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 .

Redox Proteomics Uncovers Peroxynitrite-sensitive Proteins That Help Escherichia coli to Overcome Nitrosative Stress

“…Identification and quantification were performed with Mascot (version 2.2.0, MatrixScience, London, UK) against the EcoProt database (21) and MSQuant version 1.4.3 (22).…”

“…The pre-column was then connected to a 75-m ϫ 25-cm Acclaim PepMap 100 C18, 3 m, 100-Å column (Dionex), where the peptide sample was loaded with 95% solvent A (0.1% formic acid (v/v)) and 5% solvent B (0.1% formic acid, 84% ACN) at a flow rate of 0.400 l/min by the micro pump system. Peptides were eluted with a linear gradient of 5% (22). The data analysis was divided into three steps.…”

Global Impact of Salmonella Pathogenicity Island 2-secreted Effectors on the Host Phosphoproteome

“…Data Analysis-For data analysis using MSQuant version 2.0a81 (19) Fig. 4B), phosphopeptides showing significant increases upon SteC transfection were manually validated using MSQuant.…”

Proteomic Analysis of Stem Cell Differentiation and Early Development

“…Availability of appropriate software is becoming less of an issue, because packages accepting various labeling formats are being developed Mortensen et al 2010).…”