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Historical Overview of Integrated GAG-omics and Proteomics

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Extracellular Matrix Omics

Part of the book series: Biology of Extracellular Matrix ((BEM,volume 7))

Abstract

The ECM is a complex molecular network that surrounds all cells and consists of proteins, glycoproteins, hyaluronan, glycosaminoglycans (GAGs), and proteoglycans (PGs). GAGs and PGs play vital roles in ECM-related processes such as cell migration, proliferation, adhesion, and differentiation. Among the omics technologies, including genomics, transcriptomics, and proteomics, glycomics is the least mature. Over the past two decades, with efforts from glycoscientists around world, and the advent of new glyco-techonologies, databases, tools, and methods, much progress has been made. Now, the focus is to integrate proteomics and glycomics domains in a new platform to analyze and characterize biomolecule classes and define their structural and functional roles. Towards this end, we have developed approaches that integrate analysis of GAGs and proteins towards an end goal of elucidating pathophysiological mechanisms to inform development of disease therapies and regenerative medicine. In this chapter, we provide a historical overview of our groups’ methods for glycomics, glycoproteomics, and proteomics of key ECM constituents, i.e., GAGs and PGs, as reported over the past decade.

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Abbreviations

CE:

Capillary electrophoresis

CS:

Chondroitin sulfate

DS:

Dermatan Sulfate

ECM:

Extracellular matrix

GAGs:

Glycosaminoglycans

GalNAc:

N-acetylgalactosamine

GlcA:

Glucuronic acid

GlcNAc:

N-acetylglucosamine

HA:

Hyaluronic acid

HEP:

Heparin

HILIC:

Hydrophilic interaction chromatography

HS:

Heparan sulfate

IdoA:

Iduronic acid

IMS:

Imaging mass spectrometry

IPRP:

Ion-pair reversed-phase chromatography

KS:

Keratan sulfate

LC:

Liquid chromatography

LIF:

Laser-induced fluorescence

MALDI:

Matrix-assisted laser desorption/ionization

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

MWCO:

Molecular weight cut-off filters

PGs:

Proteoglycans

PNNs:

Perineuronal nets

PTMs:

Post-translational modifications

SEC:

Size exclusion chromatography

TOF:

Time-of-flight

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Acknowledgements

This work was supported by NIH grants P41GM104602, R01MH105608, and R01GM133963.

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Authors and Affiliations

  1. Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA

    Manveen K. Sethi & Joseph Zaia

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  1. Manveen K. Sethi
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Correspondence to Joseph Zaia .

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  1. Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), Université Claude Bernard Lyon 1, Villeurbanne Cedex, Lyon, France

    Sylvie Ricard-Blum

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Sethi, M.K., Zaia, J. (2020). Historical Overview of Integrated GAG-omics and Proteomics. In: Ricard-Blum, S. (eds) Extracellular Matrix Omics. Biology of Extracellular Matrix, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-030-58330-9_5

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