Q value threshold adjustment and bug fix #2426
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This PR changes the threshold used for using the more stringent and correct q-value calculation (D+1)/T to a total of 1000 PSMs. Below that level we use D/T. This will help with top-down files that contain fewer PTMs. It is hoped that in the future, we can eliminate this threshold and use one threshold for all. Some PRs that might help would be paired target-decoy and decoy on the fly using 10X decoys.
For reference on the equation please see:
J Proteome Res. 2022 Oct 7;21(10):2412-2420. doi: 10.1021/acs.jproteome.2c00282. Epub 2022 Sep 27.
https://pubmed.ncbi.nlm.nih.gov/36166314/
Traditional Q-Value (D/T) for PSM Count < 1000