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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/17640

Title: Efficient Reduction of Candidate Matches in Peptide Spectrum Library Searching Using the Top k Most Intense Peaks
Authors: Trung Nghia, Vu
Bittremieux, Wout
Lemiere, Filip
Laukens, Kris
Issue Date: 2014
Citation: JOURNAL OF PROTEOME RESEARCH, 13 (9), p. 4175-4183
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 technical note 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 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 improvement in the speed of the search. Meanwhile, more than 9996 of the positive search results is retained. This efficient strategy to drastically improve the speed of 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.
Notes: [Trung Nghia Vu; Bittremieux, Wout; Goethals, Bart; Laukens, Kris] Univ Antwerp, Dept Math & Comp Sci, B-2020 Antwerp, Belgium. [Trung Nghia Vu; Bittremieux, Wout; Laukens, Kris] Univ Antwerp, Antwerp Univ Hosp, Biomed Informat Res Ctr Antwerp Biomina, B-2020 Antwerp, Belgium. [Valkenborg, Dirk] Flemish Inst Technol Res VITO, B-2400 Mol, Belgium. [Valkenborg, Dirk] Univ Antwerp, CFP CeProMa, B-2020 Antwerp, Belgium. [Valkenborg, Dirk] Hasselt Univ, I BioStat, B-3590 Diepenbeek, Belgium. [Lemiere, Filip] Univ Antwerp, Dept Chem, B-2020 Antwerp, Belgium.
URI: http://hdl.handle.net/1942/17640
DOI: 10.1021/pr401269z
ISI #: 000341345000028
ISSN: 1535-3893
Category: A1
Type: Journal Contribution
Validation: ecoom, 2015
Appears in Collections: Research publications

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