Journal
JOURNAL OF PROTEOME RESEARCH
Volume 7, Issue 1, Pages 293-299Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr0701198
Keywords
proteomics; protein identification; parallel database search; X!Tandem; tandem mass spectrometry; parallel X!Tandem; MPI
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Funding
- NATIONAL CENTER FOR RESEARCH RESOURCES [S10RR019895] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE ON DRUG ABUSE [P30DA018343] Funding Source: NIH RePORTER
- NCRR NIH HHS [S10 RR019895] Funding Source: Medline
- NIDA NIH HHS [P30 DA018343, 1 P30 DA018343, P30 DA018343-049002] Funding Source: Medline
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The widespread use of mass spectrometry for protein identification has created a demand for computationally efficient methods of matching mass spectrometry data to protein databases. A search using X!Tandem, a popular and representative program, can require hours or days to complete, particularly when missed cleavages and post-translational modifications are considered. Existing techniques for accelerating X!Tandem by employing parallelism are unsatisfactory for a variety of reasons. The paper describes a parallelization of X!Tandem, called X!!Tandem, that shows excellent speedups on commodity hardware and produces the same results as the original program. Furthermore, the parallelization technique used is unusual and potentially useful for parallelizing other complex programs.
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