Native top-down proteomics is enhanced by coupling separations to nMS analysis. To preserve noncovalent interactions between proteins and ligands, many traditional techniques for denaturing separations must be avoided. Therefore, a set of separation methods must be developed for native proteins and protein complexes.

Current search tools and databases neither contain nor consider non-covalent protein modification such as known cofactors and substrates. Rich information exists in various forms throughout the UniProt Knowledgebase. Tools to characterize non-covalent interactions in nTDMS must capture information from MS1, MS2 and MS3 data.