Algorithms and design strategies towards automated glycoproteomics analysis

Mass Spectrom Rev. 2017 Jul;36(4):475-498. doi: 10.1002/mas.21487. Epub 2016 Jan 4.

Abstract

Glycoproteomics involves the study of glycosylation events on protein sequences ranging from purified proteins to whole proteome scales. Understanding these complex post-translational modification (PTM) events requires elucidation of the glycan moieties (monosaccharide sequences and glycosidic linkages between residues), protein sequences, as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts. Compared with proteomics, bioinformatics for glycoproteomics is immature and many researchers still rely on tedious manual interpretation of glycoproteomics data. As sample preparation protocols and analysis techniques have matured, the number of publications on glycoproteomics and bioinformatics has increased substantially; however, the lack of consensus on tool development and code reuse limits the dissemination of bioinformatics tools because it requires significant effort to migrate a computational tool tailored for one method design to alternative methods. This review discusses algorithms and methods in glycoproteomics, and refers to the general proteomics field for potential solutions. It also introduces general strategies for tool integration and pipeline construction in order to better serve the glycoproteomics community. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:475-498, 2017.

Keywords: bioinformatics; glycoinformatics; glycoproteins; glycoproteomics; mass spectrometry.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Algorithms*
  • Carbohydrate Sequence
  • Computational Biology / instrumentation
  • Computational Biology / methods*
  • Computational Biology / standards
  • Glycomics / instrumentation
  • Glycomics / methods*
  • Glycomics / standards
  • Glycoproteins / analysis*
  • Glycoproteins / chemistry
  • Glycosides / analysis
  • Glycosides / chemistry
  • Glycosylation
  • Humans
  • Mass Spectrometry / instrumentation
  • Mass Spectrometry / methods*
  • Mass Spectrometry / standards
  • Monosaccharides / analysis
  • Monosaccharides / chemistry
  • Peptide Fragments / analysis
  • Peptide Fragments / chemistry
  • Peptide Mapping / methods
  • Peptide Mapping / statistics & numerical data
  • Protein Processing, Post-Translational*
  • Proteome / analysis
  • Proteome / chemistry
  • Software

Substances

  • Glycoproteins
  • Glycosides
  • Monosaccharides
  • Peptide Fragments
  • Proteome