Optimizing protein search engines using particle swarm optimization

Majdi Maabreh, Basheer Qolomany, Ajay Gupta, James Springstead

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

The results of protein search engines depend mainly upon a set of parameters that adjust the searching space. One of the most effective parameters is the peptide mass window tolerance (w). Most of the current search engines use a constant user-defined value for this parameter. As an alternative option, Comet search engine designers proposed a statistical technique to estimate the best tolerance window for an input spectra file. However, this technique sometimes fails in picking a value, may set the parameter to a value that results in a loss of many correct matches, and is available only for one type of mass; namely ppm. In this paper, we propose to use particle swarm optimization (PSO) to improve the coverage of search engines by picking the optimal value for this influential parameter to maximize PSMs. Our results show that this biologically-inspired algorithm can be utilized to find peptide mass window tolerance values that facilitate Comet to increase peptide spectra matches, resulting in improved peptide identification. We also show experimental evidence that an open search (i.e., wide tolerance window) does not always optimize spectra matching using the current search engines and that narrow tolerance windows improve the coverage of protein search engines.

Original languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages340-345
Number of pages6
ISBN (Electronic)9781538613245
DOIs
StatePublished - Jul 1 2017
Externally publishedYes
Event17th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2017 - Herndon, United States
Duration: Oct 23 2017Oct 25 2017

Publication series

NameProceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017
Volume2018-January

Other

Other17th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2017
Country/TerritoryUnited States
CityHerndon
Period10/23/1710/25/17

Keywords

  • Comet
  • Optimization
  • Particle swarm
  • Proteomics
  • Search engine
  • Tolerance window

ASJC Scopus subject areas

  • Signal Processing
  • Information Systems
  • Biomedical Engineering
  • Modeling and Simulation
  • Health Informatics

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