title: Glycoproteomic and glycomic databases.
abstract: Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research.
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Deniz
authors.initials: D
authors.lastname: Baycin Hizal
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wolozny
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Colao
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Elena
authors.initials: E
authors.lastname: Jacobson
authors.affiliation: Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Tian
authors.affiliation: Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
authors.forename: Sharon S
authors.initials: SS
authors.lastname: Krag
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Betenbaugh
authors.affiliation: Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
references.citation: BMC Bioinformatics. 2008 Sep 19;9:384
references.pmid: 18803830
references.citation: Glycoconj J. 2012 Aug;29(5-6):249-58
references.pmid: 22699565
references.citation: Anal Chem. 2010 Mar 15;82(6):2588-93
references.pmid: 20170179
references.citation: Arch Biochem Biophys. 1970 Apr;137(2):460-8
references.pmid: 5462146
references.citation: Source Code Biol Med. 2007 Aug 07;2:3
references.pmid: 17683623
references.citation: J Proteome Res. 2011 Mar 4;10(3):1425-31
references.pmid: 21133419
references.citation: J Proteome Res. 2011 Jun 3;10(6):2777-84
references.pmid: 21480662
references.citation: Electrophoresis. 2011 Jan;32(1):3-13
references.pmid: 21171109
references.citation: Biochemistry. 1999 Oct 12;38(41):13602-9
references.pmid: 10521267
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):511-3
references.pmid: 12520065
references.citation: Methods Mol Biol. 2006;347:125-43
references.pmid: 17072008
references.citation: Electrophoresis. 2010 Apr;31(8):1389-95
references.pmid: 20309892
references.citation: Annu Rev Biochem. 2011;80:797-823
references.pmid: 21469953
references.citation: J Neurosci. 2006 Mar 22;26(12):3319-29
references.pmid: 16554482
references.citation: Mol Cell Proteomics. 2013 Apr;12(4):874-84
references.pmid: 23325767
references.citation: Nat Biotechnol. 2003 Jun;21(6):660-6
references.pmid: 12754519
references.citation: Nat Methods. 2011 Oct 09;8(11):977-82
references.pmid: 21983924
references.citation: Rapid Commun Mass Spectrom. 2005;19(12):1730-8
references.pmid: 15912476
references.citation: Glycobiology. 2007 Apr;17(4):411-22
references.pmid: 17223647
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):332-5
references.pmid: 11125129
references.citation: Nat Protoc. 2006;1(6):3019-27
references.pmid: 17406563
references.citation: Mol Cell Proteomics. 2013 Apr;12(4):866-73
references.pmid: 23438731
references.citation: Anal Chem. 2011 Jul 1;83(13):5296-303
references.pmid: 21591763
references.citation: Genome Biol. 2006;7(8):R73
references.pmid: 16901351
references.citation: Biol Chem. 2012 Nov;393(11):1357-62
references.pmid: 23109548
references.citation: Clin Proteomics. 2008 Dec 1;4(3-4):117-136
references.pmid: 21072318
references.citation: Annu Rev Anal Chem (Palo Alto Calif). 2011;4:367-92
references.pmid: 21456971
references.citation: Glycobiology. 2006 Jun;16(6):514-23
references.pmid: 16497783
references.citation: Mol Cell Proteomics. 2010 Apr;9(4):719-27
references.pmid: 20038609
references.citation: Mol Cell Proteomics. 2011 Jan;10(1):R110.003251
references.pmid: 20736408
references.citation: Acta Chem Scand. 1970;24(5):1839-41
references.pmid: 5487824
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D373-6
