Title
Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks
Author
Faculty/Department
Faculty of Sciences. Biology
Faculty of Sciences. Chemistry
Faculty of Sciences. Mathematics and Computer Science
Publication type
article
Publication
Subject
Mathematics
Chemistry
Biology
Computer. Automation
Source (journal)
Journal of proteome research
Volume/pages
13(2014) :9 , p. 4175-4183
ISSN
1535-3893
ISI
000341345000028
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
Abstract
Spectral library searching is a popular approach for MS/MS-based peptide identification. Because the size of spectral libraries continues to grow, the performance of searching algorithms is an important issue. This paper introduces a strategy based on a minimum shared peak count between two spectra to reduce the set of admissible candidate spectra when issuing a query. A theoretical validation through a time complexity analysis and an experimental validation based on an implementation of the candidate reduction strategy show that the approach can achieve a reduction of the set of candidate spectra by (at least) an order of magnitude, resulting in a significant speed-up. Meanwhile, more than 99% of the positive search results are retained. This efficient strategy to drastically speed up spectral library searching with a negligible loss of sensitivity can be applied to any current spectral library search tool, irrespective of the employed similarity metric.
E-info
https://repository.uantwerpen.be/docman/iruaauth/432ab3/9523f571c79.pdf
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Handle