Peptide identification using vectors of small fragment ions

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.