Namely, there are two almost equivalent terms in PSI-MS fitting to that kind of fragmentation, and, further, there is a discrepancy in how MSConvert and TRFP represent these spectra. These discrepancies lead to problems with downstream tools.
It would be nice to have a community-recognized way to represent these types of spectra.
Participating in discussions about OpenMS (https://github.com/OpenMS/OpenMS/issues/7499) and TRFP (https://github.com/compomics/ThermoRawFileParser/issues/182) issues I learned that there is a certain uncertainty as to how spectra with supplemental activation (ETciD/EThcD) should be represented.
Namely, there are two almost equivalent terms in PSI-MS fitting to that kind of fragmentation, and, further, there is a discrepancy in how MSConvert and TRFP represent these spectra. These discrepancies lead to problems with downstream tools.
It would be nice to have a community-recognized way to represent these types of spectra.
I have opened an issue with PSI-MS (https://github.com/HUPO-PSI/psi-ms-CV/issues/285) to determine which CV term is preferred and I would be happy to hear your take on it.