Immunoproteomics: Methods and Protocols

380 Pages·2019·10.556 MB·English

by  Kelly M. Fulton (ed.), Susan M. Twine (ed.)

Methods in
Molecular Biology 2024
Kelly M. Fulton
Susan M. Twine Editors
Immuno-
proteomics
Methods and Protocols
Second Edition
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, UK
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Immunoproteomics
Methods and Protocols
Second Edition
Edited by
Kelly M. Fulton and Susan M. Twine
Human Health Therapeutics Research Center, National Research Council of Canada , Ottawa, ON, Canada
Editors
Kelly M. Fulton Susan M. Twine
Human Health Therapeutics Research Centre Human Health Therapeutics Research Centre
National Research Council of Canada National Research Council of Canada
Ottawa, ON, Canada Ottawa, ON, Canada
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-9596-7 ISBN 978-1-4939-9597-4 (eBook)
https://doi.org/10.1007/978-1-4939-9597-4
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Preface
The mammalian immune system has evolved to constantly survey for foreign pathogens
and abnormalities. The field of immunology has long sought to understand the extent of
the immune response. The complexity of the immune system allows pathogens to be elimi-
nated rapidly but also cancers to proliferate. The term “immunoproteomics” has been
coined to describe the study of large sets of proteins and peptides involved in the immune
system. Rapid growth of the field in the past two decades has seen the adoption of pro-
teomics, mass spectrometry, and chip-based technologies to interrogate the immune
response to infectious diseases, cancer, and autoimmunity. The resulting information has
potential to be used in diagnostics, disease progression, and correlate of protection analysis,
to name but a few applications.
The second edition of this book is aimed at scientists new to the field and those with
years of experience in immunoproteomics. Descriptions of now classical immunoproteomics
approaches are retained, many with utility as foundational techniques. This edition includes
expanded sections describing the characterization of the peptides bound to major histo-
compatibility complexes (MHC) on the surface of cells. This complement of peptides,
bound to MHC and presented to immune cells, is known as the immunopeptidome. This
field has been spurred forward by advances in speed, sensitivity, and resolution of mass
spectrometry. These advances are collectively advancing critical areas, such as cancer
immunotherapy.
The variety of techniques presented provides not only an overview of the breadth of the
field but valuable hands-on insights from specialists. Success stories will allow readers to
transfer these techniques to their own laboratories, in addition to providing a reference to
guide researchers.
Ottawa, ON, Canada Kelly M. Fulton
Susan M. Twine
v
Contents
1 Introduction to the Immune System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Scott McComb, Aude Thiriot, Bassel Akache, Lakshmi Krishnan,
and Felicity Stark
2 Immunoproteomics Methods and Techniques . . . . . . . . . . . . . . . . . . . . . . . . . 25
Kelly M. Fulton, Isabel Baltat, and Susan M. Twine
3 Classical Immunoproteomics: Serological Proteome Analysis (SERPA)
for Antigen Identification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Kelly M. Fulton, Anna Ananchenko, Lawrence Wolfraim, Shannon Martin,
and Susan M. Twine
4 Profiling of Cytokine and Chemokine Responses Using Multiplex
Bead Array Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Greg Harris and Wangxue Chen
5 Preparation of the Low Molecular Weight Serum Proteome for Mass
Spectrometry Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Timothy D. Veenstra
6 Enriching for Low-Abundance Serum Proteins Using ProteoMiner™
and Protein-Level HPLC. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Sophie Moggridge, Kelly M. Fulton, and Susan M. Twine
7 Identification of the Antigen Content of Electroimmunoprecipitates . . . . . . . . 119
N. Helena Beyer and Niels H. H. Heegaard
