title: Protein identification pipeline for the homology-driven proteomics.
abstract: Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ Orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download.
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
authors.forename: Magno
authors.initials: M
authors.lastname: Junqueira
authors.forename: Victor
authors.initials: V
authors.lastname: Spirin
authors.forename: Tiago Santana
authors.initials: TS
authors.lastname: Balbuena
authors.forename: Henrik
authors.initials: H
authors.lastname: Thomas
authors.forename: Ivan
authors.initials: I
authors.lastname: Adzhubei
authors.forename: Shamil
authors.initials: S
authors.lastname: Sunyaev
authors.forename: Andrej
authors.initials: A
authors.lastname: Shevchenko
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid / Q000379:methods; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D016678:Genome; D019476:Insect Proteins / Q000737:chemistry; D020407:Internet; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010449:Peptide Mapping; D010940:Plant Proteins / Q000737:chemistry; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D019476:Insect Proteins; D010940:Plant Proteins; D011506:Proteins