Document Outline

• PDQuest™
  • Preface
  • 1 . Introduction
    • 1.1 Overview of PDQuest
    • 1.2 Digital Data and Signal Intensity
    • 1.3 PDQuest Workflow
    • 1.4 Computer Requirements
    • 1.5 Installation
    • 1.6 Hardware Security Key (HSK)
    • 1.7 Starting the Program
    • 1.8 Software License
    • 1.9 Downloading from the Internet
    • 1.10 PDQuest Basic
    • 1.11 Contacting Bio-Rad
  • 2 . General Operation
    • 2.1 Graphical Interface
      • 2.1.a Menu Bar
      • 2.1.b Main Toolbar
      • 2.1.c Status Boxes
      • 2.1.d Secondary Toolbars
      • 2.1.e Quick Guide
    • 2.2 Keyboard Shortcuts
    • 2.3 File Commands and Functions
      • 2.3.a File Types in PDQuest
      • 2.3.b MatchSets, Scansets, and Analysis Sets
      • 2.3.c Opening Files
      • 2.3.d Closing files
      • 2.3.e Saving Files
      • 2.3.f Revert to Saved
      • 2.3.g Image Info
      • 2.3.h Reduce File Size
      • 2.3.i Exiting PDQuest
    • 2.4 Printing and Exporting
    • 2.5 Printing
      • 2.5.a Printing Images
      • 2.5.b Print Actual Size
      • 2.5.c Image Report
      • 2.5.d Video Printing
    • 2.6 Exporting
      • 2.6.a Exporting an Image
      • 2.6.b MatchSet Data
      • 2.6.c Exporting Annotations
    • 2.7 Preferences
      • 2.7.a Misc Preferences
      • 2.7.b Path Preferences
      • 2.7.c Display Preferences
      • 2.7.d Toolbar Preferences
      • 2.7.e Application Preferences
      • 2.7.f Imagers
    • 2.8 Mouse-assignable Tools
  • 3 . Viewing and Editing Images
    • 3.1 Windows and Subwindows
    • 3.2 Configuring Subwindows
    • 3.3 Assigning and Interchanging Images
    • 3.4 Tiling Windows
    • 3.5 Magnifying Images
    • 3.6 Positioning Images
      • 3.6.a Advanced View
    • 3.7 Hiding Overlays
    • 3.8 Density Tools
    • 3.9 Colors
    • 3.10 Multi-Channel Viewer
    • 3.11 3D Viewer
    • 3.12 Transform
      • 3.12.a Transform Controls
      • 3.12.b Other Transform Features
    • 3.13 Cropping Images
      • 3.13.a Advanced Crop Commands
    • 3.14 Flipping and Rotating Images
    • 3.15 Filtering Images
      • 3.15.a Filter Wizard
      • 3.15.b Selecting a Filter Directly
    • 3.16 Invert Data
    • 3.17 Text Overlays
  • 4 . Detecting and Editing Spots
    • 4.1 Selecting Spot Detection Parameters
      • 4.1.a Step 1. Give Manual Guidance
      • 4.1.b Step 2. Test Settings
      • 4.1.c Advanced Tab
      • 4.1.d Saving/Loading Parameters
      • 4.1.e Processing Gels
    • 4.2 Detecting Spots
    • 4.3 Filtered and Gaussian Images
    • 4.4 Spot Crosshairs and Ellipses
    • 4.5 Adding and Removing Spots
    • 4.6 Spot Boundary Tools
    • 4.7 Cancelling Spots
    • 4.8 Combining Spots
    • 4.9 Saturated and Faint Spots
    • 4.10 Spot Quantity
    • 4.11 Spot Quality
    • 4.12 Spot Parameters
    • 4.13 Finding Spots
  • 5 . MatchSets
    • 5.1 Creating a MatchSet
      • 5.1.a Create a MatchSet
      • 5.1.b Member Sharing
      • 5.1.c Create a MatchSet from Automated Detection and Matching
    • 5.2 Selecting the Master
    • 5.3 Matching Spots
      • 5.3.a Editing MatchSets
    • 5.4 Landmarking Spots
    • 5.5 Automated Matching
      • 5.5.a Show Symbols
      • 5.5.b Show Vector Offsets
    • 5.6 Cybergels
    • 5.7 Adding Spots to the Master
    • 5.8 Edit Match Submenu
      • 5.8.a Colony Matching
      • 5.8.b Higher Level MatchSets
    • 5.9 Matching Summary
  • 6 . Analysis Tools
    • 6.1 Spot Review Tool
    • 6.2 Image Stack Tool
    • 6.3 Scatter Plot Tool
    • 6.4 Replicate Groups
