Characterization of Plant Glycoproteins: Analysis of Plant Glycopeptide Mass Spectrometry Data with plantGlycoMS, a Package in the R Statistical Computing Environment

Methods Mol Biol. 2018:1789:205-220. doi: 10.1007/978-1-4939-7856-4_16.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Glycopeptides / analysis*
  • Glycoproteins / chemistry*
  • Glycosylation
  • Mass Spectrometry / methods*
  • Plant Proteins / chemistry*
  • Plants / chemistry*
  • Polysaccharides / analysis*
  • Software
  • Workflow

Substances

  • Glycopeptides
  • Glycoproteins
  • Plant Proteins
  • Polysaccharides