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GlycomeDB specifications

Information


Unique identifier OMICS_06786
Name GlycomeDB
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GlycomeDB

Maintainer


  • person_outline René Ranzinger

Publication for GlycomeDB

GlycomeDB citations

 (7)
library_books

pGlyco 2.0 enables precision N glycoproteomics with comprehensive quality control and one step mass spectrometry for intact glycopeptide identification

2017
Nat Commun
PMCID: 5585273
PMID: 28874712
DOI: 10.1038/s41467-017-00535-2

[…] Da), acetylation on protein N-term (+42.011 Da). The N-glycosylation sequon (N-X-S/T, X ≠ P) was modified by changing ‘N’ to ‘J’ (the two shared the same mass). The glycan database was extracted from GlycomeDB (www.glycome-db.org), total entries of N-glycan were 7884 by considering NeuGc. The protein databases used were different for each sample:The standard glycoprotein mixtures.Protein database […]

library_books

GLYDE II: The GLYcan data exchange format

2016
PMCID: 5611833
PMID: 28955652
DOI: 10.1016/j.pisc.2016.05.013

[…] LINUCS (), the BCSDB format () and LinearCode® (), as well as connection table representations, such as GlycoCT (), WURCS () and KCF () and XML representations, such as CabosML (). The development of GlycomeDB (), a meta-database for glycan structures, has been a major step towards the integration of this structural data. More recently, the GlyTouCan glycan structure repository () has been impleme […]

library_books

Mass Spectrometry Based N Glycomics of Colorectal Cancer

2015
Int J Mol Sci
PMCID: 4691109
PMID: 26690136
DOI: 10.3390/ijms161226165

[…] ntric databases into a common platform called UnicarbKB [] and UnicarbDB [], which act as centralized data repositories for glycan data and work on the interface with the already available glycomics (GlycomeDB, EUROcarbDB) and proteomics (Uniprot) databases [,]. Other glyco-related databases include Glycosciences.de, Kyoto Encyclopaedia of Gene and Genomes Glycans (KEGG Glycans), and the consortiu […]

call_split

Site Specific Glycan Microheterogeneity of Inter Alpha Trypsin Inhibitor Heavy Chain H4

2014
J Proteome Res
PMCID: 4084840
PMID: 24884609
DOI: 10.1021/pr500394z
call_split See protocol

[…] using the msconvert tool from ProteoWizard (v 2.1). The GlycoPeptideSearch (GPS) tool was used to match glycopeptides to CID MS/MS spectral data sets, with a subset of human N-glycan structures from GlycomeDB that have been annotated to indicate consistency with known glycosylation enzymes (GlycO)., Specific and semispecific in silico trypsin and endoproteinase GluC digests (for analysis of N-gly […]

library_books

Introducing glycomics data into the Semantic Web

2013
J Biomed Semantics
PMCID: 4177142
PMID: 24280648
DOI: 10.1186/2041-1480-4-39

[…] To test whether it would be possible to link lectin information with glycan structures, we used the PDB information [] in the LfDB data. Since GlycomeDB contained PDB IDs for glycan structures found in them, we could obtain the glycan structures in GlycoCT format. GlycomeDB provides references to PDB entries containing glycans which have bee […]

library_books

Correct primary structure assessment and extensive glyco profiling of cetuximab by a combination of intact, middle up, middle down and bottom up ESI and MALDI mass spectrometry techniques

2013
MAbs
PMCID: 3851223
PMID: 23924801
DOI: 10.4161/mabs.25423

[…] yielding both the precise glycan and the peptide MW from a single glycopeptides MS/MS spectrum. In step 3, Bruker’s GlycoQuest glycan search engine in ProteinScape obtained glycan identifications via GlycomeDB database searches using the glycan fragments of the glycopeptide MS/MS spectra. Several input parameters were specified for the search: the glycan type was restricted to N-glycan; taxonomy a […]

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GlycomeDB institution(s)
German Cancer Research Center, DKFZ, Core Facility, Molecular Structure Analysis, Heidelberg, Germany

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