title: Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.
abstract: 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 http://thermo-msf-parser.googlecode.com.
authors.affiliation: Department of Medical Protein Research, VIB, Ghent, Belgium.
authors.forename: Niklaas
authors.initials: N
authors.lastname: Colaert
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.forename: Kenny
authors.initials: K
authors.lastname: Helsens
authors.forename: Evy
authors.initials: E
authors.lastname: Timmerman
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D006801:Humans; D013058:Mass Spectrometry; D011381:Programming Languages; D020543:Proteome
chemical_list: D020543:Proteome