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PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

ABSTRACT: Analysis of synthetic peptide reference datasets to demonstrate the performance of PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization confidence to enable appropriate further characterization of biologic events.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Zhi Sun

LAB HEAD: Robert Moritz

PROVIDER: PXD013210 | Pride | 2019-07-18

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	HumanSRM-DP_20160511.fasta	Fasta
	TTB20160722_ISBHJOMXX001872_r01.mzML	Mzml
	TTB20160722_ISBHJOMXX001872_r01.wiff	Wiff
	TTB20160722_ISBHJOMXX001872_r01.wiff.scan	Wiff
	TTB20160722_ISBHJOMXX001873_r01.mzML	Mzml

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Publications

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline.

Shteynberg David D DD Deutsch Eric W EW Campbell David S DS Hoopmann Michael R MR Kusebauch Ulrike U Lee Dave D Mendoza Luis L Midha Mukul K MK Sun Zhi Z Whetton Anthony D AD Moritz Robert L RL

Journal of proteome research 20190722 12

Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and in addition, possible sequence ions carrying post-translational modifications (PTMs), but most do not provide confidence metrics for the exact localization of those PTMs when several possible sites are available. Localization is absolutely required for downstream molecular cell biology analysis of PTM function in vitro and in vivo. The ...[more]

PMID: 31290668

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