I'm analyzing some DIA data that was processed in DIANN, where the output is MaxLFQ intensity. I see in the documentation that DEqMS uses intensity data and number of peptide counts. How can I run DEqMS using just the MaxLFQ protein intensities and ignore the pep.count.table step? Is the pep.count.table really necessary if my list of proteins have already been filtered based on number of peptides etc.,? I may be understanding this incorrectly but DIANN output looks like it already accounts for the peptide filtering in pep.count.table.

You can't run DEqMS without the peptide counts because using the peptide counts is the whole purpose of that package. The peptide counts are not used for filtering but rather for variance modeling.

DEqMS actually consists of wrapper functions for limma. If you don't have the peptide counts, then you just run an ordinary limma analysis (as I've suggested to you previously).

Even if you did have the peptide counts, you would still be able to do same analysis as DEqMS but directly in limma. To do the DEqMS analysis directly in limma just set trend = PeptideCount when running the eBayes() step. No other change is necessary.