DIA data and MHCII

[wangjiawen2013]

Hi,

Sorry to trouble again. I never heard about slack/discord and we cannot use them in our country. So I post this question here.

Does mhcquant support Data-Independent Acquisition (DIA) data ?

If I want to analyze MHCII peptide, are there any specific parameters needs to be set ?

[jonasscheid]

Sorry to trouble again. I never heard about slack/discord and we cannot use them in our country. So I post this question here.

That is a bummer. I'll ask how chinese users can still be in touch with the nf-core Slack users.

Does mhcquant support Data-Independent Acquisition (DIA) data ?

No, currently only DDA. You can however generate spectrum libraries from DDA runs and then plug them into any DIA search engine (I jused DIA-NN 2 so far)

If I want to analyze MHCII peptide, are there any specific parameters needs to be set ?

Please check out the docs: https://nf-co.re/mhcquant/3.0.0/docs/usage/#recommended-search-settings