It looks like spectrum:
T10475_Well_A13_2025.07_16898.mgf..pkl

and spectrum:
T10475_Well_A13_2025.07_17096.mgf..pkl

are the same. This is bad news for me as TandemFit gets both of those “wrong”. The quotes because TandemFit’s match of QAGLQLQESLEPAVRLDR has 11 fragment alignments vs 2 produced by VPAPSIEDICHVLSTVCK which is the “correct” peptide.

Update: other duplicates:
T10475_Well_A12_1386.68_16898.mgf..pkl
T10475_Well_A12_1386.68_17096.mgf..pkl

T10475_Well_A03_1551.77_16898.mgf..pkl
T10475_Well_A03_1551.77_17096.mgf..pkl

T10475_Well_A11_1386.69_16898.mgf..pkl
T10475_Well_A11_1386.69_17096.mgf..pkl

T10475_Well_A10_1188.45_17096.mgf..pkl
T10475_Well_A10_1188.45_16898.mgf..pkl

T10475_Well_A10_2143.98_17096.mgf..pkl
T10475_Well_A10_2143.98_16898.mgf..pkl

Hmm… it looks like something of a pattern