An Improved Validation Protocol for Identification of Peptide Modifications Using MS/MS Based on a Detailed Investigation of In Vivo Tyrosine Nitration

摘要

The introduction of specific guidelines for reporting peptide and protein identifications has greatly enhanced the quality of publications in the area of proteomics and has provided an essential foundation for the accurate expansion of discovery-based research. Although manual validation still plays a major role in the identification of proteins and their corresponding posttranslational modifications, few uniform guidelines exist to formulate acceptable manual validation criteria. The development of such guidelines is rather complex, because a variety of factors can impact the approach used to manually validate MS/MS spectra including mass accuracy and resolving power, energy deposition mechanism for CID, implementation of dissociation, such as ECD or ETD, and other issues that may influence spectral quality (coeluting isobaric peptides, random noise, etc.) and subsequent data interpretation.