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Originally published In Press as doi:10.1074/mcp.M800065-MCP200 on August 16, 2008.
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Molecular & Cellular Proteomics 7:2442-2451, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Factors That Contribute to the Misidentification of Tyrosine Nitration by Shotgun Proteomics*,S

Stanley M. Stevens, Jr.{ddagger}, Katalin Prokai-Tatrai§ and Laszlo Prokai{ddagger},¶

From the Departments of {ddagger} Molecular Biology and Immunology and § Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas 76107

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.

The Robert A. Welch Professor of the University of North Texas Health Science Center (Grant BK-0031). To whom correspondence should be addressed: Dept. of Molecular Biology and Immunology, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107. Tel.: 817-735-2206; Fax: 817-735-2118; E-mail: lprokai{at}hsc.unt.edu


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