Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms.
MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel. The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. © 2016 by John Wiley & Sons, Inc.
Norris Cotton Cancer Center, Geisel School at Dartmouth, Lebanon, New Hampshire.
Mark E
ME
Adamo
Norris Cotton Cancer Center, Geisel School at Dartmouth, Lebanon, New Hampshire.|Department of Genetics, Geisel School at Dartmouth, Lebanon, New Hampshire.|Department of Biochemistry, Geisel School at Dartmouth, Lebanon, New Hampshire.
Scott A
SA
Gerber
D000465:Algorithms; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D030562:Databases, Protein; D012984:Software; D053719:Tandem Mass Spectrometry
GPGPU; OpenCL; database search; mass spectrometry; neutral loss; parallel computing; peptide identification; proteomics