title: Peptide identification using vectors of small fragment ions.
abstract: Traditionally, peptide identification using fragmentation spectra relies on extracting the maximum amount of information from spectra. Using different combinations of small ion masses, we show that identifying a small number of fragment ions in a spectrum is sufficient for peptide identification. We consider y2-, y3-, b2-, and b3-ions and find the combination of b2-y2 to be sufficient for many peptides. Adding either the y3- or the b3-ion increases specificity and allows reliable peptide identification in the human proteome. Fragmentation spectra and peptides are represented as n-dimensional vectors, where n is given by the number of fragment ions considered, and the peptide mass. The identification score is given by the Euclidian distance between the spectra and the matching peptide in n-dimensional space. We show that this approach, using minimal information, allows for precise and fast peptide identification.
authors.affiliation: Proteomics Group, The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Cittaro
authors.forename: Dario
authors.initials: D
authors.lastname: Borsotti
authors.forename: Alessio
authors.initials: A
authors.lastname: Maiolica
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Argenzio
authors.forename: Juri
authors.initials: J
authors.lastname: Rappsilber
mesh_terms: D006801:Humans; D007477:Ions; D013058:Mass Spectrometry; D010446:Peptide Fragments; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D013997:Time Factors
chemical_list: D007477:Ions; D010446:Peptide Fragments; D010455:Peptides