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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 VALKENBORG, Dirk GOETHALS, Bart Lemiere, Filip Laukens, Kris |
Issue Date: | 2014 | Publisher: | AMER CHEMICAL SOC | Source: | 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. | Keywords: | peptide identification; spectral library searching; query speed;Peptide identification; spectral library searching; query speed | Document URI: | http://hdl.handle.net/1942/17640 | ISSN: | 1535-3893 | e-ISSN: | 1535-3907 | DOI: | 10.1021/pr401269z | ISI #: | 000341345000028 | Rights: | © 2014 American Chemical Society. | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2015 |
Appears in Collections: | Research publications |
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