High-Throughput Glycomics and Glycoproteomics: Methods and Protocols

275 Pages·2017·9.624 MB·English

by  Gordan Lauc, Manfred Wuhrer (eds.)

Methods in
Molecular Biology 1503
Gordan Lauc
Manfred Wuhrer Editors
High Throughput
Glycomics and
Glycoproteomics
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB , UK
For further volumes:
http://www.springer.com/series/7651
High-Throughput Glycomics
and Glycoproteomics
Methods and Protocols
Edited by
Gordan Lauc
Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
Manfred Wuhrer
Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
Editors
Gordan Lauc Manfred Wuhrer
Faculty of Pharmacy and Biochemistry Center for Proteomics and Metabolomics
University of Zagreb Leiden University Medical Center
Zagreb, Croatia Leiden , The Netherlands
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-6491-8 ISBN 978-1-4939-6493-2 (eBook)
DOI 10.1007/978-1-4939-6493-2
Library of Congress Control Number: 2016948215
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Prefa ce
Carbohydrates — or glycans—are a highly abundant class of biomolecules and can be found
in various shapes and sizes in all kingdoms of life. Glycans often exist in the form of oligo-
or polysaccharides as well as glycoconjugates, i.e., with a covalent linkage of the glycan
portion to proteins or lipids. Glycans signifi cantly contribute to the structure and function
of the majority of proteins. Interindividual variability in both glycome composition and
glycome changes after environmental challenge is large, and these differences strongly
affect many physiological functions. Due to chemical and biological complexity of glycans,
the knowledge about glycans is lagging signifi cantly behind the knowledge about genes and
proteins. However, recent comprehensive report endorsed by the US National Academies
concluded that “glycans are directly involved in the pathophysiology of every major dis-
ease” and the interest in glycomics studies is growing exponentially.
The analysis of glycans is an often challenging endeavor, due to their heterogeneity, their
non-template-based synthesis, and the abundance of functionally distinct isomers which are
challenging for separation and characterisation using current analytical techniques.
Technological challenges in g lycan analysis are generally seen as the major obstacle for reveal-
ing insights into functional relevance of glycans. In the last few years several robust methods
that enable h igh-throughput analysis of glycans have been developed and glycomics is now
ready to join genomics and other o mics in genetic, epidemiological, and clinical studies.
This volume of Methods in Molecular Biology entitled H igh-Throughput Glycomics and
Glycoproteomics brings detailed protocols for the analysis of glycosylation at the level of free
glycans and glycopeptides, an essential reference for researchers planning to enter this rap-
idly evolving fi eld. The importance of glycans in eukaryotic life, with a focus on mammals
and particularly humans, is highlighted in Chapter 1 of this issue. The following chapters
largely have a focus on recent technologies that allow the characterization of larger sets of
samples, and major attention has been paid to method repeatability and robustness as well
as higher throughput with respect to sample preparation, measurement, and data analysis .
The chapters span a wide range of techniques, including the analysis of fl uorescently labeled
glycans with HPLC, LC-MS analysis of glycopeptides both for glycosylation profi ling and
for in-depth tandem mass spectrometric analysis of protein glycosylation, and the analysis
of glycans with fl uorescent labeling and capillary electrophoresis in conjunction with laser-
induced fl uorescence detection. The chapters also pay attention to specifi c sample types
including brain tissues , N-glycans from in vitro cell cultures, milk o ligosaccharides , inverte-
brate and protist N-glycans as well as p lant glycans .
We thank all the contributors, who are leading researchers in analytical g lycomics and
developers as well as expert users of the presented methods, for sharing their protocols in
this volume. We thank Dr. John Walker, the Editor-in-Chief of the Methods in Molecular
Biology series, for his guidance and continuous support.
