Automatic determination of O-glycan structure from fragmentation spectra

David Goldberg, Marshall Bern, Bensheng Li, Carlito B Lebrilla

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Glycosylation is one of the most important classes of post-translational protein modifications, but the identification of glycans is difficult because of their branched structures and numerous isomers. We describe an algorithm called Cartoonist Two that proposes structures for O-linked glycans by automatically analyzing fragmentation mass spectra. Cartoonist Two improves upon previous glycan identification software primarily in its scoring function, which can more successfully distinguish among a number of similar structures. Cartoonist Two was designed and tested with FTICR mass spectra, and includes automatic recalibration and peak selection especially tuned for such data, yet it can be easily adapted to fragmentation spectra (MS2 or MSn) from other instrument types. On a validated test set of 34 SORI-CID MSn FTICR spectra from Xenopus egg jelly, Cartoonist Two gave the manually determined structural assignment either the first or second highest score over 90% of the time. And for over 50% of these spectra, Cartoonist Two selected a unique highest scoring structure that agreed with the manually determined one.

Original languageEnglish (US)
Pages (from-to)1429-1434
Number of pages6
JournalJournal of Proteome Research
Volume5
Issue number6
DOIs
StatePublished - Jun 2006
Externally publishedYes

Fingerprint

Polysaccharides
Glycosylation
Post Translational Protein Processing
Xenopus
Isomers
Ovum
Software
Proteins

Keywords

  • Cartoon
  • FT-ICR
  • Glycomics
  • MALDI-FTMS
  • MS/MS
  • O-glycan
  • O-linked oligosaccharides
  • Tandem mass spectrometry

ASJC Scopus subject areas

  • Genetics
  • Biotechnology
  • Biochemistry

Cite this

Automatic determination of O-glycan structure from fragmentation spectra. / Goldberg, David; Bern, Marshall; Li, Bensheng; Lebrilla, Carlito B.

In: Journal of Proteome Research, Vol. 5, No. 6, 06.2006, p. 1429-1434.

Research output: Contribution to journalArticle

Goldberg, David ; Bern, Marshall ; Li, Bensheng ; Lebrilla, Carlito B. / Automatic determination of O-glycan structure from fragmentation spectra. In: Journal of Proteome Research. 2006 ; Vol. 5, No. 6. pp. 1429-1434.
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