8 Detection of Human Norovirus-Specific Antibodies Using the Luciferase
Immunoprecipitation System (LIPS) Assay. . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Christine M. Tin and Stanislav V. Sosnovtsev
9 Intact Mass Spectrometry Analysis of Immuno-Isolated Human
Therapeutic Antibodies from Serum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Christie E. Delaney, John F. Kelly, Wen Ding, and Arsalan S. Haqqani
10 Antigen Identification for Cell-Binding Antibodies Using Ligand-Directed
Crosslinking and Biotin Transfer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Tammy-Lynn Tremblay and Jennifer J. Hill
11 Whole-Genome Phage Display Libraries: A Powerful Tool
for Antigen Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Elisa Beghetto and Nicola Gargano
12 Multiplexed Detection of Autoantibodies to Glycopeptides
Using Microarray. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Johannes W. Pedersen, Alexander Nøstdal, and Hans H. Wandall
13 Construction and Screening of an Antigen-Derived Peptide Library
Displayed on Yeast Cell Surface for CD4+ T Cell Epitope Identification. . . . . . 213
Fei Wen, Mason R. Smith, and Huimin Zhao
vii
viii Contents
14 Isolation of Major Histocompatibility Complex (MHC)-Associated
Peptides by Immunoaffinity Purification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Sarah A. Penny and Stacy A. Malaker
15 Enhanced Mass Spectrometry Detection of MHC Peptides. . . . . . . . . . . . . . . . 245
Rui Chen and Jianjun Li
16 Enrichment of Phosphorylated MHC Peptides with Immobilized Metal
Affinity Chromatography and Titanium Dioxide Particles. . . . . . . . . . . . . . . . . 259
Rui Chen and Jianjun Li
17 Mass Spectrometric Identification and Molecular Modeling of Glycopeptides
Presented by MHC Class I and II Processing Pathways. . . . . . . . . . . . . . . . . . . 269
Stacy A. Malaker and Michael J. Ferracane
18 Genome-Based Bioinformatic Prediction of Major
Histocompatibility (MHC). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
Simon J. Foote
19 Enhancing Mass Spectrometry-Based MHC-I Peptide Identification
Through a Targeted Database Search Approach . . . . . . . . . . . . . . . . . . . . . . . . 301
Prathyusha Konda, J. Patrick Murphy, Morten Nielsen, and Shashi Gujar
20 Prioritization of Therapeutic Targets of Inflammation Using Proteomics,
Bioinformatics, and In Silico Cell-Cell Interactomics . . . . . . . . . . . . . . . . . . . . 309
Arsalan S. Haqqani and Danica B. Stanimirovic
21 Genomics-Driven Immunoproteomics: An Integrative Platform to Uncover
Important Biomarkers for Human Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Raghavendra Giri, Veneta Qendro, Pooja Rani, Carren Jepchumba,
Grace Bugos, Volker Stadler, and David K. Han
22 Identification of Antigens in Immune Complexes. . . . . . . . . . . . . . . . . . . . . . . 333
Nozomi Aibara and Kaname Ohyama
23 Analysis and Characterization of Immune Cells and Their Activation
Status by Whole-Cell MALDI-TOF Mass Spectrometry. . . . . . . . . . . . . . . . . . 339
Richard Ouedraogo, Julien Textoris, Laurent Gorvel, Aurélie Daumas,
Christian Capo, and Jean-Louis Mege
24 A Molecular Immunoproteomics Approach to Assess the Viral
Antigenicity of Influenza . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
Kevin M. Downard
25 Immunoproteomic Biomarkers: From Publication to Personalized
Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
Devanand M. Pinto
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
Contributors
Nozomi AibArA • Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki,
Japan
bAssel AkAche • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
ANNA ANANcheNko • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
isAbel bAltAt • Human Health Therapeutics Research Centre, National Research Council
of Canada, Ottawa, ON, Canada
elisA beghetto • IRBM Science Park, Rome, Italy
N. heleNA beyer • Department of Autoimmunology and Biomarkers, Statens Serum
Institut, Copenhagen, Denmark
grAce bugos • Department of Cell Biology, Center for Vascular Biology, University
