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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Unknown modification error #983

Open dtabang opened 6 months ago

dtabang commented 6 months ago

Hi, I am using DIA-NN 1.8.1 in the GUI to do spectral library searching of dia-PASEF files. My library contains 10 different PTMs and I have not had previous issues with searches using libraries (generated with FragPipe) with subsets of these PTMs. This time I get an "unknown modification" error. Are there additional parameters to change from default to make my search work? Thanks. Log below:

03_29_2024 09_46_08.txt

vdemichev commented 6 months ago

Unknown modification in combination with PTM scoring causes an error. Solutions: don't use PTM scoring (probably no practical sense in enabling it here) or declare extra modifications in addition to common ones (UniMod:1, 42, 35 - all these are recognised by DIA-NN) using --mod.

dtabang commented 6 months ago

Is PTM scoring enabled by default on the DIA-NN GUI? I didn't write anything to enable it under additional options. Is this box also where to add info on the extra modifications?

vdemichev commented 6 months ago

It gets enabled if you select sertain PTMs in the GUI. You can see if this is the case by the presence of --monitor-mod in the command line printed by the GUI in the log as well as by messages outputed by DIA-NN when it starts processing. Extra mods can be added by supplying --var-mod and --monitor-mod commands in the 'Additional options' field in the GUI, please see the docs for the info on these commands.