    • 6.5 Group Consensus
      • 6.5.a Review Individual Spots
      • 6.5.b Achieving Consensus
      • 6.5.c Global Actions
    • 6.6 Sample Database
      • 6.6.a Associating Sample to Gels
      • 6.6.b Classes
      • 6.6.c Copying a Sample Database from another MatchSet
      • 6.6.d Sample Pairs
    • 6.7 Normalization
      • 6.7.a Scaling Factor
      • 6.7.b Normalization Methods
    • 6.8 MrpI Data
    • 6.9 Standard Spot Numbers
    • 6.10 Database Spot Numbers
  • 7 . Analysis Sets and Annotations
    • 7.1 Analysis Sets
      • 7.1.a Analysis Set Manager
      • 7.1.b Creating an Analysis Set
      • 7.1.c Qualitative Analysis Sets
      • 7.1.d Quantitative Analysis Sets
      • 7.1.e Statistical Analysis Sets
      • 7.1.f Arbitrary Analysis Sets
      • 7.1.g Boolean Analysis Sets
      • 7.1.h Matching Analysis Sets
    • 7.2 Annotation Tool
      • 7.2.a Opening the Annotation Tool
      • 7.2.b Annotation Categories
      • 7.2.c Selecting a Category
      • 7.2.d Selecting Spot(s)
      • 7.2.e Entering an Annotation
      • 7.2.f Importing Annotations
      • 7.2.g Reviewing Annotations in the MatchSet
    • 7.3 Browsing Annotations
    • 7.4 Creating Annotations from Analysis Sets
    • 7.5 Printing Annotations
    • 7.6 Transferring Annotations
  • 8 . Basic Excision Tool
    • 8.1 Spot Cutter Setup
      • 8.1.a Focus Cutter Camera
      • 8.1.b Set Cutting Tip Height
      • 8.1.c Spot Cutter Settings
      • 8.1.d Spot Cutter Calibration
    • 8.2 Cutting Spots
      • 8.2.a Step 1. Acquiring the Image
      • 8.2.b Step 2. Specifying Cuts
      • 8.2.c Step 3. Set Cutter Options
      • 8.2.d Step 4. Set Wash Options
      • 8.2.e Performing a Cut Run
      • 8.2.f Recutting Spots
      • 8.2.g Saving the Image
    • 8.3 Other Spot Cutter Controls
  • 9 . Integrated Excision Tool
    • 9.1 Excision Gel Selection
      • 9.1.a Step 1. Select Analysis Set
      • 9.1.b Step 2. Set Selection Mode
      • 9.1.c Step 3. Specify Cuts
      • 9.1.d Performing the Cuts
    • 9.2 Integrated Excision Tool
      • 9.2.a Spot Cutter Setup
      • 9.2.b Spot Cutter Calibration
      • 9.2.c Cutting Spots
      • 9.2.d Exporting the Cut List
  • 10 . Mass Spectrometry Analysis
    • 10.1 Creating a MassLynx Batch File
    • 10.2 Importing MassLynx Results
    • 10.3 Mass Spec Score Overlay
    • 10.4 Protein Probe
    • 10.5 Import Mascot Results
      • 10.5.a Options
  • 11 . Graphs and Reports
    • 11.1 Configure Graphs
      • 11.1.a Adding and Editing Configurations
    • 11.2 Histogram Graphs
      • 11.2.a Data Displayed in the Histogram
      • 11.2.b Types of Graphs
    • 11.3 A-B Overlay
    • 11.4 Quantity Table Report
      • 11.4.a Quantity Graph Report
    • 11.5 Master Image Report
    • 11.6 Scatter Plot Report
  • Appendix A Gel Doc 2000
    • A.1 Gel Doc Acquisition Window
    • A.2 Step I. Position Gel
    • A.3 Step II. Select Image Mode
    • A.4 Step III. Acquire Image
    • A.5 Step IV. Optimize Display
    • A.6 Step V. Analysis
    • A.7 Step VI. Select Output
    • A.8 Exposure Status
    • A.9 Options
  • Appendix B ChemiDoc
    • B.1 ChemiDoc Acquisition Window
    • B.2 Step I. Position Gel
    • B.3 Step II. Image Mode
    • B.4 Step III. Acquire Image
    • B.5 Step IV. Optimize Display
    • B.6 Step V. Analysis
    • B.7 Step VI. Select Output
    • B.8 Exposure Status
    • B.9 Options
  • Appendix C ChemiDoc XRS
    • C.1 ChemiDoc XRS Acquisition Window
    • C.2 Step I. Select Application
      • C.2.a. Custom Applications
    • C.3 Step II. Position Gel
    • C.4 Step III. Acquire Image
      • C.4.a. Exposure Status
    • C.5 Options
      • C.5.a. Imaging Area
      • C.5.b. Reminder
      • C.5.c. Dark Subtraction
      • C.5.d. Save Options
      • C.5.e. Auto-scale Transform
      • C.5.f. Auto Exposure Threshold
    • C.6 Other Features
  • Appendix D GS-700 Imaging Densitometer
    • D.1 GS-700 Acquisition Window
    • D.2 Step I. Select Application
    • D.3 Step II. Select Scan Area
    • D.4 Step III. Select Resolution
    • D.5 Acquire the Image
    • D.6 Calibration
      • D.6.a Editing the Step Tablet
      • D.6.b Calibration Settings
    • D.7 Other Options
  • Appendix E GS-710 Imaging Densitometer
    • E.1 GS-710 Acquisition Window
    • E.2 Step I. Select Application
    • E.3 Step II. Select Scan Area
    • E.4 Step III. Select Resolution
    • E.5 Calibration
      • E.5.a Editing the Step Tablet
      • E.5.b Calibration Settings
    • E.6 Acquire the Image
    • E.7 Other Options
  • Appendix F GS-800 Imaging Densitometer
    • F.1 GS-800 Acquisition Window
    • F.2 Step I. Select Application
    • F.3 Step II. Select Scan Area
    • F.4 Step III. Select Resolution
    • F.5 Calibration
      • F.5.a Step Tablet Values
      • F.5.b Other Calibration Settings
    • F.6 Acquire the Image
    • F.7 Other Options
  • Appendix G Fluor-S MultiImager
    • G.1 Fluor-S Acquisition Window
    • G.2 Step I. Select Application
    • G.3 Step II. Position/Focus
    • G.4 Step III. Set Exposure Time
    • G.5 Acquire the Image
    • G.6 Options
      • G.6.a Dark Subtraction Type
      • G.6.b Live Exposure Mode
      • G.6.c Save
      • G.6.d Imaging Area Size
      • G.6.e Auto-scale Transform
    • G.7 Other Features
  • Appendix H Fluor-S MAX MultiImager
    • H.1 Fluor-S MAX Acquisition Window
    • H.2 Step I. Select Application
    • H.3 Step II. Position/Focus
    • H.4 Step III. Set Exposure Time
    • H.5 Acquire the Image
    • H.6 Options
      • H.6.a Dark Subtraction Type
      • H.6.b Live Exposure Mode
      • H.6.c Save
      • H.6.d Imaging Area Size
      • H.6.e Auto-scale Transform
    • H.7 Other Features
  • Appendix I Personal Molecular Imager FX
    • I.1 Personal FX Acquisition Window
    • I.2 Step I. Select Scan Area
    • I.3 Step II. Select Resolution
    • I.4 Acquire the Image
    • I.5 Options
  • Appendix J Molecular Imager FX Family (FX Pro, FX Pro Plus and Molecular FX)
    • J.1 FX Acquisition Window
    • J.2 Step I. Select Application
      • J.2.a Selecting a Channel
      • J.2.b Selecting an Application
    • J.3 Step II. Select Scan Area
    • J.4 Step III. Select Resolution
    • J.5 Acquire the Image
    • J.6 Options
  • Appendix K VersaDoc
    • K.1 VersaDoc Acquisition Window
    • K.2 Step I. Select Application
      • K.2.a. Selecting a Channel
      • K.2.b. Selecting an Application
    • K.3 Step II. Position/Focus
    • K.4 Step III. Set Exposure Time
    • K.5 Acquire the Image
    • K.6 Options
      • K.6.a. Dark Subtraction Type
      • K.6.b. Save
      • K.6.c. Imaging Area Size
      • K.6.d. Auto-scale Transform
    • K.7 Other Features
  • Appendix L Calibration and Merging
    • L.1 Calibrating Gels
      • L.1.a Calibration Strip Data
      • L.1.b Scan Information
      • L.1.c Sampling the Calibration Strip Segments
      • L.1.d Plot the Calibration Curve
      • L.1.e Repeat for Each Calstrip
    • L.2 Merging Multiple Exposures
  • Appendix M Cross-Platform File Exchange
    • M.1 Macintosh to PC
    • M.2 PC to Macintosh