Manual

Delta2D 4.0

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DECODON GmbH

December 2008
Copyright ©2000-2008 DECODON GmbH. DECODON makes no representations, express or implied, with respect to this documentation or the software it describes, including without limitations, any implied warranties of merchantability or fitness for a particular purpose, all of which are expressly disclaimed. Users should recognize that all complex software systems and their documentation contain errors and omissions. DECODON shall not be responsible under any circumstances for providing information on or corrections to errors and omissions discovered at any time in this document or the software it describes, whether or not they are aware of the errors and omissions. DECODON does not recommend the use of the software described in this document for applications in which errors or omissions could threaten life, injury or significant loss. DECODON, the DECODON logo, Delta2D, SmartVectors are trademarks or registered trademarks of DECODON GmbH in Germany and in several other countries all over the world. The use of general descriptive names, trademarks, etc., in this publication, even if the former are not especially identified, is not to be taken as a sign that such names, as understood by the Trade Marks and Merchandise Marks Act, may accordingly be used by anyone. Where those designations appear in this work and DECODON was aware of a trademark claim, the designations follow the capitalization style used by the manufacturer. Linux is a trademark of Linus Torvalds. Apple, Mac, MacOS, Macintosh are trademarks of Apple Computer, Inc., registered in the U.S. and other countries. JAVA and Solaris are registered trademarks of Sun Microsystems, Inc., 901 San Antonio Road, Palo Alto, CA 94303 USA. Microsoft, WINDOWS, NT, PowerPoint, Excel, Vista are registered trademarks of Microsoft Corporation. UNIX is a registered trademark of The Open Group. All other products mentioned are trademarks or registered trademarks of their respective companies. Some software products marketed by DECODON GmbH and its distributors may contain proprietary software components of other software vendors.

About Delta2D
 The Challenge
 Delta2D: Dedicated to Innovation
 Modern User Interface
How to use this manual
Contents
1 Strategy for Analyzing Gel Images with Delta2D
2 Install and start Delta2D
 2.1 Available Computing Platforms
 2.2 Installation Steps for Microsoft Windows
 2.3 Start Delta2D
 2.4 License Registration
 2.5 Adjusting Memory Settings
 2.6 Checking for Software Updates
 2.7 Updating an Existing Installation of Delta2D
3 Workflow of Delta2D 4.0
 3.1 Setup Project
 3.2 Setup Gel Image Warping
 3.3 Create Direct Warpings
 3.4 Create the Consensus Spot Pattern
 3.5 Analyze Expression Profiles
 3.6 Present Results
 3.7 Exporting Results to Other Applications
4 Main Menu and Toolbars
 4.1 The Main Menu
 4.2 The Main Toolbar
5 The Windows
 5.1 Workflow
 5.2 Project Explorer
 5.3 Light Table
 5.4 Warping Setup
 5.5 Dual View
 5.6 Quantitation Table
 5.7 Gel Image Regions
 5.8 Expression Profiles
 5.9 Color Coding
 5.10 Job Manager
 5.11 Analysis
 5.12 Project Matrix
 5.13 Arrange Windows
6 The Gel Pool
 6.1 Adding Gel Images to the Pool
 6.2 Assigning Gel Image Attributes
7 Image Fusion
 Why image fusion makes your work much more efficient
 Image fusion algorithms
8 Working with Spots
 8.1 Sorting and Selecting Spots
 8.2 Selecting Spots in the Dual View
 8.3 Hiding Spots
 8.4 Canceling Spots
 8.5 Marking Spots
 8.6 Counting
 8.7 Filtering
 8.8 Scatter Plots
 8.9 Spot Picking
9 Working with Spot Annotations
 9.1 Creating a Label
 9.2 Labels and Spots
 9.3 Working with Labels
 9.4 Formatting Labels
 9.5 Creating and Using a Proteome Map with Spot Identifications
 9.6 Support for Protein Identification by Mass Spectrometry
 9.7 Scouts: Finding Information in Web Resources
10 Options
 10.1 Delta2D
 10.2 General
 10.3 Memory
 10.4 Keymap
11 Advanced Topic: Scripting
 11.1 File Commands
 11.2 Image Processing Commands
 11.3 Commands for Controlling Windows
 11.4 Remote Control Commands
12 Advanced Topic: Greyscale Calibration
13 Useful Tips
 Create Your Own Pool Before You Start to Work with Delta2D
 Adapt the Memory Settings of Delta2D
 Working with Big Images
 Accurate Scanning Will Be Recompensed
 Working with Different Versions of Delta2D on the Same Data
 Tuning Spot Detection
A Example Files
B Contact Information
C Acknowledgments
D Lists of Figures and Tables, Index
List of Figures
List of Tables