Documentation

Getting Started

1. Prerequisites
   • Make sure you have the Java Runtime Environment (JRE) version 1.5 or higher installed.
   • Ensure that the machine you are planning to use has sufficient memory. We recommend at least 1024 MB of RAM.
2. Downloads
   • Download the latest release of Prequips.
   • Download the sample data set.
3. Installation
   • Extract the downloaded Prequips ZIP archive into a directory of your choice. A new subdirectory named "prequips_xxx" will be created ("xxx" will be replaced by the version and the OS identifier, e.g. "macosx" or "win32").
   • Execute the Prequips application (prequips.app, prequips.exe, ...). A splash screen will appear within a few seconds.

"How To" Screencasts

The screencasts are in Apple QuickTime format and require a free Apple QuickTime Player to play.

• How To Create a Project
• How To Use the Gaggle with Prequips
• How To Use the Visualization Tools
• How To Work with a Multi Sample Analysis
• How To Create a Master Table (Inclusion List Builder)
• How To Create an Inclusion List (Inclusion List Builder)
• How To Map Peptides to the Master Table (Inclusion List Builder)
• How To Export Peptide Mappings (Inclusion List Builder)

File Formats

Currently there are data providers for mzXML (spectrum data), pepXML (peptide data), BioWorks tab-delimited (peptide and protein data) and protXML (protein data) files. In addition to the core data the following information can be imported by meta information providers:

• PeptideProphet results (pepXML)
• Sequest results (pepXML)
• Libra results (protXML)
• ProteinProphet results (protXML)
• Protein annotation (protXML)

Presentations

• PowerPoint slides of a Systems Biology Case Study
• PowerPoint slides introducing the Inclusion List Builder