Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics.

ABSTRACT: In shotgun proteomics, peptides are typically identified using database searching, which involves scoring acquired tandem mass spectra against peptides derived from standard protein sequence databases such as Uniprot, Refseq, or Ensembl. In this strategy, the sensitivity of peptide identification is known to be affected by the size of the search space. Therefore, creating a targeted sequence database containing only peptides likely to be present in the analyzed sample can be a useful technique for improving the sensitivity of peptide identification. In this study, we describe how targeted peptide databases can be created based on the frequency of identification in the global proteome machine database (GPMDB), the largest publicly available repository of peptide and protein identification d

SUBMITTER: Shanmugam AK 

PROVIDER: S-EPMC4748730 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature