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Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results
dc.contributor.authorda Veiga Leprevost, Felipe
dc.contributor.authorBarbosa, Valmir C.
dc.contributor.authorCarvalho, Paulo Costa
dc.date.accessioned2020-01-13T15:06:03Z
dc.date.available2020-01-13T15:06:03Z
dc.date.issued2015-09
dc.identifier.citationda Veiga Leprevost, Felipe; Barbosa, Valmir C.; Carvalho, Paulo Costa (2015). "Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results." Current Protocols in Bioinformatics 51(1): 13.27.1-13.27.9.
dc.identifier.issn1934-3396
dc.identifier.issn1934-340X
dc.identifier.urihttps://hdl.handle.net/2027.42/152617
dc.description.abstractPepExplorer aids in the biological interpretation of de novo sequencing results; this is accomplished by assembling a list of homolog proteins obtained by aligning results from widely adopted de novo sequencing tools against a target‐decoy sequence database. Our tool relies on pattern recognition to ensure that the results satisfy a user‐given false‐discovery rate (FDR). For this, it employs a radial basis function neural network that considers the precursor charge states, de novo sequencing scores, the peptide lengths, and alignment scores. PepExplorer is recommended for studies addressing organisms with no genomic sequence available. PepExplorer is integrated into the PatternLab for proteomics environment, which makes available various tools for downstream data analysis, including the resources for quantitative and differential proteomics. © 2015 by John Wiley & Sons, Inc.
dc.publisherWiley Periodicals, Inc.
dc.publisherHumana Press
dc.subject.otherde novo sequencing
dc.subject.otherproteomics
dc.subject.othermass spectrometry
dc.titleUsing PepExplorer to Filter and Organize De Novo Peptide Sequencing Results
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelGenetics
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biology
dc.subject.hlbtoplevelScience
dc.subject.hlbtoplevelHealth Sciences
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/152617/1/cpbi1327.pdf
dc.identifier.doi10.1002/0471250953.bi1327s51
dc.identifier.sourceCurrent Protocols in Bioinformatics
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dc.owningcollnameInterdisciplinary and Peer-Reviewed


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