vdemichev
commented
1 year ago Hi Klemens,
Indeed, recent versions of DIA-NN distributions no longer contain a manual, i.e. all the docs are on github. The --cut command is how the cleavage specificity is configured in recent versions https://github.com/vdemichev/DiaNN#command-line-reference.
Best, Vadim
Dear DIANN Developers, Thank you very much for developing and providing support for DIA-NN. It is an invaluable tool in our group!
I have a question for some samples which were digested with both trypsin and GluC: I think the manual is outdated? manual: "Protease Several built-in options are available for the in silico digest. Alternatively, one can specify custom cleavage specificity, e.g. “--cut-after KR --no-cut-before P” corresponds to a tryptic digest. Multiple proteases are not supported, however DIA-NN can be provided with an in silico digest in the FASTA format instead of the FASTA database."
When I modifify this command to my samples: --cut-after KRE --no-cut-before P
then the command is not recognized:
[DIA-NN output] ..... In silico digest will involve cuts at K,R .... WARNING: unrecognised option [--cut-after KRE] WARNING: unrecognised option [--no-cut-before P] .....
looking at the command line when executing a "normal" trypsin digestion I would modify the command to: --cut K,R,E,!P
yielding: [DIA-NN output] ... In silico digest will involve cuts at E,K,R But excluding cuts at P ....
Which looks much better, but now I am wondering whether this is correct and the manual is outdated or whether I haveoverlooked sth and the analysis might be wrong.
Any help would be appreciated!
Kind Regards Klemens