The global proteomics was done one a TIMSTOF with diaPASEF and analysis in SpectroNaut. The glycoproteomics was done following some sort of chemical enrichment thing followed by TMT proteomics. It's a big 'ol pile of files.
I was looking for how they would normalize the glycopeptides against the whole protein concentrations and they actually include that part in the method section! Our puppy just scratched our kid, sounds minor, but I've got to stop typing here even though I haven't got to how they used some combination of ETD and HCD to do the glycan and TMT based quan. Worth checking out though!
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