| Title | Faster SEQUEST searching for peptide identification from tandem mass spectra. |
| Publication Type | Journal Article |
| Year of Publication | 2011 |
| Authors | Diament BJ, Noble W S |
| Journal | Journal of proteome research |
| Volume | 10 |
| Issue | 9 |
| Pagination | 3871-9 |
| Date or Month Published | 2011 Sep 2 |
| ISSN | 1535-3907 |
| Keywords | Algorithms, Databases, Protein, Peptide Fragments, Peptide Mapping, Proteomics, Reproducibility of Results, Software, Tandem Mass Spectrometry |
| 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. |
| DOI | 10.1021/pr101196n |
| Downloads | http://www.ncbi.nlm.nih.gov/pubmed/21761931?dopt=Abstract |
| Alternate Journal | J. Proteome Res. |
| Citation Key | 7855 |
| PubMed ID | 21761931 |
