BD CellQuest Pro Software User's Guide

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Transcript of BD CellQuest Pro Software User's Guide

  • http://www.bdbiosciePart No. 349226 Rev. AJuly 2002

    BD Biosciences2350 Qume DriveSan Jose, CA 95131-1807USATel (877) 232-8995Fax (408) 954-2347BD CellQuest ProSoftware

    Users Guidences.com/

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  • 2002, Becton, Dickinson and Company. All rights reserved. No part of this publication may be reproduced, transmitted, transcribed, stored in retrieval systems, or translated into any language or computer language, in any form or by any means: electronic, mechanical, magnetic, optical, chemical, manual, or otherwise, without prior written permission from BD Biosciences.

    The information in this guide is subject to change without notice. BD Biosciences reserves the right to change its products and services at any time to incorporate the latest technological developments. Although this guide has been prepared with every precaution to ensure accuracy, BD Biosciences assumes no liability for any errors or omissions, nor for any damages resulting from the application or use of this information. BD Biosciences welcomes customer input on corrections and suggestions for improvement.

    BD CellQuest Pro software 2002, Becton, Dickinson and Company. This software is the property of Becton, Dickinson and Company. Each sale of a stored unit of this software grants the purchaser a nontransferable, nonexclusive, personal license. This software may not be duplicated, reproduced, or copied in any form or by any means whatsoever, except as otherwise permitted by law.

    This program was written with MacApp, Apple Computer, Inc. The MacApp software is proprietary to Apple Computer, Inc. and is licensed to BD Biosciences for distribution only for use in combination with this software.

    Apple Computer, Inc. makes no warranties whatsoever, either expressed or implied, regarding this product, including warranties with respect to its merchantability or its fitness for any particular purpose.

    BD, the BD logo, BD CaliBRITE, BD CellQuest, BD CloneCyt, BD FACS, BD FACSCalibur, BD FACScan, BD FACSComp, BD FACSConvert, BD FACSDiVa, BD FACSort, BD FACStation, BD FACSVantage, BD MultiSET, BD ProCOUNT, BD QuantiBRITE, and BD SimulSET are trademarks of Becton, Dickinson and Company.

    Apple, Mac, Macintosh, and Power Macintosh are trademarks of Apple Computer, Inc., registered in the US and other countries. Finder is a trademark of Apple Computer, Inc.

    Adobe and Acrobat are registered trademarks of Adobe Systems Incorporated.

    All other company and product names might be trademarks of the respective companies with which they are associated.

    Guide updated by Linda Jackson; edited by Kim Gautho; produced by Pushpa MacFarlane.

    History

    Revision Date Change Made

    A 11/00 New software features

    349226 8/02 Revised for Mac OS X

  • Contents

    About This Guide ix

    Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

    Technical Assistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

    Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

    Chapter 1: Introduction 13

    Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

    Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

    Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

    Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

    Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

    Other Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

    Installing BD CellQuest Pro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

    Installing BD Inits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

    Launching BD CellQuest Pro Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

    Registering the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

    Quitting BD CellQuest Pro Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

    Chapter 2: Becoming Familiar with BD CellQuest Pro Software 23

    BD CellQuest Pro Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

    Default File Naming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

    Experiment Document Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

    Tool Palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

    View Area Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30iii

  • Inspector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

    Changing Text Style and Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

    Changing Object Geometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

    Customizing Experiment Documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

    Document Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

    Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

    Text Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

    Color Palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

    Banners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

    Grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

    Chapter 3: BD CellQuest Pro Plots 49

    Plot Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

    Creating Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

    Deleting Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

    Formatting Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

    Dot Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

    Contour Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

    Density Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

    3D Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

    Plot Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

    Formatting Histograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

    Creating Overlaid Histograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

    Using Histogram Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

    Saving Experiment Documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

    Saving Experiment Documents as Templates . . . . . . . . . . . . . . . . . . . . . 73

    Saving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75iv BD CellQuest Pro Software Users Guide

  • Chapter 4: Optimizing Instrument Electronics 77

    Performing Instrument Quality Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

    Instrument Controls in BD CellQuest Pro . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

    Adjusting Instrument Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

    Adjusting Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

    Adjusting Amplifiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

    Adjusting Threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

    Adjusting Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

    Optimizing the Instrument for Biological Samples . . . . . . . . . . . . . . . . . . . . 85

    Starting Up the Cytometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

    Setting Up an Acquisition Experiment Document . . . . . . . . . . . . . . . . . . 86

    Restoring Calib Settings to the Cytometer . . . . . . . . . . . . . . . . . . . . . . . 88

    Adjusting FSC, SSC, and FSC Threshold . . . . . . . . . . . . . . . . . . . . . . . . 90

    Gating on the Population of Interest . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

    Adjusting Fluorescence Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

    Adjusting Fluorescence Compensation . . . . . . . . . . . . . . . . . . . .