Faster SEQUEST searching for peptide identification from tandem mass spectra

Benjamin J. Diament and William Stafford Noble

Journal of Proteome Research. 10(9):3871-9, 2011.


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.

Tide is available in a stand-alone version or as part of Crux.
Journal of Proteome Research