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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Un-specific cutting #679

Open lzy604 opened 1 year ago

lzy604 commented 1 year ago

Dear DiaNN developer,

I used the command line to run the DIANN, and I want to know if the DIANN can be used to detect the un-specific cutting, which means every kind of cleavage might exist.

--cut [specificty 1],[specificity 2],... specifies cleavage specificity for the in silico digest. Cleavage sites (pairs of amino acids) are listed separated by commas, '' indicates any amino acid, and '!' indicates that the respective site will not be cleaved. Examples: "--cut K,R,!P" - canonical tryptic specificity, "--cut " - digest disabled

I wonder the digest disabled mode is the meaning of a long protein do not digest any more and they are very long ones?

vdemichev commented 1 year ago

No, non-specific digest searches will likely not work well with DIA-NN. I would suggest to try MSFragger-DIA which is part of FragPipe for this, but in general it's not the best idea for DIA, regardless of the processing software.