Hmmm ... you seem to be missing something. Briefly, a mass spec only measures ions. So by definition, all molecules are broken into ions, or they are missed by the detector. Now, molecular ions may form, but they're not formed from molecules, that's just what we call a molecule, that has a charge, that the system detects. You probably having trouble, because you're conflating atomic mass spec, of the sort used to understand the elements and their isotopes, and compound mass spec, which we use to understand (usually) large molecules.