For our small molecules we certainly do µHPLC-/MS and -MS² for routine decoding; MALDI we use mainly for analytics of biomolecules such as peptides, nucleic acids and proteins (as most labs do); I did also work with nano HPLC, MECK and CE in the past. We also did a bit of carbohydrate analytics based on UV-detection as boric acid complexes. For our purpose, these are mainly analytical methods to check on the quality of our reagents that we then use in our single molecule experiments.