I have seen many researchers use (and instruct on how to use) Limma for analyzing genomics data. What are the changes that need to be made to the way Limma is used for analyzing Proteomics data?

Thank you so much.

This will depend on what data you intend to use. If you have spectral counts, limma is not a good choice (see msmsTests instead). Otherwise, limma can be used as is for proteomics data. What you will need to do is to process/normalise your data, ... according to the mass spectrometry and quantitation you have used. But that's independent of limma, really.