Protein C

Tide is written in standard C++ including the standard template libraries. All code is single-threaded; parallel execution is achievable by running multiple program instances simultaneously. During development, timing and profiling experiments were done on a 2.4 GHz Dual Pentium processor with 4 GB of memory running Linux. Final timing measurements were performed on 2.33GHz Dual Xeon processor with 8GB memory running Linux, with all code compiled in 64-bit mode.
Two benchmark datasets were used for both development and final timing: a “yeast” set, and a larger “worm” set. The yeast set was acquired on an LTQ ion trap mass spectrometer from a tryptic digest of an unfractionated S. cerevisiae lysate and analyzed using a 4-h reverse-phase separation, yielding 37,641 spectra [25 (link)], from which 10,000 spectra were randomly sampled. These spectra were searched against a protein database consisting of the predicted open reading frames from S. cerevisiae (released 2004-04-02, 6298 proteins). The worm benchmark was derived from a 24-h MudPIT analysis of C. elegans proteins containing 207,804 spectra, from which 10,000 spectra were randomly sampled. These spectra were searched against a protein database consisting of the predicted open reading frames from C. elegans and common contaminants (Wormpep v160, 27,499 proteins). The spectra and databases comprising these benchmarks are available at http://noble.gs.washington.edu/proj/tide.
Peptide indexes were generated from each benchmark protein database for use with Tide and Crux. The indexes contained tryptic peptides of length 6–50 amino acids and mass 200.0–7200.0 Da. These same search parameters were applied to the SEQUEST searches. Except where noted, a precursor mass tolerance window of ±3.0 Daltons and a fully tryptic peptide database were used in all experiments. Tide and Crux experiments were run with full X_Corr calculation on all candidate matches. SEQUEST experiments were run with the preliminary scoring pass S_p.