Is it possible to differentiate acid form from its salt form when you characterize a compound by LC-MS? Thanks for the comments.

The only way I can figure, would be to look for the counter-ion. If the counterion is something like sodium or potassium, you'll have a hard time with LC/MS. If it's an organic molecule, you'll have better luck. I've tried briefly a time or two, and was unable to see "naked" sodium or potassium ions by LC/MS. On the other hand, I have seen anions like chloride and H2PO4- in negative ESI.

MG,

Thanks for your response. The counter ion of my compound is NH4+. Will ESI(+) be sensitive to look at it in such low mass range?

I've never tried to look for NH4+, so I don't know. If you want to try the experiment, be sure you're not using any ammonium salts in your mobile phase or diluent, and flush your lines really well as they have probably had ammonium salts in them before (if yours is like most LC/MS systems). If your compound is precious, you might want to start by injecting some ammonium acetate or ammonium formate solutions to see if you can detect NH4+ ions. I would expect the ammonium to be unretained on an RP column, but maybe some of the more experienced chromatographers here have a better feel for how it would behave.

Let me add that, although this is a neat experiment, I have never heard of anyone doing this to get useful quantitative information. That doesn't mean it isn't possible, but it might be difficult.

Something else you could do that is more likely to be useful, would be to get a pure standard of the acid form (if possible), and use it to quantitate the mass of the free acid in your "test sample". However much free acid you find in your test sample, the rest is the counterion plus other impurities.

In order to find the difference between an acid form and a salt form of an analyte, you should look at the problem differently: in most reliable and reproducible chromatographic methods, the ions are separated from each other (e.g. when you use a buffer in the mobile phase in reversed-phase HPLC). Thus the problem is a question of determining the presence or the absence of ammonia. You could do this by ion chromatography.
I don't know what your MS will do at the mass of 18+. This should be reasonably specific, but I have no clue if the instruments work down there.
If you do not work with a buffer or some other means to control the pH and the ionization of your compounds, strange things happen with salts in reversed-phase chromatography. For an analytical problem, I recommend not to do get into this area. Way too complicated!

No! Unless you have an instrument specifically designed for this purpose, there's really no chance it will work at mass 18. Generally, instruments are designed so that the sensitivity is rather poor below mass 100 in order to minimize problems with background from solvent and reagents. Dionex sells a mass spectrometer (the MSQ) with an extended low mass range which can detect low molecular weight molecules. The lower limit of molecular weight on this instrument is 18, so ostensibly this might seem plausible on this instrument. However, ammonium ion is commonly used as a "volatile buffer ion" and its detection in an electrospray system is extremely unlikely even on such an instrument given the volatility of ammonium ion.