Connecticut School of Medicine, Farmington, CT, USA
christiAN cApo • Aix Marseille Université, Unité de Recherche sur les Maladies
Infectieuses Tropicales et Emergentes, CNRS UMR 7278, IRD 198, INSERM U1095,
Marseille, France
rui cheN • Human Health Therapeutics Research Centre, National Research Council
Canada, Ottawa, ON, Canada
WANgxue cheN • Human Health and Therapeutics Research Center, National Research
Council of Canada, Ottawa, ON, Canada
Aurélie DAumAs • Aix Marseille Université, Unité de Recherche sur les Maladies
Infectieuses Tropicales et Emergentes, CNRS UMR 7278, IRD 198, INSERM U1095,
Marseille, France
christie e. DelANey • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
WeN DiNg • Human Health Therapeutics Research Centre, National Research Council of
Canada, Ottawa, ON, Canada
keviN m. DoWNArD • Infectious Disease Responses Laboratory, POWCS, Medicine,
University of New South Wales, Sydney, NSW, Australia
michAel J. FerrAcANe • Department of Chemistry, University of Redlands, Redlands,
CA, USA
simoN J. Foote • Human Health Therapeutics Research Centre, National Research
Council Canada, Ottawa, ON, Canada
kelly m. FultoN • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
NicolA gArgANo • Alfasigma S.p.A, Rome, Italy
rAghAveNDrA giri • Department of Cell Biology, Center for Vascular Biology, University
Connecticut School of Medicine, Farmington, CT, USA
ix
x Contributors
lAureNt gorvel • Aix Marseille Université, Unité de Recherche sur les Maladies
Infectieuses Tropicales et Emergentes, CNRS UMR 7278, IRD 198, INSERM U1095,
Marseille, France
shAshi guJAr • Department of Microbiology and Immunology, Dalhousie University,
Halifax, NS, Canada; Department of Pathology, Dalhousie University, Halifax, NS,
Canada; Department of Biology, Dalhousie University, Halifax, NS, Canada; Centre for
Innovative and Collaborative Health Services Research, IWK Health Centre, Halifax,
NS, Canada
DAviD k. hAN • Department of Cell Biology, Center for Vascular Biology, University
Connecticut School of Medicine, Farmington, CT, USA
ArsAlAN s. hAqqANi • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
greg hArris • Human Health and Therapeutics Research Center, National Research
Council of Canada, Ottawa, ON, Canada
Niels h. h. heegAArD • Department of Autoimmunology and Biomarkers, Statens
Serum Institut, Copenhagen, Denmark; Department of Clinical Biochemistry, University
of Southern Denmark, Odense, Denmark
JeNNiFer J. hill • Human Health Therapeutics, National Research Council Canada,
Ottawa, ON, Canada
cArreN JepchumbA • Department of Cell Biology, Center for Vascular Biology, University
Connecticut School of Medicine, Farmington, CT, USA
JohN F. kelly • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
prAthyushA koNDA • Department of Microbiology and Immunology, Dalhousie
University, Halifax, NS, Canada
lAkshmi krishNAN • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
JiANJuN li • Human Health Therapeutics Research Centre, National Research Council
Canada, Ottawa, ON, Canada
stAcy A. mAlAker • Department of Chemistry, Stanford University, Stanford, CA, USA
shANNoN mArtiN • Dynport Vaccine Company LLC, Frederick, MD, USA
scott mccomb • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
JeAN-louis mege • Aix Marseille Université, Unité de Recherche sur les Maladies
Infectieuses Tropicales et Emergentes, CNRS UMR 7278, IRD 198, INSERM U1095,
Marseille, France
sophie moggriDge • Human Health Therapeutics Research Centre, National Research
Council of Canada, Ottawa, ON, Canada
J. pAtrick murphy • Department of Pathology, Dalhousie University, Halifax, NS,
Canada
morteN NielseN • Department of Bio and Health Informatics, Technical University of
Denmark, Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad
Nacional de San Martín, Buenos Aires, Argentina
AlexANDer NøstDAl • Department of Cellular and Molecular Medicine, Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
kANAme ohyAmA • Graduate School of Biomedical Sciences, Nagasaki University,
Nagasaki, Japan