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The tricky part when dealing with the combined results is how to control the quality. In PEAKS 6, we introduced a very easy to use filter in the inChorus result to help resolving this issue. To use this feature, 'Search decoy database from PEAKS' option must be selected for individual search engines when performing inChorus search.
In the 'inChorus' summary view, there is a 'Edit filters' button to control the FDR at the PSM level.
Click the button, a dialog with filter details will be displayed.
The easiest way is to select the target inChorus FDR and PEAKS will automatically determine the appropriate score threshold for each individual search engine so that the combined result has the FDR the user specified. PEAKS also gives users the flexibility to select the score threshold for individual engines manually. When the filters are applied, the overall FDR of the combined result will be calculated.
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