Zagreb, Croatia Gordan Lauc
Leiden, The Netherlands Manfred Wuhrer
v
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 U biquitous Importance of Protein Glycosylation. . . . . . . . . . . . . . . . . . . . . . . 1
Jasminka Krištić and Gordan Lauc
2 L aboratory Experimental Design for a Glycomic Study . . . . . . . . . . . . . . . . . . 1 3
Ivo Ugrina , H arry Campbell , and Frano Vučković
3 H igh-Throughput Analysis of the IgG N-Glycome by UPLC-FLR . . . . . . . . . 2 1
Maja Pučić-Baković
4 H igh-Throughput Analysis of IgG Fc Glycopeptides by LC–MS . . . . . . . . . . . 3 1
David Falck , B as C. Jansen , N oortje de Haan ,
and M anfred Wuhrer
5 S ialic Acid Derivatization for the Rapid Subclass- and Sialic Acid
Linkage-Specific MALDI-TOF-MS Analysis of IgG Fc-Glycopeptides. . . . . . . 49
Noortje de Haan , K arli R. Reiding , and Manfred Wuhrer
6 T he Use of Multiple Reaction Monitoring on QQQ-MS for the Analysis
of Protein- and Site-Specific Glycosylation Patterns in Serum . . . . . . . . . . . . . 63
L. Renee Ruhaak
7 A nalysis of Permethylated Glycan by Liquid Chromatography (LC)
and Mass Spectrometry (MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Shiyue Zhou , K erry M. Wooding , and Yehia Mechref
8 H igh-Throughput Analysis of the Plasma N -Glycome by UHPLC . . . . . . . . . 9 7
Barbara Adamczyk , H enning Stöckmann , R óisín O’Flaherty ,
Niclas G. Karlsson , and Pauline M. Rudd
9 S ite-Specific N - and O -Glycopeptide Analysis Using an Integrated
C18-PGC-LC-ESI-QTOF-MS/MS Approach . . . . . . . . . . . . . . . . . . . . . . . . 109
Kathrin Stavenhagen , H annes Hinneburg , D aniel Kolarich ,
and M anfred Wuhrer
10 A nalysis of Milk Oligosaccharides by Mass Spectrometry. . . . . . . . . . . . . . . . . 1 21
Lauren D. Wu , L . Renee Ruhaak , and Carlito B. Lebrilla
11 N - and O -Glycomics from Minor Amounts of Formalin-F ixed,
Paraffin-Embedded Tissue Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 31
Hannes Hinneburg , F alko Schirmeister , P etra Korać , and Daniel Kolarich
12 C arbohydrate Microarray Technology Applied to High-T hroughput
Mapping of Plant Cell Wall Glycans Using Comprehensive
Microarray Polymer Profiling (CoMPP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Stjepan Krešimir Kračun , J onatan Ulrik Fangel , M aja Gro Rydahl ,
Henriette Lodberg Pedersen , S ilvia Vidal-Melgosa ,
and W illiam G eorge Tycho Willats
vii
viii Contents
13 A nalysis of Invertebrate and Protist N -Glycans . . . . . . . . . . . . . . . . . . . . . . . . 1 67
Alba Hykollari , K atharina Paschinger , B arbara Eckmair ,
and I ain B. H. Wilson
14 H igh-Throughput and High-Sensitivity Mass Spectrometry-B ased
N -Glycomics of Mammalian Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Stephanie Holst , G abi W. van Pelt , W ilma E. Mesker , R ob A. Tollenaar ,
Ana I. Belo , I rma van Die , Y oann Rombouts , and Manfred Wuhrer
15 A nalysis of N -Glycosylation of Total Membrane Proteins. . . . . . . . . . . . . . . . . 1 97
Tamara Pavić and Olga G ornik
16 H ILIC-UPLC Analysis of Brain Tissue N -Glycans. . . . . . . . . . . . . . . . . . . . . . 2 07
Thomas Klarić and Ivan Gudelj
17 A utomated Integration of a UPLC Glycomic Profile. . . . . . . . . . . . . . . . . . . . 217
Anna Agakova , F rano Vučković , L ucija Klarić , G ordan Lauc ,
and F elix Agakov
18 D atabases and Associated Tools for Glycomics and Glycoproteomics. . . . . . . . 2 35
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 , and Niclas G. Karlsson
19 H igh-Throughput N -Glycan Analysis with Rapid Magnetic
Bead-Based Sample Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Marton Szigeti and Andras Guttman
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 73
Contributors
JODIE L. ABRAHAMS • Biomolecular Frontiers Research Centre, M acquarie University ,
North Ryde, N SW , A ustralia
BARBARA ADAMCZYK • Department of Medical Biochemistry and Cell Biology, Institute
of Biomedicine, Sahlgrenska Academy , U niversity of Gothenburg , G othenburg, S weden ;
