I'm attempting to do a DDA search with MSFragger. My overall workflow is as in the thread I started last week (FATAL: An exception occurred: 'c' is not a valid amino acid), and works fine with those old data. The same workflow also works fine with most of the new data I have collected. With some files, however, I will get 0 PSMs returned from the decoy search, which results in an error message when Percolator gets to that file (Error: no decoy PSMs were provided). I have attached the log from an attempt at running the search with one of the files in question (several files will trigger the same error message). This might, in part, reflect the small size of my database and relatively low sample complexity (289 peptides), but is there some way that I can adjust settings to encourage MSFragger / Percolator to find at least 1 PSM among the decoys so the search can complete with all files?