Yes I will be neutralising my samples.
My mobile phase is 0.1% Formic Acid and 0.01%TFA in water and Methanol, so it is not exactly a buffer system.
Do you think I can still run the samples on MS-Ms or do I risk damaging the MS probe due to HCL/NaOH
If you'll be neutralizing it, then your main concern is the [Na+] concentration. What kind of concentrations are we talking here?
A small injection that contains non-volatile electrolytes, followed by a long enough chromatographic run, is unlikely to cause any rapid accumulation in the source as long as you do regular maintenance anyway. Moreover, once you are sure of your method you can divert flow to waste until some point between the end of the void volume and the elution of your first peak. In RPLC you can expect most elemental ions to elute with the void.
I don't know much about degradation, but the most common acid or base induced reactions are hydrolysis. Maybe your compounds of interest are just very stable to hydrolysis. What about oxidation, reduction, photodegradation etc?
For example I was analyzing some water samples for several pesticides including aldicarb and I prepared a calibration in DI water with 0.1% formic acid. Aldicarb did not degrade in my calibration solution, but my spike into the water sample had very poor aldicarb recovery. If I waited an hour after spiking, it was totally gone. On a whim I scanned for aldicarb sulfoxide and found it eluting at an earlier time in the spike but not my standards. I then tried spiking our own local drinking water and found the same thing happening albeit at a much slower rate. Turns out that in chlorinated water, aldicarb oxidizes very easily.