# Why do we subtract the mass of one proton in mass spectrometry (negative mode)?

This is probably very basic, but I have been given the understanding that we subtract the mass of only one proton when looking for our compound in a mass spectrometry (negative mode). I dont really understand why we are only subtracting the mass of one proton when our compound could potentially loose more than one proton at higher pH?

In example, the amino acid glutamate, would it not loose or gain more than one proton is a negative (higher pH) or positive (lower pH) mode mass spectrometry (MS)? Perhaps I have misunderstood the concept of negative and positive mode for MS?

• Higher pH is rarely used in LCMS due to possibility of damaging column packing usually made of $\ce{SiO2}.$ – andselisk Jun 9 at 9:07
• This question concerns the MS, not the column, but some columns do tolerate higher pH as far as I understand it? – CuriousTree Jun 9 at 9:10
• I concluded from "mass spectrometry chromatogram" that you are asking about LCMS meaning the backend is a chromatographic column. And from from I heard, there is rarely a need to go with higher pH for amino acid assays and switching to other packing material like $\ce{ZrO2},$ which are usually considerably more expensive and have their own quirks. – andselisk Jun 9 at 9:14
• ah okay, thanks for the input! I also assume the higher or lower pH is relative (i.e. not always extreme), but in general sticking to a neutral pH range is more common. Im not all that familiar with this topic, so I will remove the 'chromatography' word to clarify my question. – CuriousTree Jun 9 at 9:34