Online quantitative proteomics p -value calculator for permutation-based statistical testing of peptide ratios

David Chen, Anup Shah, Hien Nguyen, Dorothy Loo, Kerry L. Inder, Michelle M. Hill

Research output: Contribution to journalArticleResearchpeer-review

12 Citations (Scopus)


The utility of high-throughput quantitative proteomics to identify differentially abundant proteins en-masse relies on suitable and accessible statistical methodology, which remains mostly an unmet need. We present a free web-based tool, called Quantitative Proteomics p-value Calculator (QPPC), designed for accessibility and usability by proteomics scientists and biologists. Being an online tool, there is no requirement for software installation. Furthermore, QPPC accepts generic peptide ratio data generated by any mass spectrometer and database search engine. Importantly, QPPC utilizes the permutation test that we recently found to be superior to other methods for analysis of peptide ratios because it does not assume normal distributions.1 QPPC assists the user in selecting significantly altered proteins based on numerical fold change, or standard deviation from the mean or median, together with the permutation p-value. Output is in the form of comma separated values files, along with graphical visualization using volcano plots and histograms. We evaluate the optimal parameters for use of QPPC, including the permutation level and the effect of outlier and contaminant peptides on p-value variability. The optimal parameters defined are deployed as default for the web-tool at

Original languageEnglish
Pages (from-to)4184-4191
Number of pages8
JournalJournal of Proteome Research
Issue number9
Publication statusPublished - 5 Sept 2014
Externally publishedYes


  • bioinformatics
  • quantitative proteomics
  • statistics

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