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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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plexDIA --channels option with variable modifications #1169

Open dong-gi-jang opened 2 months ago

dong-gi-jang commented 2 months ago

Dear DiaNN team,

Thank you for developing amazing tool.

I'm trying to analyze plexDIA experiments. It works well when using fixed modifications, such as SILAC.

However, it seems that the --channels option is not supported for variable modifications. The following error appears when i use a var-mod in --channels option:

ERROR: label family must be among the fixed mods applied

In my experiments, chemical probes are not fully incorporated in all the same amino acid residues, like ISOTOP-ABPP experiments.

Is there any way to overcome this issue?

Best, Dong-Gi Jang

vdemichev commented 2 months ago

Hi Dong-Gi,

One needs to use very specific syntax with --channels, i.e. declaring the label family as --fixed-mod is part of the syntax. However, if you have a situation, for example, when a label might not be fully present, you can prepare the library with labels already present (specified as --var-mod) and then proceed as in Scenario 2 Step 2 here https://github.com/vdemichev/DiaNN?tab=readme-ov-file#multiplexing-using-plexdia. That is, --var-mod in initial library preparation, but then --fixed-mod when using --channels.

Best, Vadim

dong-gi-jang commented 2 months ago

Hi Vadim,

Thank you for the detailed response! That approach seems very reasonable.

Best, Dong-Gi