title: Effects of modified digestion schemes on the identification of proteins from complex mixtures.
abstract: In shotgun proteomics, a complex protein mixture is digested to peptides, separated, and identified by microcapillary liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this technology, complete protein digestion is often assumed. We show that, to the contrary, modifications to a standard digestion protocol demonstrate large, reproducible improvements in protein identification, a result consistent with digestion being a limiting factor in the efficiency of protein identification.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Aaron A
authors.initials: AA
authors.lastname: Klammer
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
mesh_terms: D045424:Complex Mixtures / Q000032:analysis* / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D013058:Mass Spectrometry; D010447:Peptide Hydrolases; D011506:Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics
chemical_list: D045424:Complex Mixtures; D029968:Escherichia coli Proteins; D011506:Proteins; D010447:Peptide Hydrolases