Figure 3.

Combining multiple scores from a search engine improves peptide identification rate. Tandem mass spectra from three different samples were matched to IPI human protein database (version 3.47) using MyriMatch, Sequest, and Mascot search engines (see Materials and Methods for additional details). Peptide identifications from all search engines were loaded into IDPicker. For each search engine, IDPicker was configured to use either its primary score or a combination of its scores to identify peptides at an FDR ≤5%. Panels A–I show the percent overlap between valid peptide identifications when IDPicker was using either a single score or multiple scores from respective search engines. Combining multiple scores from a search engine yielded more peptide identifications from all samples. There were few peptide identifications that were identified only when using the primary score of a search engine but not the score combination.