title: Effectively addressing complex proteomic search spaces with peptide spectrum matching.
abstract: CONCLUSIONS
  Protein identification by mass spectrometry is commonly accomplished using a peptide sequence matching search algorithm, whose sensitivity varies inversely with the size of the sequence database and the number of post-translational modifications considered. We present the Spectrum Identification Machine, a peptide sequence matching tool that capitalizes on the high-intensity b1-fragment ion of tandem mass spectra of peptides coupled in solution with phenylisotiocyanate to confidently sequence the first amino acid and ultimately reduce the search space. We demonstrate that in complex search spaces, a gain of some 120% in sensitivity can be achieved.
  
  
  BACKGROUND
  All data generated and the software are freely available for academic use at http://proteomics.fiocruz.br/software/sim.
  
  
  BACKGROUND
  paulo@pcarvalho.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil.
authors: Diogo
authors: D
authors: Borges
authors: Yasset
authors: Y
authors: Perez-Riverol
authors: Fabio C S
authors: FC
authors: Nogueira
authors: Gilberto B
authors: GB
authors: Domont
authors: Jesus
authors: J
authors: Noda
authors: Felipe
authors: F
authors: da Veiga Leprevost
authors: Vladimir
authors: V
authors: Besada
authors: Felipe M G
authors: FM
authors: França
authors: Valmir C
authors: VC
authors: Barbosa
authors: Aniel
authors: A
authors: Sánchez
authors: Paulo C
authors: PC
authors: Carvalho
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000032:analysis* / Q000737:chemistry; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D010455:Peptides