Annotation with multiple condition characteristics

[brookegenovese]

Hi MSstats team,
Thanks for all your work on this tool!

I have a complex study design and I'm trying to ascertain the best modeling strategy for this data with MSstats. This is a DIA label-free dataset with no repeated measures (n=37) with three disease states (control, disease1, and disease2) but I have additional metadata, such as sex, day post infection, and batch designations, that I'd like to retain. Would I need to code these in under Condition on the annotation file as [disease state]_[sex]_[dpi]and would this strategy carry through the groupComparison function?

Thanks very much for any guidance you have here!