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The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyse and validate quantitative proteomics information. All code, binaries and documentation is freely available at http://thermo-msf-parser.googlecode.com.
Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L. thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files. J Proteome Res. 2011 Jun 30. [Epub ahead of print]