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 language | English (US) |
|---|---|
| Pages (from-to) | 1429-1434 |
| Number of pages | 6 |
| Journal | Journal of Proteome Research |
| Volume | 5 |
| Issue number | 6 |
| DOIs | |
| State | Published - Jun 2006 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - Automatic determination of O-glycan structure from fragmentation spectra
AU - Goldberg, David
AU - Bern, Marshall
AU - Li, Bensheng
AU - Lebrilla, Carlito B
PY - 2006/6
Y1 - 2006/6
N2 - 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.
AB - 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.
KW - Cartoon
KW - FT-ICR
KW - Glycomics
KW - MALDI-FTMS
KW - MS/MS
KW - O-glycan
KW - O-linked oligosaccharides
KW - Tandem mass spectrometry
UR - http://www.scopus.com/inward/record.url?scp=33745004837&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33745004837&partnerID=8YFLogxK
U2 - 10.1021/pr060035j
DO - 10.1021/pr060035j
M3 - Article
VL - 5
SP - 1429
EP - 1434
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
IS - 6
ER -