FDR, Decoy Hits, and Forward/Decoy FASTAs in Scaffold

Most modern search tools (eg, MaxQuant, Mascot, Proteome Discoverer, etc) have an on-the-fly decoy search option, wherein it reverses or randomizes the FASTA sequences while it searches.

If you use this feature, you can simply use the same forward FASTA you used in the search in Scaffold. Note that your decoy hits will not be annotated. If you want them annotated, you will need to use a forward/decoy concatenated FASTA.

If the on-the-fly decoy function is not available or wasn't used, and you want to get decoys, then you must use a forward/decoy concatenated FASTA in both the search engine and Scaffold.

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