I've read Why don't the manufacturers do these? a place for ideas... (BTW, great topic - please write more) and one of the ideas was:

lmh wrote:
Calculate the inner product of an LC-MS spectrum and the same spectrum shifted X units left. Soooo useful for neutral losses. This just means take a copy of the spectrum, move it X units leftwards, multiply each intensity of ion in the region where the two spectra overlap by its corresponding value in the other unshifted spectrum, and sum all the values. If you have a peak that fragments to something X units lighter (source fragmentation), it will be intense in both the unshifted and the shifted spectrum, and you get a big signal. This really does work, and is a valuable addition to single quads, and useful in ion-traps, where it will pick up things that weren't chosen for data-dependent fragmentation.
I have some questions:
1. Why do we want to multiply instead of adding the signals like we do for the isotopes? All these masses could relate to the same substance:
2. When extracting EIC - I assume all these fragments should be summed up to result in a bigger peak, right?
3. Shouldn't the detection of neutral loss be done automatically w/o manual intervention? Finding repeating patterns within the scan isn't too hard (that's where we'd multiply to get the inner product) though it will take more time to calculate.. Or do chemists want to have full control over this?
4. If the neutral loss contained Br or Cl this would result in a different isotopic pattern - would chemists try to figure out such neutral loss as well? I mean - is it practical?