An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.

By Lukas N. Mueller, Mi Youn Kim Brusniak, D. Mani, R. Aebersold. Journal of Proteome Research, 2008

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Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline (2012, methodology): “It is currently being used in the National Cancer Institute Clinical Proteomic Technology Assessment for Cancer program to assess reproducibility and accuracy of large scale proteomic experiments across multiple sites and laboratories 2 (http://proteomics. cancer.gov/programs/cptacnetwork).”
Decoding signalling networks by mass spectrometry-based proteomics (2010, background): “Several successful applications of label-free analysis have nevertheless been reporte”
Less label, more free: Approaches in label‐free quantitative mass spectrometry (2011, unknown): “For a recent review primarily focused on software tools for MS quantitation see [14].”
Correlation of mRNA and protein in complex biological samples (2009, unknown): “A large variety of MS data analysis software packages exist, also comprising statistical tools for data analysis (for an overview see [81,83–85]).”
Mass Spectrometry-Based Label-Free Quantitative Proteomics (2009, methodology): “The open source programs include MapQuant, MZmine, MsInspect, OpenMs, MSight, SuperHirn, and PEPPeR [41, 42].”
Proteomics by mass spectrometry: approaches, advances, and applications. (2009, background): “Automated quantification of complex proteomes necessitates additional software solutions (192).”