Often Proteome Discoverer 2.1 users will want to generate results compatible with Scaffold and other programs without having to perform the search multiple times. The following steps allow for data to be loaded successfully into Scaffold and the creation of a pdResult file that is compatible with other programs.
- In the processing workflow FDR node make sure the Max DeltaCN is set to 1
- In the separate MSF files node the max DeltaCN can also be set. Set the value to 0.05 here
That is all there is to it. The resulting files should be in the correct format to load into Scaffold and the pdResult file should be in the correct format for use in additional programs.