Peptide ID with Multiple Engines


If you have access to another database search engine, then the inChorus function of PEAKS can make use of it by combining the database search results of PEAKS DB and with the other search engines.The combination of multiple engines will not only increase the coverage, but also the confidence since the engines using independent algorithms and therefore confirm each others results (Figure 1). In fact, PEAKS inChorus can directly invoke many of the supported engines and display all results in a united graphical user interface. This saves the tedious manual work of running different engines and loading their results separately.

Multiple Engine Proteomics Search Workflow

Figure 1: inChorus Workflow
PEAKS inChorus combines the multiple engine proteomics search results from Mascot, X!Tandem, OMSSA, and Proteome Discoverer (Sequest). It can call Mascot, X!Tandem, and OMSSA directly and the results are automatically retrieved and combined by PEAKS inChorus.

Result Display

Multiple engine proteomics search results are displayed in a unified interface (Figure 2), with the engine icons indicating which engine or engines identified the same peptide-spectrum match (PSM). A blue background indicates that the engine assigned a higher-than-threshold score to the corresponding PSM and a white background indicates the score is lower than threshold from that engine.

Figure 2: inChorus Engine Display: PEAKS inChorus also makes the result validation and filtration extremely easy. Users can simply specify the target false discovery rate (FDR) and the algorithm will automatically adjust the score threshold for each engine to meet the target FDR. For example, if the target FDR is 1%, then the algorithm will choose individual engines’ thresholds so that (1) all engines have the same FDR and (2) the combined FDR is 1%. (Figure 3) Advanced users can also set individual engine’s score threshold by themselves. Another advantage of PEAKS inChorus is the “de novo only” peptides. These are the highly confident de novo sequencing results from the spectra that cannot be confidently interpreted by any of the combined search engines. These “de novo only” peptides potentially lead to novel discoveries.

Figure 3: inChorus Results Summary