title: The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches.
abstract: Mass spectrometry-driven BLAST (MS BLAST) is a database search protocol for identifying unknown proteins by sequence similarity to homologous proteins available in a database. MS BLAST utilizes redundant, degenerate, and partially inaccurate peptide sequence data obtained by de novo interpretation of tandem mass spectra and has become a powerful tool in functional proteomic research. Using computational modeling, we evaluated the potential of MS BLAST for proteome-wide identification of unknown proteins. We determined how the success rate of protein identification depends on the full-length sequence identity between the queried protein and its closest homologue in a database. We also estimated phylogenetic distances between organisms under study and related reference organisms with completely sequenced genomes that allow substantial coverage of unknown proteomes.
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. habermann@mpi-cbg.de
authors.forename: Bianca
authors.initials: B
authors.lastname: Habermann
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Oegema
authors.forename: Shamil
authors.initials: S
authors.lastname: Sunyaev
authors.forename: Andrej
authors.initials: A
authors.lastname: Shevchenko
mesh_terms: D000818:Animals; D003198:Computer Simulation; D016208:Databases, Factual; D006801:Humans; D008962:Models, Theoretical; D010449:Peptide Mapping; D011209:Power, Psychological; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013045:Species Specificity; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D020543:Proteome