references.pmid: 21045056
references.citation: Liver Int. 2014 Jan;34(1):147-60
references.pmid: 23902602
references.citation: Development. 2008 May;135(10):1745-9
references.pmid: 18403407
references.citation: Anal Bioanal Chem. 2010 Aug;397(8):3457-81
references.pmid: 20225063
references.citation: J Proteome Res. 2009 Jul;8(7):3764-70
references.pmid: 19435342
references.citation: Methods Mol Biol. 2013;1022:387-402
references.pmid: 23765677
references.citation: Nature. 1998 Jan 29;391(6666):455-60
references.pmid: 9461212
references.citation: Analyst. 2013 Nov 7;138(21):6454-62
references.pmid: 24027776
references.citation: Expert Rev Proteomics. 2010 Oct;7(5):761-74
references.pmid: 20973647
references.citation: Glycobiology. 2006 May;16(5):82R-90R
references.pmid: 16478800
references.citation: J Biochem. 2008 Aug;144(2):139-47
references.pmid: 18390573
references.citation: Biochem Biophys Res Commun. 2003 Dec 19;312(3):601-7
references.pmid: 14680807
references.citation: Nat Biotechnol. 2003 Aug;21(8):879-83
references.pmid: 12894204
references.citation: FEBS J. 2010 Jan;277(1):95-105
references.pmid: 19919546
references.citation: Mol Biosyst. 2012 Nov;8(11):2850-6
references.pmid: 22892896
references.citation: J Inherit Metab Dis. 2011 Aug;34(4):853-8
references.pmid: 21384229
references.citation: Int J Proteomics. 2011;2011:601937
references.pmid: 22084691
references.citation: BioDrugs. 2010 Feb 1;24(1):9-21
references.pmid: 20055529
references.citation: Biomolecules. 2013 Feb 21;3(1):198-225
references.pmid: 24970165
references.citation: Proteomics. 2011 Feb;11(4):631-43
references.pmid: 21241022
references.citation: J Proteome Res. 2010 Apr 5;9(4):2037-41
references.pmid: 20143869
references.citation: Glycobiology. 2006 Feb;16(2):117-31
references.pmid: 16237199
references.citation: Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8256-61
references.pmid: 18550810
references.citation: Nat Methods. 2009 Nov;6(11):809-11
references.pmid: 19838169
references.citation: Anal Chem. 2011 Nov 15;83(22):8509-16
references.pmid: 21975078
references.citation: J Proteome Res. 2011 May 6;10(5):2612-24
references.pmid: 21469647
references.citation: Cell. 2010 May 28;141(5):897-907
references.pmid: 20510933
references.citation: Nat Biotechnol. 2003 Jun;21(6):667-72
references.pmid: 12754521
references.citation: J Proteome Res. 2010 Nov 5;9(11):5837-47
references.pmid: 20828161
references.citation: J Proteome Res. 2010 Oct 1;9(10):4952-9
references.pmid: 20698584
references.citation: Glycobiology. 2005 Feb;15(2):153-64
references.pmid: 15385431
references.citation: Mol Cell Proteomics. 2007 Dec;6(12):2100-9
references.pmid: 17761667
references.citation: Anal Bioanal Chem. 2012 May;403(5):1291-302
references.pmid: 21647803
references.citation: Bioinformatics. 2008 May 1;24(9):1214-6
references.pmid: 18344517
references.citation: Expert Opin Drug Discov. 2009 Jul 1;4(7):715-726
references.pmid: 19774094
references.citation: EMBO J. 2013 May 15;32(10):1478-88
references.pmid: 23584533
references.citation: BMC Bioinformatics. 2011 Apr 06;12:91
references.pmid: 21466708
references.citation: Mol Cell Proteomics. 2013 May;12(5):1294-305
references.pmid: 23389048
references.citation: J Proteome Res. 2003 Nov-Dec;2(6):618-25
references.pmid: 14692455
references.citation: Proteomics Clin Appl. 2010 Feb;4(2):124-32
references.pmid: 21137038
references.citation: Nucleic Acids Res. 1999 Jan 1;27(1):370-2
references.pmid: 9847232
references.citation: Gene. 1998 Sep 14;217(1-2):117-25
references.pmid: 9795179