title: The implications of proteolytic background for shotgun proteomics.
abstract: The analysis by liquid chromatography coupled to tandem mass spectrometry of complex peptide mixtures, generated by proteolysis of protein samples, is the main proteomics method used today. The approach is based on the assumption that each protein present in a sample reproducibly and predictably generates a relatively small number of peptides that can be identified by mass spectrometry. In this study this assumption was examined by a targeted peptide sequencing strategy using inclusion lists to trigger peptide fragmentation attempts. It was found that the number of peptides observed from a single protein is at least one order of magnitude greater than previously assumed. This unexpected complexity of proteomics samples implies substantial technical challenges, explains some perplexing results in the proteomics literature, and prompts the need for developing alternative experimental strategies for the rapid and comprehensive analysis of proteomes.
authors.affiliation: Institute of Molecular Systems Biology, ETH Zürich, CH-8093, Zürich, Switzerland.
authors.forename: Paola
authors.initials: P
authors.lastname: Picotti
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Bruno
authors.initials: B
authors.lastname: Domon
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016632:Apolipoprotein A-I / Q000737:chemistry; D002852:Chromatography, Ion Exchange / Q000379:methods; D002853:Chromatography, Liquid / Q000379:methods; D007477:Ions; D007782:Lactoglobulins / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D020543:Proteome; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods*; D013552:Swine; D014357:Trypsin / Q000737:chemistry
chemical_list: D016632:Apolipoprotein A-I; D007477:Ions; D007782:Lactoglobulins; D010455:Peptides; D020543:Proteome; D014357:Trypsin