Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs.
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BMC bioinformatics, ISSN: 1471-2105, Vol: 15, Issue: 1, Page: 121
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- Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics; Computer Sciences
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Tandem mass spectrometry-based database searching is currently the main method for protein identification in shotgun proteomics. The explosive growth of protein and peptide databases, which is a result of genome translations, enzymatic digestions, and post-translational modifications (PTMs), is making computational efficiency in database searching a serious challenge. Profile analysis shows that most search engines spend 50%-90% of their total time on the scoring module, and that the spectrum dot product (SDP) based scoring module is the most widely used. As a general purpose and high performance parallel hardware, graphics processing units (GPUs) are promising platforms for speeding up database searches in the protein identification process.