Astral Phospho Questions

[JackLeerson]

Hi all,

Just got a few questions about running astral phospho analyses.

1. Correct formatting of variable modifications:
   Are Phospho@STY and Phospho@S;Phospho@T;Phospho@Y equivalent?

2. If intending to do phospho analysis, I assume the library_prediction.peptdeep_model_type should be set to phospho? What change does this actually make?

3. Does the library generated depend at all on the phospho raw files you are providing, or will it be the same every time when you generate the library (so long as you set the same seed).

4. Should general.astral_ms1 be set to true? What does this actually do?

5. Is there anything else that should be changed from defaults to better work with phospho data? I've attached my config in case that helps.
   phospho_test.txt

6. Bonus Question: What does enabling MBR do with DIA data? It was my impression (and I thought this was true for maxquant), that this only really made sense for DDA data?

Thanks and sorry for all the questions!!
Jack