When determining the mass of the order of 500 Da on the Orbitrap, the measured masses of the starting compound and some of its fragments are less than the calculated ones by 0.018 Da. Could this be due to the dissociation of a proton from our compound in a mass spectrometer? Could Orbitrap indeed see it?
Hi there
You can probably give more details
How long it has been since you calibrated the instrument?
Is the analysis performed after chromatographic separation or in infusion mode?
Depending on the instrument the mass accuracy (error) should be within the specs of the instrument (36ppm for your 0.018Da @500Da)
Is the experiment done in positive or negative mode?
Hope this helps
Hello. Thank you, we do not have such mistakes. I would like to know in principle - if one mass is flying, and during the flight one hydrogen flies, whether Orbitrap will see a reduced mass.
A mass difference of 0.018 Da (in general) is very good depending on what resolving power mode you are running. Since you say that its a systematic shift of 0.018 Da for the precursor and product ions, you probably just need to recalibrate your mass scale.
Because mass spectrometry analyzes gas-phase ions, of course you can lose a Hydrogen or other funny effects not normally seen in solvent-based chemistry. You just have to be able to rationalize that chemistry.
Thank you. But if in one dimension, one mass is exact, while others have a mass defect, then the calibration has nothing to do with it.
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