Factors that contribute to the misidentification of tyrosine nitration by shotgun proteomics

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Abstract

The high selectivity and throughput of tandem mass spectrometry allow for rapid identification and localization of various posttranslational protein modifications from complex mixtures by shotgun approaches. Although sequence database search algorithms provide necessary support to process the potentially enormous quantity of MS/MS spectra generated from large scale tandem mass spectrometry experiments, false positive identifications of peptide modifications may exist even after implementation of stringent identification criteria. In this report, we describe factors that lead to misinterpretation of MS/MS spectra as well as common chemical and experimental artifacts that generate false positives using the proteomics-based identification of tyrosine nitration as an example. In addition to the proposed manual validation criteria, the importance of peptide synthesis and subsequent MS/MS characterization for validation of peptide nitration demonstrated by several examples from earlier publications is also presented.

Original languageEnglish
Pages (from-to)2442-2451
Number of pages10
JournalMolecular and Cellular Proteomics
Volume7
Issue number12
DOIs
StatePublished - 1 Dec 2008

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