SWEET-DB: an attempt to create annotated data collections for carbohydrates

Loss, Alexander; Bunsmann, Peter; Böhne, Andreas; Loß, Annika; Schwarzer, Eberhard; Lang, Elke; Lieth, Claus‐Wilhelm von der

doi:10.1093/nar/30.1.405

Cited by 74 publications

(12 citation statements)

References 19 publications

(15 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It includes most of the theoretically possible spectra of Nand O-glycans, which were extracted from SweetDB. 17,18) e Oligosaccharide Subtree Constraint Algorithm ("OSCAR") restructures analyst-selected fragments into branching or linkage glycan structures and provides a de novo algorithm for identifying a glycan structure without being limited by presumed biosynthetic structures. In particular, OSCAR can interpret MSn data for permethylated O-linked oligosaccharides, but the disadvantage is that it cannot process LC-MS data smoothly.…”

Section: Ms Approaches For Released Glycan Analysismentioning

confidence: 99%

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

Tsai

Chen

2017

Mass Spectrometry

View full text Add to dashboard Cite

e purpose of this review is to provide updated information regarding bioinformatic so ware for the use in the characterization of glycosylated structures since 2013. A comprehensive review by Woodin et al. Analyst 138: 2793Analyst 138: -2803Analyst 138: , 2013 described two main approaches that are introduced for starting researchers in this area; analysis of released glycans and the identi cation of glycopeptide in enzymatic digests, respectively. Complementary to that report, this review focuses on mass spectrometry related bioinformatics tools for the characterization of N-linked and O-linked glycopeptides. Speci cally, it also provides information regarding automated tools that can be used for glycan pro ling using mass spectrometry.

show abstract

Section: Ms Approaches For Released Glycan Analysismentioning

confidence: 99%

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

Tsai

Chen

2017

Mass Spectrometry

View full text Add to dashboard Cite

show abstract

“…The Carbank institutors also implemented regular updates with information from new publications. Unfortunately, a funding crisis stopped this effort in the 1990s and the project was discontinued, but the assembled data lived on in the next-generation databases including SWEET-DB 46 and GlycosuiteDB 47 (later incorporated into UniCarbKB 48 and GlyConnect 49 , both having the same agenda as their ancestor. Then, integrative initiatives arose with the goal of centralising scattered data (e.g.…”

Section: The Current Landscape Of Glycomic E-infrastructuresmentioning

confidence: 99%

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

et al. 2019

View full text Add to dashboard Cite

The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.

show abstract

“…Glycosciences.DB , formerly known as SweetDB (7), was one of the first efforts to collect information on carbohydrate structures and make them available online. The database is part of the Glycosciences.de web portal (8), where it is freely accessible at http://www.glycosciences.de/database/.…”

Section: Introductionmentioning

confidence: 99%

Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)

Böhm

Bohne-Lang

Frank

et al. 2018

Nucleic Acids Research

View full text Add to dashboard Cite

Glycosciences.DB, the glycan structure database of the Glycosciences.de portal, collects various kinds of data on glycan structures, including carbohydrate moieties from worldwide Protein Data Bank (wwPDB) structures. This way it forms a bridge between glycomics and proteomics resources. A major update of this database combines a redesigned web interface with a series of new functions. These include separate entry pages not only for glycan structures but also for literature references and wwPDB entries, improved substructure search options, a newly available keyword search covering all types of entries in one query, and new types of information that is added to glycan structures. These new features are described in detail in this article, and options how users can provide information to the database are discussed as well. Glycosciences.DB is available at http://www.glycosciences.de/database/ and can be freely accessed.

show abstract

SWEET-DB: an attempt to create annotated data collections for carbohydrates

Cited by 74 publications

References 19 publications

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)

Contact Info

Product

Resources

About