Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms. Issue 1 (7th September 2016)

• Record Type: Journal Article
• Authors: Adamo, Mark E.; Gerber, Scott A.
• Editors: Bateman, Alex; Pearson, William R.; Stein, Lincoln D.; Stormo, Gary D.; Yates, John R.
• Is Part Of: Current protocols in bioinformatics. Volume 55:Issue 1(2016)
• Page Start: 13.29.1
• Page End: 13.29.23
• Publication Date: 2016-09-07
• Subjects: database search -- GPGPU -- mass spectrometry -- neutral loss -- OpenCL -- parallel computing -- peptide identification -- proteomics; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.15
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: 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.