TY - JOUR
T1 - Factors that contribute to the misidentification of tyrosine nitration by shotgun proteomics
AU - Stevens, Stanley M.
AU - Prokai-Tatrai, Katalinm
AU - Prokai, Laszlo
PY - 2008/12
Y1 - 2008/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=58149291366&partnerID=8YFLogxK
U2 - 10.1074/mcp.M800065-MCP200
DO - 10.1074/mcp.M800065-MCP200
M3 - Article
C2 - 18708664
AN - SCOPUS:58149291366
SN - 1535-9476
VL - 7
SP - 2442
EP - 2451
JO - Molecular and Cellular Proteomics
JF - Molecular and Cellular Proteomics
IS - 12
ER -