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. Author manuscript; available in PMC: 2010 Aug 1.
Published in final edited form as: J Proteome Res. 2009 Aug;8(8):3872–3881. doi: 10.1021/pr900360j

Figure 4.

Figure 4

Comparison of IDPicker and PeptideProphet score combination methods. Tandem mass spectra from three different samples were matched to the IPI human protein database (version 3.47) using the Sequest search engine (see Materials and Methods). The search results were separately processed by IDPicker and PeptideProphet. Both algorithms were configured to filter PSMs using a 5% FDR threshold. The total number of confident PSMs identified by both algorithms in each replicate of all three data sets is shown above. IDPicker produced more confident PSMs than PeptideProphet in some data sets and vice versa, but the algorithms performed similarly in all data sets, with a maximum difference of 5.7%. The simple nonparametric score combination method implemented in IDPicker performs as well as the complex probabilistic frameworks implemented in PeptideProphet, but the IDPicker score combination method can be more easily extended to combine multiple search scores from new search engines.