Advancements of Mass Spectrometry in Biomedical Research

805 Pages·2019·63.964 MB·English

by  Alisa G. Woods, Costel C. Darie

Advances in Experimental Medicine and Biology 1140
Alisa G. Woods
Costel C. Darie Editors
Advancements of
Mass Spectrometry
in Biomedical
Research
Second Edition
Advances in Experimental Medicine
and Biology
Volume 1140
Editorial Board Member:
IRUN R. COHEN, The Weizmann Institute of Science, Rehovot, Israel
ABEL LAJTHA, N.S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
JOHN D. LAMBRIS, University of Pennsylvania, Philadelphia, PA, USA
RODOLFO PAOLETTI, University of Milan, Milan, Italy
NIMA REZAEI, Tehran University of Medical Sciences, Children’s Medical
Center Hospital, Tehran, Iran
More information about this series at http://www.springer.com/series/5584
Alisa G. Woods • Costel C. Darie
Editors
Advancements of Mass
Spectrometry in Biomedical
Research
Second Edition
Editors
Alisa G. Woods Costel C. Darie
Biochemistry and Proteomics Group Biochemistry and Proteomics Group
Department of Chemistry and Biomolecular Department of Chemistry and Biomolecular
Science Science
Clarkson University Clarkson University
Potsdam, NY, USA Potsdam, NY, USA
ISSN 0065-2598 ISSN 2214-8019 (electronic)
Advances in Experimental Medicine and Biology
ISBN 978-3-030-15949-8 ISBN 978-3-030-15950-4 (eBook)
https://doi.org/10.1007/978-3-030-15950-4
© Springer Nature Switzerland AG 2014, 2019
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To Professor Dr. Vlad Artenie
(University of Iasi, Romania),
to late Professor Dr. Wolfgang Haehnel
(University of Freiburg, Germany),
and to Dr. Kenneth R. Woods,
an inspirational biochemist.
Also, to the past and current members of Darie Lab,
as well as to its many supporters.
Preface
The use of mass spectrometry (MS) is becoming increasingly important for biomedical
research and for clinical applications. Detection of exogenous substances, such as toxins, can
be performed by MS and was perhaps the initial use of this technology in biomedicine.
However identification of endogenous, disease-related molecules is also possible. With the
advent of the genetic revolution, the proteomic revolution has followed in close succession.
Mass spectrometers are essential for proteomic discovery, and other “omic” fields (such as
glycomics, metabolomics, lipidomics, and many more) are exploding with new information.
The sensitivity of mass spectrometers and increasingly more sophisticated bioinformatics tools
are opening up this field to untold possibilities for biomedical researchers and clinicians.
In the spirit of this revolution in biomedicine, we have assembled this comprehensive work,
which largely focuses on the application of MS to “omics” analysis in biomedicine. We start
with broad descriptions of the field, definitions of the machinery, and then delve into the vari-
ous methods and approaches that can be utilized. Aspects of molecular analysis are considered
(i.e. whether to use label-based or label-free analysis, or 1D-PAGE versus 2D-PAGE analysis),
and then options are explored on how MS can be applied to understanding and specific dis-
eases and disorders.
Numerous MS-based methodologies are now available to researchers, and this text reviews
many cutting-edge and relevant technologies. Dudley, Ju, and Neagu focus on the application
of matrix-assisted laser desorption/ionization (MALDI) in biomedicine. Xu’s, Wood’s,
Melman’s, Darie’s, and Luque-Garcia’s teams explore methods for full sequence analysis in
proteins, mutated proteins, conjugated/derivatized proteins, and membrane proteins, while
Gethings and Connolly examine how peak capacity can be best maximized and Spellman’s
group is focused on biomarker discovery. Brown’s lab describes lipidomics, Mihasan’s team
focuses on bacterial proteomics, Arcaro’s team describes breast milk proteomics, and
Kendrick’s team focuses on two-dimensional electrophoresis coupled with proteomics. While
Neubert’s and Haley’s groups explore the use of stable isotope labeling by amino acids in cell
culture (SILAC) for protein quantification using MS, Mihasan et al. discuss the complemen-
tary use of computational structural biology in MS, and Dupree et al. focus on environmental
proteomics and proteogenomics.
