title: 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 data. We demonstrate that targeted peptide databases can be easily integrated into existing proteome analysis workflows and describe a computational strategy for minimizing any loss of peptide identifications arising from potential search space incompleteness in the targeted search spaces. We demonstrate the performance of our workflow using several data sets of varying size and sample complexity.
authors.affiliation: Department of Computational Medicine and Bioinformatics and ‡Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Avinash K
authors.initials: AK
authors.lastname: Shanmugam
authors.affiliation: Department of Computational Medicine and Bioinformatics and ‡Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
mesh_terms: D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D030562:Databases, Protein / Q000706:statistics & numerical data; D006367:HeLa Cells; D006801:Humans; D020014:K562 Cells; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data; D057386:Search Engine; D016415:Sequence Alignment; D053719:Tandem Mass Spectrometry / Q000379:methods* / Q000706:statistics & numerical data; D057188:Workflow
chemical_list: D010455:Peptides
keywords: GPMDB; RNA-Seq; combined searches; integrative analysis; search space restriction; tandem mass spectrometry; targeted databases