Thank you @jjjvanderhooft for your comments and advice. Indeed the moiety being cleaved off will often ionize in one mode only, in which case it will be seen as a neutral loss in one mode and as a peak (with possible fragments) in the other. This should be taken into account but so far I haven't had enough data to classify the information based on that.
I have been looking for a comprehensive list of neutral losses commonly seen in MS/MS spectra but haven't been able to find one. Instead, I've started to compile a list on my own with some additional information, such as the functional groups to which the neutral loss may be related and how the moieties may be further fragmented. You can access and use the list in Excel format using the OneDrive link below and expand it freely. Also, any good source for additional information is most welcome.