I have no idea of what you are working with....What is the phase of your species, etc...
However, you could look into isotopic labeling with NMR (assuming your compound can be determined using NMR).
MS gives you the fragments...putting them together can require further confirmational analysis.
Structural determination may require several analyses used in tandem. NMR, FTIR, UV/Vis, MS, etc...
Of course, I would always go with XRF and XRD whenever possible (faster and sample prep is simple).