Search times as a function of job complexity. Complexity is measured as dot products - the score of one spectrum against one peptide. Complexity depends on the number of spectra, the size of the protein database and the modifications and cleavages searched. The measured spectra files used for benchmarking our implementation were picked out of the public experiments of the PRIDE (Proteomics Identifications Database) proteomics repository. The PRIDE accession numbers of the 3 experiments used for making Figure 3 are: 7962, 15459, 10295. The PRIDE xml files containing spectra were downloaded from the PRIDE website and were opened in the PRIDE Inspector . The mgf export functionality of PRIDE Inspector was used to generate the mgf files used in the searches, with only human tissue samples or cell lines being used to generate the mass spectra.
Lewis et al. BMC Bioinformatics 2012 13:324 doi:10.1186/1471-2105-13-324