What ions do I expect

This page applies only to AP-ESI and APCI. Those familiar with GC-MS will probably have used electron ionization, which forms a radical ion of the same mass as the neutral molecule. ES and APCI are different, in that they form conventional, non-radical ions. These are "quasi-molecular" ions, in that the molecule has not been fragmented in any way, but has become an ion by loss of a hydrogen ion, or by gain of some adduct, hydrogen, sodium etc. Therefore the mass is not that of the neutral molecule. Examples are given below.

Electrospray ionization is mostly about releasing ions created in solution into the gaseous phase. At the tip of the spray-nozzle, where the ions are about to enter the large electric field some quite complicated electrochemistry occurs, and potentially neutral molecules can be ionised. Nevertheless this is the conventional electrochemistry you would expect to see in solution, so the ions you see in electrospray mass spectrometry are exactly the sorts of ions you would see normally. Acid groups lose their proton and yield negative ions. Organic acids with -COOH groups, and things with phosphate groups therefore produce useful negative ions. Here for example is Glucose 6-phosphate:

Glucose 6-phosphate has a formula C₆H₁₃O₉P, so its Molecular Weight is 260. It shows up as G6P^-, after loss of one H⁺ at 259 Daltons. Some of the other peaks in this spectrum make sense. For instance, 519 is probably a dimer of G6P: (2 × 260) - H⁺ = 519.

This is very common. At high concentration (here 0.1mM), things often form dimers during ionisation. The dimer has several potential acid groups. 541 is probably a sodium salt of the dimer. It is 22amu above 519, indicating a 519-dimer that has lost another proton (-1) and in its place gained a sodium (+23). This is also very common, even if you think your sample contains no sodium. The source of the world's sodium is located somewhere in our LC system.

112.9 is a contaminant. These are also very common, and not just in our home-made spectra. It is worth checking a bit of baseline somewhere outside the region of interest to see what ions are present in the solvents and system at large.

198.9 although tiny is actually interesting. It is a fragment.

A useful characteristic of electrospray ionisation is that the ions are formed electrochemically in the nozzle, which means that they can still happen, even when they wouldn't have been present in high concentrations in the original sample. An weakly acidic analyte shouldn't by rights show up well when there's formic acid in the solvent, but fortunately it often does.

Atmospheric pressure chemical ionisation (APCI) is also a friendly method of ionisation that yields ions you would not be surprised to see in solution. It usually works by ionisation of the solvent, which then interacts with analyte molecules, for instance donating hydrogen ions to them. Again negative things tend to lose hydrogens. But APCI is most popular in its positive mode, where the ions are usually the molecule with an adduct, H⁺ and Na⁺ being the most common. Again, do not be surprised if you see sodium adducts in a chromatography run that theoretically contains no sodium at all. Peaks separated by 22amu (Na⁺ - H⁺) are diagnostic.

Further information is available on masses of ions.