NIBRT GlycoScience Group, NIBRT–The National Institute for Bioprocessing Research
and Training, Blackrock, Co. , D ublin, I reland
FELIX AGAKOV • Pharmatics Limited , E dinburgh, U K
ANNA AGAKOVA • Pharmatics Limited , E dinburgh, U K
DAVIDE ALOCCI • Proteome Informatics Group , S IB Swiss Institute of Bioinformatics ,
Geneva, S witzerland
ANA I. BELO • Department of Molecular Cell Biology and Immunology, V U University
Medical Centre , A msterdam, T he Netherlands
HARRY CAMPBELL • Center for Global Health Research, Usher Institute of Population
Health Sciences and Informatics , U niversity of Edinburgh , E dinburgh, U K
MATTHEW P. CAMPBELL • Biomolecular Frontiers Research Centre, M acquarie University ,
North Ryde, N SW , A ustralia
BARBARA ECKMAIR • Department für Chemie, Universität für Bodenkultur , Vienna, Austria
DAVID FALCK • Center for Proteomics and Metabolomics, L eiden University Medical Center ,
Leiden, T he Netherlands
JONATAN ULRIK FANGEL • Section for Plant Glycobiology, Department for Plant and
Environmental Sciences, U niversity of Copenhagen , F rederiksberg C, D enmark
IVAN GUDELJ • Genos Glycoscience Research Laboratory , Z agreb, C roatia
ANDRAS GUTTMAN • Horvath Csaba Laboratory of Bioseparation Sciences, U niversity
of Debrecen , D ebrecen, H ungary ; M TA-PE Translational Glycomics Group,
University of Pannonia , V eszprem, H ungary ; S CIEX , B rea, C A , U SA
OLGA GORNIK • Faculty of Pharmacy and Biochemistry , U niversity of Zagreb , Z agreb,
Croatia
NOORTJE D E HAAN • Center for Proteomics and Metabolomics, Leiden University Medical
Center , L eiden, T he Netherlands
HANNES HINNEBURG • Department of Biomolecular Systems, M ax Planck Institute
of Colloids and Interfaces , P otsdam, G ermany ; D epartment of Biology, Chemistry,
Pharmacy, Institute of Chemistry and Biochemistry , F reie Universität Berlin , B erlin,
Germany
STEPHANIE HOLST • Center for Proteomics and Metabolomics, L eiden University Medical
Center , L eiden, T he Netherlands
ALBA HYKOLLARI • Department für Chemie, U niversität für Bodenkultur , V ienna, A ustria
BAS C. JANSEN • Center for Proteomics and Metabolomics, L eiden University Medical
Center , L eiden, T he Netherlands
CHUNSHENG JIN • Department of Medical Biochemistry and Cell Biology, Institute
of Biomedicine, Sahlgrenska Academy , U niversity of Gothenburg , G othenburg, S weden
ix
x Contributors
NICLAS G. KARLSSON • Department of Medical Biochemistry and Cell Biology, Institute
of Biomedicine, Sahlgrenska Academy , U niversity of Gothenburg , G othenburg, S weden
THOMAS KLARIĆ • Genos Glycoscience Research Laboratory , Z agreb, C roatia
LUCIJA KLARIĆ • Genos Glycoscience Research Laboratory , Z agreb, C roatia
DANIEL KOLARICH • Department of Biomolecular Systems, M ax Planck Institute of Colloids
and Interfaces , P otsdam, G ermany
PETRA KORAĆ • Division of Molecular Biology, Department of Biology, Faculty of Science ,
University of Zagreb , Z agreb, C roatia
STJEPAN KREŠIMIR KRAČUN • Section for Plant Glycobiology, Department for Plant and
Environmental Sciences, U niversity of Copenhagen , F rederiksberg C, D enmark
JASMINKA KRIŠTIĆ • Genos Glycoscience Research Laboratory , Z agreb, C roatia
GORDAN LAUC • Faculty of Pharmacy and Biochemistry , U niversity of Zagreb , Z agreb,
Croatia ; G enos Glycoscience Research Laboratory , Z agreb, C roatia
CARLITO B . L EBRILLA • Department of Chemistry , University of California , Davis , CA , USA
FREDERIQUE LISACEK • Proteome Informatics Group , S IB Swiss Institute of Bioinformatics ,
Geneva, S witzerland
MIGUEL A. ROJAS MACIAS • Department of Medical Biochemistry and Cell Biology, Institute
of Biomedicine, Sahlgrenska Academy , U niversity of Gothenburg , G othenburg, S weden
JULIEN MARIETHOZ • Proteome Informatics Group , S IB Swiss Institute of Bioinformatics ,
Geneva, S witzerland
YEHIA MECHREF • Department of Chemistry and Biochemistry , T exas Tech University ,
Lubbock, T X, U SA
WILMA E. MESKER • Department of Surgery , L eiden University Medical Center , L eiden,
The Netherlands
