title: Gas phase conformation can have an influence on peptide fragmentation.
abstract: In the post-genomic era, mass spectrometry is destined to fulfil a central role in biomedical research, and it is in the area of protein identification that mass spectrometry is now most rapidly expanding. An important identification method is to subject a protein to proteolysis and determine the resulting peptide masses and/or primary structure. From such determinations proteins can be identified. Tandem mass spectrometry (MS/MS) is used to determine primary structure and, for high-throughput identification, computer-based automated strategies are a prerequisite. Computer programs are available for such identifications, where simulated MS/MS spectra of amino acid sequences within a database are generated and compared to experimental spectra. Such algorithms take into account empirical rules for peptide fragmentation, rather than specific gas-phase ion chemistry. For example, fragmentation of each peptide bond is usually considered to be equally facile. In reality, this is not the case. Gas-phase ion chemistry bears an important role in determining the abundance of fragment ions in MS/MS spectra. In this communication, the gas-phase ion chemistry responsible for the facile cleavage between Gln and Gly residues is investigated, particularly in relation to Proline Rich Protein-1.
authors.affiliation: Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. william.griffiths@mbb.ki.se
authors.forename: W J
authors.initials: WJ
authors.lastname: Griffiths
authors.forename: A P
authors.initials: AP
authors.lastname: Jonsson
mesh_terms: D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry*; D010449:Peptide Mapping; D021241:Spectrometry, Mass, Electrospray Ionization; D014357:Trypsin / Q000737:chemistry
chemical_list: D010446:Peptide Fragments; D014357:Trypsin