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QuPE is a repository and algorithmic framework to store and analyze isotopic labeled tandem mass spectrometry-based (LC-MS/MS) quantitative proteomics experiements. Mass spectrometry data can be imported either via mzData, mzXML, or the Mascot generic format in a data model adapted to the the HUPO proteomics standards initiative (PSI). QuPE provides protein identification by database searches facilitating an integrated Mascot search engine and the consecutive calculation of protein abundance ratios. Statistical evaluation of the quantified stable-isotope labeled samples (15N, 13C, SILAC) includes significance test, multivariate analysis methods such as analysis of variance, principal component analysis, and various cluster analysis and validation methods.

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Funding: Service provision and maintenance funded by de.NBI.