Any issue with processing MS2 spectra with Peakonly?

[ghfzvc]

I understand that the code explicitly parses for ms_level=1 spectra, but would there be any issue with modifying the code to process ms_level=2?

Is there something unique about the code that would make targeted metabolomics more challenging to classify and integrate peaks for?

[valen320]

I didn't really understand your question. peakonly finds features, i.e. calculate areas of peaks in MS1 space of untargeted MS (unknown m/z's). For targeted MS you already have known list of masses to monitor for. That means, you don't have to search for unknown m/z's, just calculate areas for that list. It is easy to process even with vendor's software.