Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags.

ABSTRACT: Identifying proteins and their modification states and with known levels of confidence remains as a significant challenge for proteomics. Random or decoy peptide databases are increasingly being used to estimate the false discovery rate (FDR), e.g., from liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses of tryptic digests. We show that this approach can significantly underestimate the FDR and describe an approach for more confident protein identifications that uses unique partial sequences derived from a combination of database searching and amino acid residue sequencing using high-accuracy MS/MS data. Applied to a Saccharomyces cerevisiae tryptic digest, the approach provided 3 132 confident peptide identifications ( approximately 5% modified in some fashion), covering 57

SUBMITTER: Shen Y 

PROVIDER: S-EPMC2600587 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature