A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins

Hyun Joo An, John S. Tillinghast, David L. Woodruff, David M Rocke, Carlito B Lebrilla

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

A new computer program, GlycoX, was developed to aid in the determination of the glycosylation sites and oligosaccharide heterogeneity in glycoproteins. After digestion with the nonspecific protease, each glycan at a specific glycosylation site contains a small peptide tag that identifies the location of the glycan. GlycoX was developed in MATLAB requiring the entry of the exact masses of the glycopeptide and the glycan spectra in the form of a mass-intensity table and taking advantage of the accurate mass capability of the mass analyzer, in this case a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer. This program computes not only the glycosylation site but also the composition of the glycans at each site. Several glycoproteins were used to determine the efficacy of GlycoX. These glycoproteins range from the simple, with one site of glycosylation, to the more complex, with multiple (three) sites of glycosylation. The results obtained using the computer program were the same as those determined manually. Model glycoproteins yielded the correct results, and new glycoproteins with unknown glycosylation were examined with the site of glycosylation and the corresponding glycans determined. Furthermore, other functions in GlycoX, including an auto-isotope filter to identify monoisotopic peaks and an oligosaccharide calculator to obtain the oligosaccharide composition, are demonstrated.

Original languageEnglish (US)
Pages (from-to)2800-2808
Number of pages9
JournalJournal of Proteome Research
Volume5
Issue number10
DOIs
StatePublished - Oct 2006

Fingerprint

Glycosylation
Oligosaccharides
Computer program listings
Glycoproteins
Software
Polysaccharides
Cyclotrons
Cyclotron resonance
Glycopeptides
Mass spectrometers
Fourier Analysis
Chemical analysis
Isotopes
MATLAB
Digestion
Fourier transforms
Peptide Hydrolases
Ions
Peptides

Keywords

  • Glycosylation site
  • Isotope filter
  • Mass spectrometry
  • Oligosaccharide calculator
  • Oligosaccharide heterogeneity
  • Software

ASJC Scopus subject areas

  • Genetics
  • Biotechnology
  • Biochemistry

Cite this

A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins. / An, Hyun Joo; Tillinghast, John S.; Woodruff, David L.; Rocke, David M; Lebrilla, Carlito B.

In: Journal of Proteome Research, Vol. 5, No. 10, 10.2006, p. 2800-2808.

Research output: Contribution to journalArticle

An, Hyun Joo ; Tillinghast, John S. ; Woodruff, David L. ; Rocke, David M ; Lebrilla, Carlito B. / A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins. In: Journal of Proteome Research. 2006 ; Vol. 5, No. 10. pp. 2800-2808.
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