Different aspects of proteins and other molecules can be studied using MS. Petre explores
protein structures and interactions, Drochioiu’s team explores metal-peptides interactions,
Furdui’s team explores the use of MS in redox precision medicine, and Munteanu et al. explore
protein complexes, while Zamfir has tackled the use of MS to understand gangliosides.
Ngounou Wetie et al., Yakubu et al., and Aslebagh et al. examine the analysis of protein post-
translational modifications and protein-protein interactions and Samways focuses on MS-based
analysis of ion channel structure and function. Spellman describes the workflow for biomarker
discovery in a pharmaceutical company, while Ferguson et al. focus on its use for understand-
ing small molecules. Small molecules are also explored by members of Mesaros, Dudley,
Darie, and Boolani teams.
Focusing on health promotion, Andrei and colleagues examine how MS can be used to
analyze biomedically relevant stilbenes from wine. With regard to increased understanding of
diseases and disorders and of the environment that we live in, chapters by Monien, Arcaro,
vii
viii Preface
Channaveerappa, Boolani, Cristea, or Crimmins describe the use of MS for analysis in cancer
adductomics, breast cancer, sleep apnea, mental fatigue, development, or environmental
exposure. Topics covered include quantifying DNA adducts, analysis of breast milk, tissue
proteomics in sleep apnea, salivary proteomics in mental fatigue subjects, developmental pro-
teomics, or nontargeted screening of legacy contaminants in environmental monitoring
programs.
Deinhardt examines how MS can be used to understand neuronal signaling, which could
apply to numerous neurological and psychiatric conditions, while Sokolowska et al. study how
MS can facilitate the understanding of a novel central nervous system protein. We then explore
more applied uses of MS in the central nervous system, specifically, how biomarker discovery
may be directly performed for neurodevelopmental disorders (Wormwood et al.) and be used
to understand and potentially diagnose depression (Woods et al.).
In the realm of diagnostics and therapeutics, it is worth noting the contributions from
authors that are part of biotechnology and pharmaceutical industry. Companies like Waters
Corporation, Bruker Daltonics, or Mobilion are focusing on making better mass spectrometers
with more applications; others like Merck & Co and Biogen are focused on basic research and
drug development; and other companies like Kendrick Labs focus on custom proteomics anal-
ysis for protein identification, characterization, and quantification.
We finally end with a particularly important chapter on bottlenecks in proteomics, topics
that are encountered by almost all researchers but that are almost never discussed in publica-
tions. Since the editors’ university is primarily an undergraduate institution and MS is usually
not a focus on teaching undergraduate students, we decided to show some examples of the
MS-based applications in protein and small molecule analysis designed for teaching under-
graduate students (Jayathirtha et al.). We do envision that very soon in the near future MS will
be a required course at the undergraduate level at almost every university that wants to be
competitive.
We thus present to the reader a comprehensive text, examining the many uses of MS in
biomedicine, with the hope that this will be useful to both researchers and clinicians. As this
exciting field further expands, so will the potential applications for using MS to understand
medical issues and to address them, through exploration, as well as eventual clinical prognosis,
diagnosis, and monitoring. We look forward to an exciting era of MS-based discovery and
application.
