title: Shotgun protein identification and quantification by mass spectrometry in neuroproteomics.
abstract: Shotgun proteomics is based on identification and quantification of peptides from digested proteins using tandem mass spectrometry. In this chapter, we discuss computational methods to analyze tandem mass spectra of peptides, including database searching, de novo peptide sequencing, hybrid approaches, library searching, and unrestricted modification search. A special focus is given to database searching programs, since they are the most widely used. The process of inferring proteins from identified peptides is then discussed. We also provide description of key steps in the quantitative analysis of mass spectrometry proteomics data. These methods are valuable tools for discovery and hypothesis-driven analyses in neuroproteomics.
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA.
authors.forename: Bingwen
authors.initials: B
authors.lastname: Lu
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.forename: Sung Kyu
authors.initials: SK
authors.lastname: Park
authors.forename: Daniel B
authors.initials: DB
authors.lastname: McClatchy
authors.forename: Lujian
authors.initials: L
authors.lastname: Liao
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000032:analysis* / Q000235:genetics; D010455:Peptides / Q000032:analysis / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D009419:Nerve Tissue Proteins; D010455:Peptides