When adding a substance with just EMW, is it a mass of M or M+H?

[ctapobep]

If Substance added as just an EMW (which isn't advised!), we can treat it either as the original M (in Da, that's how Peaksel actually works) or as M+H (as m/z). Each approach has its pros and cons which are described below. When going through the explanations consider the situation when we have both ES+ and ES- in an injection.

Substance's EMW is the actual mass of the substance

Pros:

• If user knows a mass of the substance, they can just enter that mass. Peaksel will add/subtract the respective fragments for the user.
• We can create EICs for both modes. Though if we guessed the substance mass incorrectly, the 2nd chromatogram will be empty.
• Theoretically, since we know the mass of the substance, we can add all other possible masses of the substance according to the fragments. This isn't necessarily correct, especially if we want to consider fragment loss - we don't really know if that fragment was present in the analyte. But user could see the whole distribution of masses and select/unselect the m/z that we presented them with. And maybe the user can then change their mind and switch to another m/z which fits the actual isotope pattern better. But still - we keep working with patterns, not just one value.
• Furthermore in the future we could develop smarter algorithm, and when user clicks on the spectrum - guess which ion species that actually is by the presence of neighboring m/z.

Cons:

• When clicking on the spectrum, we actually add a substance with a different mass - not what user clicked on. And that mass isn't necessarily the true mass of the substance because it's only our assumption that the original m/z was for $M+H$ or $M-H$.
• Suppose the ionizing fragment is something that has an isotope distribution of its own ($[M+Cl]⁻$), then when clicking on the spectrum, we have to decide which isotope the user clicked on. And the choice may be incorrect.

Entered EMW is the ionized m/z (M+H or M-H)

Whatever user enters - we just extract that value from the spectra. This approach assumes that only one ion is considered for each ionization mode, even if the processing method contains more ions/neutral fragments. If user wants more ions, they have to add them manually one by one instead of relying on fragments (H, Na, BOC, etc) and their permutation.

Pros:

• This is an honest approach, because Peaksel doesn't really know the true mass of the substance.
• When adding a substance by clicking on the spectrum, we don't modify the EMW. User sees whatever they clicked on.

Cons:

• If there are 2 ionization modes enabled, we can create an EIC only for the one the user clicked on.
• Additional complication if the value is entered manually in the Add Substance dialog. Then which mode we think this value is for? We'd have to complicate user's life and make him choose the mode explicitly?
• In the Mass Spec settings of the substance we'd have to show only one mode, and potentially allow adding the ion for another mode. But if that's done, then what's going to be the the substance display name? By default it'll stay as the initial m/z. Weird and confusing.
• What if it's an upload for the whole batch? How to determine the mode for which the upload is happening? More columns in the CSV?