Truncation data analysis

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Suresh Poudel

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Jun 5, 2026, 10:38:03 AM (6 days ago) Jun 5

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Dear All,

I am using semi-digested option in comet to get the truncated peptides. Jimmy et al. does this option really need allowed_missed_cleavage paramater? It should not really care right as we are not looking at fully tryptic? How does comet work here, does it still take this option and should we put 5 just to make it look every possiblities?

Thank you.

Jimmy Eng

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Jun 5, 2026, 3:42:00 PM (5 days ago) Jun 5

to Comet ms/ms db search support

The "allowed_missed_cleavage" rule is applied irrespective of the "num_enzyme_termini" setting. This means one can still place a limit on the number of missed cleavage sites in a semi-tryptic peptide. If you do not want to put any constraints on the number of internal missed cleavages, just set that parameter value to some large value, e.g. "allowed_missed_cleavage = 50".