Tests run fine and can see in the console output that ms2 scans are happening, but in the resulting mzML there are no ms2 scans.
Possibly the old problem that empty scans don't get written into the file?
Suggested fix: have at least one fragment in the scan.
Tests run fine and can see in the console output that ms2 scans are happening, but in the resulting mzML there are no ms2 scans. Possibly the old problem that empty scans don't get written into the file? Suggested fix: have at least one fragment in the scan.