I’m experimenting with the MSMSFit scoring and am going down what looks like a very promising road. Interesting: When examining OutputFile2.pkl against chr4.fasta a peptide, GSWYSMRK, came up with a high MSMSFit score that HMM_Score somewhat overlooks (it gets an HMM score of about 60 depending on the peak cleaning method). What is interesting is that GSWYSMRK starts at 15571189, which is right where HGTDDGVVWMNWK ends which, I think, strongly implies that it is a valid hit.