Peptide identification using vectors of small fragment ions

Davide Cittaro, Dario Borsotti, Alessio Maiolica, Elisabetta Argenzio, Juri Rappsilber

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)1006-1011
Number of pages6
JournalJournal of Proteome Research
Issue number3
Publication statusPublished - May 2005


  • Attribute vectors
  • Database search
  • Mass spectrometry
  • Peptide fragmentation
  • Peptide identification

ASJC Scopus subject areas

  • Genetics
  • Biotechnology
  • Biochemistry


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