When using the error tolerant search function in Mascot, we have a high (>700 total matches value) for "non-specific cleavage".
Does anyone else use this search function and if so, what do you do with examples of high scoring matches like "non-specific cleavage"?
Yazan Haddad
when you have scarce or low number of hits, increasing the error tolerance will give you more possible results but with less confidence. for me I think the next step is to check the peptides one by one with BLAST to see if any of them can be of biological significance.
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Peter Allen Faull
Thank you Yazan but we do not have scarce/low number of hits. Quite the opposite as we have high numbers.
Regards, Peter
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