Work

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

Year: 2011

Type: article

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.

Source: Journal of Proteome Research

DOI: 10.1021/pr101196n

Authors: Benjamin J. Diament, William Stafford Noble

Institution: University of Washington

Language: English

Topic: Advanced Proteomics Techniques and Applications

Subfield: Spectroscopy

Field: Chemistry

Domain: Physical Sciences

Open Access status: green

Funders: National Institutes of Health, National Human Genome Research Institute, National Institute of General Medical Sciences, National Institute of Biomedical Imaging and Bioengineering

Awards: Machine learning analysis of tandem mass spectra, Machine learning analysis of tandem mass spectra, Interdisciplinary Training in Genome Sciences