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.
To use FragMixer:
FragMixer accepts output files (.DAT files) from the Mascot search engine (www.matrixscience.com).
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.
Three types of .DAT files (outputs from Mascot) can be analysed with this tool.
Bertrand Ameline de Cadeville has brought modifications to the published version of FragMixer, to allow in particular batch mode processing of several DAT files, automated export of results files and easy visualization of the MS/MS spectra annotated by Mascot from within the results pages of FragMixer. We gladly acknowledge the assistance of Mathias Vandenbogaert and Veronique Hourdel.
Download FragMixer v2.0 from here. The associated User Guide can be accessed here.