ELAINE MULLEN • The MITRE Corporation , M cLean, V A, U SA
RÓISÍN O’FLAHERTY • NIBRT GlycoScience Group, NIBRT–The National Institute for
Bioprocessing Research and Training, Blackrock, Co. , D ublin, I reland
NICOLLE H. PACKER • Biomolecular Frontiers Research Centre, M acquarie University ,
North Ryde, N SW , A ustralia
KATHARINA PASCHINGER • Department für Chemie, U niversität für Bodenkultur , V ienna,
Austria
TAMARA PAVIĆ • Faculty of Pharmacy and Biochemistry , U niversity of Zagreb , Z agreb,
Croatia
HENRIETTE LODBERG PEDERSEN • Section for Plant Glycobiology, Department for Plant
and Environmental Sciences, U niversity of Copenhagen , F rederiksberg C, D enmark
MAJA PUČIĆ-BAKOVIĆ • Genos Glycoscience Research Laboratory , Z agreb, C roatia
KARLI R. REIDING • Center for Proteomics and Metabolomics, Leiden University Medical
Center , L eiden, T he Netherlands
YOANN ROMBOUTS • Center for Proteomics and Metabolomics, L eiden University Medical
Center , L eiden, T he Netherlands ; U niversity Lille, CNRS, UMR 8576, UGSF, Unite de
Glycobiologie Structurale et Fonctionnelle , L ille , F rance
PAULINE M. RUDD • NIBRT GlycoScience Group, NIBRT–The National Institute for
Bioprocessing Research and Training, Blackrock, Co. , D ublin, I reland
L. RENEE RUHAAK • Department of Translational Molecular Pathology, U T MD
Anderson Cancer Center , H ouston, T X, U SA ; D epartment of Chemistry , U C Davis ,
Davis , C A , U SA
MAJA GRO RYDAHL • Section for Plant Glycobiology, Department for Plant
and Environmental Sciences, U niversity of Copenhagen , F rederiksberg C, D enmark
Contributors xi
FALKO SCHIRMEISTER • Department of Biomolecular Systems, M ax Planck Institute
of Colloids and Interfaces , P otsdam, G ermany ; D epartment of Biology, Chemistry,
Pharmacy, Institute of Chemistry and Biochemistry , F reie Universität Berlin , B erlin,
Germany
JONAS STÅHLE • Department of Organic Chemistry, Arrhenius Laboratory, S tockholm
University , S tockholm, S weden
KATHRIN STAVENHAGEN • Division of BioAnalytical Chemistry , V U University Amsterdam ,
Amsterdam, T he Netherlands ; C enter for Proteomics and Metabolomics, L eiden
University Medical Center , L eiden, T he Netherlands
HENNING STÖCKMANN • NIBRT GlycoScience Group, NIBRT–The National Institute
for Bioprocessing Research and Training, Blackrock, Co. , D ublin, I reland ; A bbVie Inc. ,
North Chicago, I L, U SA
MARTON SZIGETI • Horvath Csaba Laboratory of Bioseparation Sciences, U niversity
of Debrecen , D ebrecen, H ungary
ROB A. TOLLENAAR • Department of Surgery , L eiden University Medical Center , L eiden,
The Netherlands
IVO UGRINA • Genos Glycoscience Research Laboratory , Z agreb, C roatia
IRMA V AN DIE • Department of Molecular Cell Biology and Immunology, V U University
Medical Center , A msterdam, T he Netherlands
GABI W. V AN PELT • Department of Surgery , L eiden University Medical Center , L eiden,
The Netherlands
SILVIA VIDAL-MELGOSA • Section for Plant Glycobiology, Department for Plant
and Environmental Sciences, U niversity of Copenhagen , F rederiksberg C, D enmark
FRANO VUČKOVIĆ • Genos Glycoscience Research Laboratory , Z agreb, C roatia
GÖRAN WIDMALM • Department of Organic Chemistry, Arrhenius Laboratory, S tockholm
University , S tockholm, S weden
WILLIAM GEORGE TYCHO WILLATS • Section for Plant Glycobiology, Department for Plant
and Environmental Sciences, U niversity of Copenhagen , F rederiksberg C, D enmark
IAIN B.H. WILSON • Department für Chemie, U niversität für Bodenkultur , V ienna,
Austria
KERRY M. WOODING • Department of Chemistry and Biochemistry , T exas Tech University ,
Lubbock, T X, U SA
LAUREN D. WU • Department of Chemistry , U niversity of California , D avis , C A , U SA
MANFRED WUHRER • Division of BioAnalytical Chemistry , V U University Amsterdam ,
Amsterdam, T he Netherlands ; C enter for Proteomics and Metabolomics, Leiden
University Medical Center , L eiden, T he Netherlands
SHIYUE ZHOU • Department of Chemistry and Biochemistry , T exas Tech University ,
Lubbock, T X, U SA