title: Faster SEQUEST searching for peptide identification from tandem mass spectra.
abstract: Computational analysis of mass spectra remains the bottleneck in many proteomics experiments. SEQUEST was one of the earliest software packages to identify peptides from mass spectra by searching a database of known peptides. Though still popular, SEQUEST performs slowly. Crux and TurboSEQUEST have successfully sped up SEQUEST by adding a precomputed index to the search, but the demand for ever-faster peptide identification software continues to grow. Tide, introduced here, is a software program that implements the SEQUEST algorithm for peptide identification and that achieves a dramatic speedup over Crux and SEQUEST. The optimization strategies detailed here employ a combination of algorithmic and software engineering techniques to achieve speeds up to 170 times faster than a recent version of SEQUEST that uses indexing. For example, on a single Xeon CPU, Tide searches 10,000 spectra against a tryptic database of 27,499 Caenorhabditis elegans proteins at a rate of 1550 spectra per second, which compares favorably with a rate of 8.8 spectra per second for a recent version of SEQUEST with index running on the same hardware.
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Diament
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D010446:Peptide Fragments / Q000737:chemistry*; D010449:Peptide Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010446:Peptide Fragments