title: Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
abstract: MALDI-quadrupole time-of-flight mass spectrometry was applied to identify proteins from organisms whose genomes are still unknown. The identification was carried out by successively searching a sequence database-first with a peptide mass fingerprint, then with a packet of noninterpreted MS/MS spectra, and finally with peptide sequences obtained by automated interpretation of the MS/MS spectra. A "MS BLAST" homology searching protocol was developed to overcome specific limitations imposed by mass spectrometric data, such as the limited accuracy of de novo sequence predictions. This approach was tested in a small-scale proteomic project involving the identification of 15 bands of gel-separated proteins from the methylotrophic yeast Pichia pastoris, whose genome has not yet been sequenced and which is only distantly related to other fungi.
authors.affiliation: Peptide and Protein Group, European Molecular Biology Laboratory, Heidelberg, Germany. shevchenko@EMBL-Heidelberg.de
authors.forename: A
authors.initials: A
authors.lastname: Shevchenko
authors.forename: S
authors.initials: S
authors.lastname: Sunyaev
authors.forename: A
authors.initials: A
authors.lastname: Loboda
authors.forename: A
authors.initials: A
authors.lastname: Shevchenko
authors.forename: P
authors.initials: P
authors.lastname: Bork
authors.forename: W
authors.initials: W
authors.lastname: Ens
authors.forename: K G
authors.initials: KG
authors.lastname: Standing
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D016208:Databases, Factual; D004285:Dogs; D016681:Genome, Fungal; D007668:Kidney / Q000166:cytology; D008565:Membrane Proteins / Q000737:chemistry; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000295:instrumentation / Q000379:methods; D010843:Pichia / Q000235:genetics*; D020543:Proteome / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014357:Trypsin / Q000378:metabolism
chemical_list: D008565:Membrane Proteins; D020543:Proteome; D014357:Trypsin