Peptide identification using vectors of small fragment ions

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

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)1006-1011
Number of pages6
JournalJournal of Proteome Research
Volume4
Issue number3
DOIs
Publication statusPublished - May 2005

Keywords

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

ASJC Scopus subject areas

  • Genetics
  • Biotechnology
  • Biochemistry

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    Cittaro, D., Borsotti, D., Maiolica, A., Argenzio, E., & Rappsilber, J. (2005). Peptide identification using vectors of small fragment ions. Journal of Proteome Research, 4(3), 1006-1011. https://doi.org/10.1021/pr0500152