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 language | English |
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Pages (from-to) | 1006-1011 |
Number of pages | 6 |
Journal | Journal of Proteome Research |
Volume | 4 |
Issue number | 3 |
DOIs | |
Publication status | Published - May 2005 |
Keywords
- Attribute vectors
- Database search
- Mass spectrometry
- Peptide fragmentation
- Peptide identification
ASJC Scopus subject areas
- Genetics
- Biotechnology
- Biochemistry