plantGlycoMS is a set of tools, implemented in R, which is used to assess and validate glycopeptide spectrum matches (gPSMs). Validity of gPSMs is based on characteristic fragmentation patterns of glycopeptides (gPSMvalidator), adherence of the glycan moiety to the known N-glycan biosynthesis pathway in plants (pGlycoFilter), and elution of the glycopeptide within the observed retention time window of other glycopeptides sharing the same peptide backbone (rt.Restrict). plantGlycoMS also contains a tool for relative quantitation of glycoforms based on selected ion chromatograms of glycopeptide ion precursors in the mass spectrometry level 1 data (glycoRQ). This protocol walks the user through this workflow with example mass spectrometry data obtained for a plant glycoprotein.
Keywords: Glycopeptide; Glycoprotein; Glycoproteomics; Mass spectrometry; N-glycosylation; Plant; R statistical computing environment.