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MSQuant, an open source platform for mass spectrometry-based quantitative proteomics

Research output: Contribution to journalJournal articleResearchpeer-review

  • Peter Mortensen
  • Joost W Gouw
  • Jesper Velgaard Olsen
  • Shao-En Ong
  • Kristoffer T.G. Rigbolt
  • Jakob Bunkenborg
  • Jürgen Cox
  • Leonard J Foster
  • Albert J R Heck
  • Blagoy Blagoev
  • Jens S Andersen
  • Matthias Mann
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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 .
Original languageEnglish
JournalJournal of Proteome Research
Issue number1
Pages (from-to)393-403
Number of pages11
Publication statusPublished - 2010
Externally publishedYes

    Research areas

  • Algorithms, Databases, Protein, Isotope Labeling, Mass Spectrometry, Proteins, Proteomics, Reproducibility of Results, Software, User-Computer Interface

ID: 42358399