X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers.
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.
Bjornson
Robert D
RD
Yale University, Department of Computer Science, P.O. Box 208285, New Haven, Connecticut 06520-8285, USA. robert.bjornson@yale.edu
Carriero
Nicholas J
NJ
Colangelo
Christopher
C
Shifman
Mark
M
Cheung
Kei-Hoi
KH
Miller
Perry L
PL
Williams
Kenneth
K
D030562:Databases, Protein; D008722:Methods; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis*; D012984:Software / Q000592:standards*; D053719:Tandem Mass Spectrometry; D013997:Time Factors
D011506:Proteins