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J Proteome Res. 2011 Aug 5;10(8):3840-3. doi: 10.1021/pr2005154. Epub 2011 Jul 11.

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

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Department of Medical Protein Research, VIB, Ghent, Belgium.


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 analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at

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