Alternative methods for verifying the results of the mass spectrometric identification of peptides in shotgun proteomics
2010 (English)In: Journal of Analytical Chemistry, ISSN 1061-9348, E-ISSN 1608-3199, Vol. 65, no 14, 1462-1468 p.Article in journal (Refereed) Published
Database search is the most popular approach used for the identification of peptides in contemporary shotgun proteomics; it utilizes only mass spectrometric data. In this work, we introduce three criteria for the verification of peptide identification; these are based on the analysis of data orthogonal to tandem mass spectra. The first one utilizes chromatographic retention times of peptides. The development of such approaches has been hindered by the relatively low accuracy of retention time prediction algorithms. In this work, we suggest the use of two independent models of the liquid chromatography of peptides, which increase the reliability of the results. The second criterion utilizes the mean number of missed tryptic cleavages per peptide. The third one results from the analysis of the difference between theoretical and experimentally measured peptide masses. The proposed criteria were applied to the tandem mass spectra of tryptic peptides from rat kidney tissue, which were processed by the Mascot search engine. All the criteria showed that Mascot significantly overestimated the reliability of an identification. This conclusion was supported by the PeptideProphet algorithm.
Place, publisher, year, edition, pages
2010. Vol. 65, no 14, 1462-1468 p.
proteomics, Mascot, mass spectrometry, liquid chromatography, retention time prediction
IdentifiersURN: urn:nbn:se:uu:diva-148612DOI: 10.1134/S1061934810140042ISI: 000287150000004OAI: oai:DiVA.org:uu-148612DiVA: diva2:402475