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dc.contributor.authorChen, David
dc.contributor.authorShah, Anup
dc.contributor.authorHien, Nguyen
dc.contributor.authorLoo, Dorothy
dc.contributor.authorInder, Kerry L
dc.contributor.authorHill, Michelle M
dc.date.accessioned2017-11-27T12:00:44Z
dc.date.available2017-11-27T12:00:44Z
dc.date.issued2014
dc.identifier.issn1535-3893
dc.identifier.doi10.1021/pr500525e
dc.identifier.urihttp://hdl.handle.net/10072/65208
dc.description.abstractThe 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 http://qppc.di.uq.edu.au/.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.publisherAmerican Chemical Society
dc.publisher.placeUnited States
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom4184
dc.relation.ispartofpageto4191
dc.relation.ispartofissue9
dc.relation.ispartofjournalJournal of Proteome Research
dc.relation.ispartofvolume13
dc.rights.retentionY
dc.subject.fieldofresearchBioinformatics
dc.subject.fieldofresearchBiological Sciences
dc.subject.fieldofresearchChemical Sciences
dc.subject.fieldofresearchcode060102
dc.subject.fieldofresearchcode06
dc.subject.fieldofresearchcode03
dc.titleOnline Quantitative Proteomics p-value Calculator for Permutation-Based Statistical Testing of Peptide Ratios
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
dc.description.versionPost-print
gro.rights.copyrightThis document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of Proteome Research, copyright 2014 American Chemical Society after peer review. To access the final edited and published work see http://dx.doi.org/10.1021/pr500525e.
gro.hasfulltextFull Text
gro.griffith.authorChen, David


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