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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Can DIA-NN detect non-standard amino acids #1099

Open lmin-2023 opened 3 months ago

lmin-2023 commented 3 months ago

Hi Vadim,

Thanks for providing the exceptional software for the community.

I have a question about whether DIA-NN can detect proteins/peptides containing non-standard amino acids? If yes, what will be the best way to incorporate this into a predicted spectral library and search later on?

Thanks very much, Leah

vdemichev commented 3 months ago

Hi Leah,

Selenocysteine - fine. Everything else - not really. I would suggest to declare them as variable modifications of standard ones. Note also that you can filter predicted libraries https://github.com/vdemichev/DiaNN/issues/1084, e.g. only retain specific peptides with modifications.

Best, Vadim

lmin-2023 commented 3 months ago

Hi Vadim,

Thanks for the fast response. Here is an example that I found for adding a modification on UniMod list: --var-mod UniMod:35,15.994915,M. I am wondering what the syntax will be for adding a modification that is not on the UniMod list? Can the UniMod accession number be left as blank?

Best, Leah

vdemichev commented 3 months ago

Can be anything as a modification name, e.g. --var-mod MetOx,15.994915,M. The only situation when you want the UniMod name is when you know DIA-NN's deep learning predictor was trained on the modification in question, and then you want it to recognise it. But in your use-case this will not be the case anyway, so can just provide arbitrary names.

lmin-2023 commented 3 months ago

Great! Thank you so much!