Databases and associated tools for glycomics and glycoproteomics

Frederique Lisacek; Julien Mariethoz; Davide Alocci; Pauline M. Rudd; Jodie L. Abrahams; Matthew P. Campbell; Nicolle H. Packer; Jonas Ståhle; Göran Widmalm; Elaine Mullen; Barbara Adamczyk; Miguel A. Rojas-Macias; Chunsheng Jin; Niclas G. Karlsson

doi:10.1007/978-1-4939-6493-2_18

Databases and associated tools for glycomics and glycoproteomics

Frederique Lisacek, Julien Mariethoz, Davide Alocci, Pauline M. Rudd, Jodie L. Abrahams, Matthew P. Campbell, Nicolle H. Packer, Jonas Ståhle, Göran Widmalm, Elaine Mullen, Barbara Adamczyk, Miguel A. Rojas-Macias, Chunsheng Jin, Niclas G. Karlsson^*

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

49 Citations (Scopus)

Abstract

The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (Sugar Bind).

Original language	English
Title of host publication	High-throughput glycomics and glycoproteomics
Subtitle of host publication	Methods and protocols
Editors	Gordan Lauc, Manfred Wuhrer
Place of Publication	New York
Publisher	Humana Press Inc.
Chapter	18
Pages	235-264
Number of pages	30
ISBN (Electronic)	9781493964932
ISBN (Print)	9781493964918
DOIs	https://doi.org/10.1007/978-1-4939-6493-2_18
Publication status	Published - 2017

Publication series

Name	Methods in Molecular Biology
Volume	1503
ISSN (Print)	10643745

Keywords

Databases
Glycobioinformatics
HPLC
Mass spectrometry
NMR
Oligosaccharide
Omics

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10.1007/978-1-4939-6493-2_18

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Lisacek, F., Mariethoz, J., Alocci, D., Rudd, P. M., Abrahams, J. L., Campbell, M. P., Packer, N. H., Ståhle, J., Widmalm, G., Mullen, E., Adamczyk, B., Rojas-Macias, M. A., Jin, C., & Karlsson, N. G. (2017). Databases and associated tools for glycomics and glycoproteomics. In G. Lauc, & M. Wuhrer (Eds.), High-throughput glycomics and glycoproteomics: Methods and protocols (pp. 235-264). (Methods in Molecular Biology; Vol. 1503). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6493-2_18

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title = "Databases and associated tools for glycomics and glycoproteomics",

abstract = "The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (Sugar Bind).",

keywords = "Databases, Glycobioinformatics, HPLC, Mass spectrometry, NMR, Oligosaccharide, Omics",

author = "Frederique Lisacek and Julien Mariethoz and Davide Alocci and Rudd, {Pauline M.} and Abrahams, {Jodie L.} and Campbell, {Matthew P.} and Packer, {Nicolle H.} and Jonas St{\aa}hle and G{\"o}ran Widmalm and Elaine Mullen and Barbara Adamczyk and Rojas-Macias, {Miguel A.} and Chunsheng Jin and Karlsson, {Niclas G.}",

year = "2017",

doi = "10.1007/978-1-4939-6493-2_18",

language = "English",

isbn = "9781493964918",

series = "Methods in Molecular Biology",

publisher = "Humana Press Inc.",

pages = "235--264",

editor = "Gordan Lauc and Manfred Wuhrer",

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Lisacek, F, Mariethoz, J, Alocci, D, Rudd, PM, Abrahams, JL, Campbell, MP, Packer, NH, Ståhle, J, Widmalm, G, Mullen, E, Adamczyk, B, Rojas-Macias, MA, Jin, C & Karlsson, NG 2017, Databases and associated tools for glycomics and glycoproteomics. in G Lauc & M Wuhrer (eds), High-throughput glycomics and glycoproteomics: Methods and protocols. Methods in Molecular Biology, vol. 1503, Humana Press Inc., New York, pp. 235-264. https://doi.org/10.1007/978-1-4939-6493-2_18

Databases and associated tools for glycomics and glycoproteomics. / Lisacek, Frederique; Mariethoz, Julien; Alocci, Davide et al.
High-throughput glycomics and glycoproteomics: Methods and protocols. ed. / Gordan Lauc; Manfred Wuhrer. New York: Humana Press Inc., 2017. p. 235-264 (Methods in Molecular Biology; Vol. 1503).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

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AU - Mariethoz, Julien

AU - Alocci, Davide

AU - Rudd, Pauline M.

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AU - Campbell, Matthew P.

AU - Packer, Nicolle H.

AU - Ståhle, Jonas

AU - Widmalm, Göran

AU - Mullen, Elaine

AU - Adamczyk, Barbara

AU - Rojas-Macias, Miguel A.

AU - Jin, Chunsheng

AU - Karlsson, Niclas G.

PY - 2017

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AB - The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (Sugar Bind).

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KW - Glycobioinformatics

KW - HPLC

KW - Mass spectrometry

KW - NMR

KW - Oligosaccharide

KW - Omics

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DO - 10.1007/978-1-4939-6493-2_18

M3 - Chapter

C2 - 27743371

AN - SCOPUS:84991677937

SN - 9781493964918

T3 - Methods in Molecular Biology

SP - 235

EP - 264

BT - High-throughput glycomics and glycoproteomics

A2 - Lauc, Gordan

A2 - Wuhrer, Manfred

PB - Humana Press Inc.

CY - New York

ER -

Databases and associated tools for glycomics and glycoproteomics

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