Waters DataConnect mzML format appears different depending on version

[chrashwood]

Initial development was performed on Waters .raw files subjected to either DataConnect (unsure of which version) or MSConvert. Both situations were covered in v1.1.

Recently, Waters raw data has been made available (https://glycopost.glycosmos.org/entry/GPST000467) so I downloaded and tested the Waters DataConnect (v2.1) process. Unfortunately, the formatting of the scans is different to what was originally accounted for in GlyCombo, so if v2.1 of DataConnect is used, it will crash.

Specific problem
Compatible:
<spectrum index="7" id="merged=7 function=2 process=0 spectra=1-3 scan=8" defaultArrayLength="874" dataProcessingRef="pwiz_Reader_Waters_conversion">
Not compatible:
<spectrum index="404" id="merged=404 function=2 process=0 scans=1-2" defaultArrayLength="346">

Current workaround: Use MSConvert instead or another version of DataConnect that doesn't crash GlyCombo.

Once we are sure about the versions of DataConnect and the different kinds of Waters mzML output, we will have a more comprehensive solution prepared.