title: MSQuant, an open source platform for mass spectrometry-based quantitative proteomics.
abstract: Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environment, called MSQuant, which allows visualization and validation of peptide identification results directly on the raw mass spectrometric data. MSQuant iteratively recalibrates MS data thereby significantly increasing mass accuracy leading to fewer false positive peptide identifications. Algorithms to increase data quality include an MS(3) score for peptide identification and a post-translational modification (PTM) score that determines the probability that a modification such as phosphorylation is placed at a specific residue in an identified peptide. MSQuant supports relative protein quantitation based on precursor ion intensities, including element labels (e.g., (15)N), residue labels (e.g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net .
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Center for Experimental Bioinformatics, Odense, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Peter
authors.initials: P
authors.lastname: Mortensen
authors.forename: Joost W
authors.initials: JW
authors.lastname: Gouw
authors.forename: Jesper V
authors.initials: JV
authors.lastname: Olsen
authors.forename: Shao-En
authors.initials: SE
authors.lastname: Ong
authors.forename: Kristoffer T G
authors.initials: KT
authors.lastname: Rigbolt
authors.forename: Jakob
authors.initials: J
authors.lastname: Bunkenborg
authors.forename: Jürgen
authors.initials: J
authors.lastname: Cox
authors.forename: Leonard J
authors.initials: LJ
authors.lastname: Foster
authors.forename: Albert J R
authors.initials: AJ
authors.lastname: Heck
authors.forename: Blagoy
authors.initials: B
authors.lastname: Blagoev
authors.forename: Jens S
authors.initials: JS
authors.lastname: Andersen
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D007553:Isotope Labeling; D013058:Mass Spectrometry / Q000379:methods*; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins