Chemical rule-based filtering of MS/MS spectra

Reiz, Beáta and Kertész-Farkas, Attila and Pongor, Sándor (2013) Chemical rule-based filtering of MS/MS spectra. BIOINFORMATICS, 29 (7). pp. 925-932. ISSN 1367-4803

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Motivation: Identification of proteins by mass spectrometry-based proteomics requires automated interpretation of peptide tandem mass spectrometry spectra. The effectiveness of peptide identification can be greatly improved by filtering out extraneous noise peaks before the subsequent database searching steps. Results: Here we present a novel chemical rule-based filtering algorithm, termed CRF, which makes use of the predictable patterns (rules) of collision-induced peptide fragmentation. The algorithm selects peak pairs that obey the common fragmentation rules within plausible limits of mass tolerance as well as peak intensity and produces spectra that can be subsequently submitted to any search engine. CRF increases the positive predictive value and decreases the number of random matches and thus improves performance by 15-20% in terms of peptide annotation using search engines, such as X!Tandem. Importantly, the algorithm also achieves data compression rates of similar to 75%.

Item Type: Article
Subjects: Q Science / természettudomány > QH Natural history / természetrajz > QH301 Biology / biológia
Depositing User: MTMT SWORD
Date Deposited: 18 Nov 2013 14:38
Last Modified: 19 Nov 2013 11:53

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