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Hi Rita,Here's the percolator command I use to process comet output (actually for a different experiment but the issue is the same):crux percolator --overwrite T --subset-max-train 1000000 --klammer F --maxiter 10 --output-dir ./P3856/percolator-output-pasef-recalibrated --picked-protein ./fasta/Human_Yeast_Ecoli.fasta --protein T --protein-enzyme trypsin --search-input auto --verbosity 30 --fileroot P3856 ./comet-output-pasef-recalibrated/P3856_YHE211_1_Slot1-1_1_5104.comet.pinThe comet command I use is this:crux comet --parameter-file ./comet/TimsTOF-recalibration.params --output-dir ./comet-output-pasef-recalibrated --fileroot "P3856_YHE211_1_Slot1-1_1_5104" ./exp-P3856-run-P3856_YHE211_1_Slot1-1_1_5104-features-pasef-recalibrated.mgf ./fasta/Human_Yeast_Ecoli.fastaAttached is the MGF.Thanks,Daryl.