My group's started using limpa and we're considering adopting it for all our proteomics analyses. We have some data with PTMs (most commonly phosphorylation) - is there a way to study these protein modifications with limpa or use limpa's methods as part of such an analysis? Thanks for the package!

Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with dpcImpute(), to tell limpa you want to keep each row separate instead of summarizing at the protein level. Otherwise the whole pipeline is unchanged.