Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs.

Citation data:

BMC bioinformatics, ISSN: 1471-2105, Vol: 15, Issue: 1, Page: 121

Publication Year:
2014
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Repository URL:
https://repository.hkbu.edu.hk/hkbu_staff_publication/1520
PMID:
24773593
DOI:
10.1186/1471-2105-15-121
PMCID:
PMC4049470
Author(s):
Li, You; Chi, Hao; Xia, Leihao; Chu, Xiaowen
Publisher(s):
Springer Nature; BioMed Central
Tags:
Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics; Computer Sciences
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article description
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.