest to Process Images

This chapter describes how to modify specific image views in the ImageQuest main window

in order to more carefully target your analysis towards the location and intensity of the

analyte.

Contents

•Changing the Spectra View Range

•Changing an Optical Image View

•Changing the 2D Setup View

•Changing the 3D View

•Changing a Combo File View

2 Using ImageQuest to Process Images

Changing the Spectra View Range

12 ImageQuest User Guide Thermo Scientific

Changing the Spectra View Range

You can control the range of the X and Y display axes using either menu commands or toolbar

button commands. Use the following buttons to control the range of the display for spectra

and chromatograms:

Zoom in Y from the current baseline to show more detail.

Zoom out Y to show more data.

Normalize Y intensity scale.

Zoom in X at the center to show more detail.

Zoom out X at the center to show more data.

Display all data on X-axis or all text in report.

Reset scaling to full scale for both X- and Y-axes.

Display Y-axis data in normalized mode.

Display Y-axis in creep mode.

Display Y-axis in fixed mode.

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Thermo Fisher Scientific ImageQuest 1.0.1 User guide

Thermo Fisher Scientific ImageQuest 1.0.1 User guide

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