MSQuant, an open source platform for mass spectrometry-based quantitative proteomics.
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 .
Mortensen
Peter
P
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Center for Experimental Bioinformatics, Odense, Campusvej 55, DK-5230 Odense M, Denmark.
Gouw
Joost W
JW
Olsen
Jesper V
JV
Ong
Shao-En
SE
Rigbolt
Kristoffer T G
KT
Bunkenborg
Jakob
J
Cox
Jürgen
J
Foster
Leonard J
LJ
Heck
Albert J R
AJ
Blagoev
Blagoy
B
Andersen
Jens S
JS
Mann
Matthias
M
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
D011506:Proteins