Peptide identification using vectors of small fragment ions |
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Authors: | Cittaro Davide Borsotti Dario Maiolica Alessio Argenzio Elisabetta Rappsilber Juri |
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Affiliation: | Proteomics Group, The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy. |
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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. |
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