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:
· 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).
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.