"How can you infer what the molecule is made of by preserving it? Without ionizing it?
Correct. The problem is that TOO MUCH fragmentation loses needed information. You want at least SOME of the parent molecules to be intact or largely so, yet be ionized. So you have somewhat contradictory needs, and are working on balancing them.
And the bigger the molecule, the more difficult that balancing act gets.
"Do you hit the molecule with different wavelength photons?
AFAIK, that has not been used, or not widely used. Lasers HAVE been used to blast things off surfaces to get composition analysis, as with metal samples.
Cool. Thanks for explaining it to me.