FragMixer

FragMixer is a tool to better identify phosphopeptides using multiple MS/MS fragmentation modes.


Contents

Requirements

How to use FragMixer

Tutorial

Examples of input files


Requirements

FragMixer is a standalone application written in Java. It requires Java 1.6 (or newer). To install Java just click here.
We tested FragMixer on systems running with Windows XP or Windows 7 or with Linux.
If you have problems with other systems, please contact us.

How to use FragMixer

To use FragMixer:

You just need to download the .ZIP file here,

Unzip the .ZIP file,

Double click on the .BAT or .SH file.

FragMixer accepts output files (.DAT files) from the Mascot search engine (www.matrixscience.com).

Tutorial

FragMixer was developed as a tool downstream of Mascot, to help determine the most probable phosphorylation sites within phosphopeptides. It can handle identification results from LC-MS/MS runs which consisted of acquiring one single spectrum (MSn-only) or pairs of spectra (such as MS2/MSA or MSA/ETD) on precursor ions.

This help is more specifically detailed for the handling of LC-MS/MS analyses consisting of spectrum pairs. The contents of the reports generated by FragMixer from LC-MS/MS analyses made up of one single scan type (MSn-only analyses) can be easily deduced. 

Examples of input files

Three types of .DAT files (outputs from Mascot) can be analysed with this tool.

 





Institut PASTEUR, Paris ip
Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR CNRS 8587, Evry lambe
URGV Plant Genomics, INRA, CNRS, Evry urgv