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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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The role of in-silico prediction-specific commands in library-based DIA-NN mode #630

Open michaelsteidel86 opened 1 year ago

michaelsteidel86 commented 1 year ago

Dear Vadim,

I took note that in the "library-based" DIA-NN mode - meaning no fasta digest is performed and in-silico predicition is turned off - (while a library is provided as input, and re-annotation is activated) there are always "prediction-specific" commands passed to DIA-NN, and are displayed in the log-file:

Using default settings these are always:

--met-excision --cut K,R --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4

Just wondering - are these commands only related to the in-silico predicition - and consequently being ignored in the library-mode? Alternatively, are these parameters used for any "filtering" of the spectral library provided?

Thanks Michael

vdemichev commented 1 year ago

Hi Michael,

--cut will affect also 'Reannotate'. --unimod4 declares a modification, this can also affect things potentially in some scenarios (see --monitor-mod and --channels docs).

Best, Vadim