Warning

This project is not maintained anymore and may not be compatible with the current version of OMSSA.

Please use SearchGUI instead.

Introduction

A GUI for the OMSSA MS/MS search engine for easy integration of OMSSA into existing data analysis pipelines. For downstream visualization and/or processing of the OMSSA search results, you might be interested in OMSSA Parser.

Details

Download the file omssa_gui-1.0.jar and xpp3-1.1.3.4-RC3.jar on the right of this page to the same folder, then double-click the OMSSAGUI file to start the software.

7/10/08 The formatdb executable from the NCBI has been added here for convenience.

7/21/08 A new version of the manual has been uploaded.

7/13/09 Please be sure once you download that the xpp3 jar is not renamed in the download process, and if it is, rename it back to the filename shown here. We are not sure why the website occasionally does this, but it is an easy fix.

The code was compiled using Sun's Java JDK 1.5.

Working code is guaranteed by a complete JUnit 3.8 testing suite.

Setup

OMSSA must be installed for this GUI to be used. To get OMSSA, go to

http://pubchem.ncbi.nlm.nih.gov/omssa/download.htm

Also, the formatdb.exe program must be downloaded and placed in the same directory as the OMSSA executable, omssacl.exe. The formatdb.exe program is part of the BLAST release, which can be found here:

ftp://ftp.ncbi.nih.gov/blast/executables/release/2.2.18

To install Java, go to

http://java.sun.com/javase/downloads/index.jsp

Please send questions, comments, or suggestions to rtharak1 AT jhu.edu

For further information, please see our technical brief in Proteomics 12'08: "OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine."