title: Determination of partial amino acid composition from tandem mass spectra for use in peptide identification strategies.
abstract: We demonstrate a new approach to the determination of amino acid composition from tandem mass spectrometrically fragmented peptides using both experimental and simulated data. The approach has been developed to be used as a search-space filter in a protein identification pipeline with the aim of increased performance above that which could be attained by using immonium ion information. Three automated methods have been developed and tested: one based upon a simple peak traversal, in which all intense ion peaks are treated as being either a b- or y-ion using a wide mass tolerance; a second which uses a much narrower tolerance and does not perform transformations of ion peaks to the complementary type; and the unique fragments method which allows for b- or y-ion type to be inferred and corroborated using a scan of the other ions present in each peptide spectrum. The combination of these methods is shown to provide a high-accuracy set of amino acid predictions using both experimental and simulated data sets. These high quality predictions, with an accuracy of over 85%, may be used to identify peptide fragments that are hard to identify using other methods. The data simulation algorithm is also shown post priori to be a good model of noiseless tandem mass spectrometric peptide data.
authors.affiliation: Cranfield University, Cranfield Centre for Bioinformatics and IT, Silsoe, Beds, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Shadforth
authors.forename: Kieran
authors.initials: K
authors.lastname: Todd
authors.forename: Daniel
authors.initials: D
authors.lastname: Crowther
authors.forename: Conrad
authors.initials: C
authors.lastname: Bessant
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D010455:Peptides