Potsdam, NY, USA Alisa G. Woods
Potsdam, NY, USA Costel C. Darie
Contents
1 Mass Spectrometry for Proteomics- Based Investigation . . . . . . . . . . . . . . . . . . . . . 1
Alisa G. Woods, Izabela Sokolowska, Armand G. Ngounou Wetie,
Devika Channaveerappa, Emmalyn J. Dupree, Madhuri Jayathirtha,
Roshanak Aslebagh, Kelly L. Wormwood, and Costel C. Darie
2 MALDI Profiling and Applications in Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Ed Dudley
3 Applications of Matrix-Assisted Laser Desorption Ionization
In-Source Decay Mass Spectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Yue Ju
4 Proteome Imaging: From Classic to Modern Mass
Spectrometry-Based Molecular Histology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Anca-Narcisa Neagu
5 Mass Spectrometry-Based Tissue Imaging of Small Molecules . . . . . . . . . . . . . . . 99
Carly N. Ferguson, Joseph W. M. Fowler, Jonathan F. Waxer, Richard A. Gatti,
and Joseph A. Loo
6 Sequencing Proteins from Bottom to Top: Combining
Techniques for Full Sequence Analysis of Glucokinase . . . . . . . . . . . . . . . . . . . . . .111
Emily R. Sekera and Troy D. Wood
7 Proteomics and Non-proteomics Approaches to Study Stable
and Transient Protein-Protein Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Armand G. Ngounou Wetie, Izabela Sokolowska, Devika Channaveerappa,
Emmalyn J. Dupree, Madhuri Jayathirtha, Alisa G. Woods, and Costel C. Darie
8 Contribution of Mass Spectrometry- Based Proteomics
to Discoveries in Developmental Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .143
Yutaka Hashimoto, Todd M. Greco, and Ileana M. Cristea
9 Profiling Optimal Conditions for Capturing EDEM Proteins
Complexes in Melanoma Using Mass Spectrometry . . . . . . . . . . . . . . . . . . . . . . . .155
Cristian V. A. Munteanu, Gabriela N. Chiriţoiu, Andrei- Jose Petrescu,
and Ștefana M. Petrescu
10 The Methods Employed in Mass Spectrometric Analysis of Posttranslational
Modifications (PTMs) and Protein–Protein Interactions (PPIs) . . . . . . . . . . . . . .169
Rama R. Yakubu, Edward Nieves, and Louis M. Weiss
11 Identification of Posttranslational Modifications (PTMs) of Proteins
by Mass Spectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .199
Roshanak Aslebagh, Kelly L. Wormwood, Devika Channaveerappa, Armand G.
Ngounou Wetie, Alisa G. Woods, and Costel C. Darie
ix
x Contents
12 S equence Variant and Posttranslational Modification Analysis During
Cell Line Selection via High-Throughput Peptide Mapping . . . . . . . . . . . . . . . . .225
Chong-Feng Xu, Yan Wang, Pete Bryngelson, Zoran Sosic, and Li Zang
13 S elective Derivatization of Hexahistidine-Tagged Recombinant Proteins . . . . . . .237
Vasantha Krishna Kadambar and Artem Melman
14 I nvestigation of Antibody-Drug Conjugates by Mass Spectrometry . . . . . . . . . . .251
Madhuri Jayathirtha and Costel C. Darie
15 M ass Spectrometry- and Computational Structural Biology-Based
Investigation of Proteins and Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .265
Marius Mihăşan, Kelly L. Wormwood, Izabela Sokolowska, Urmi Roy,
Alisa G. Woods, and Costel C. Darie
16 S trategies for Membrane Protein Analysis by Mass Spectrometry . . . . . . . . . . . .289
Rafael C. Prados-Rosales, Guillermo Aragoneses-Cazorla, Hector Estevez,
Estefania Garcia-Calvo, Andres Machuca, and Jose L. Luque-Garcia
17 T he Potential for Ion Mobility in Pharmaceutical and Clinical Analyses . . . . . . .299
Kelly L. Wormwood, Liulin Deng, Ahmed M. Hamid, Daniel DeBord,
and Laura Maxon
18 A pplication of Ion Mobility Mass Spectrometry in Lipidomics . . . . . . . . . . . . . . .317
Fereshteh Zandkarimi and Lewis M. Brown
19 M ass Spectrometry in Advancement of Redox Precision Medicine . . . . . . . . . . . .327
Xiaofei Chen, Jingyun Lee, Hanzhi Wu, Allen W. Tsang,
and Cristina M. Furdui
20 A pplications for Mass Spectrometry in the Study of Ion Channel
Structure and Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .359
Damien S. K. Samways
21 I mmuno-Affinity Mass Spectrometry: A Novel Approaches
with Biomedical Relevance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .377
Laura Ion and Brînduşa Alina Petre
22 D eveloping Well-Annotated Species- Specific Protein Databases
Using Comparative Proteogenomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .389
Emmalyn J. Dupree, Bernard S. Crimmins, Thomas M. Holsen,
and Costel C. Darie
23 S toichiometry of Heavy Metal Binding to Peptides Involved
in Alzheimer’s Disease: Mass Spectrometric Evidence . . . . . . . . . . . . . . . . . . . . . .401
Monica Jureschi, Ancuta Veronica Lupaescu, Laura Ion, Brînduşa Alina Petre,
and Gabi Drochioiu
24 R ole of Mass Spectrometry in Investigating a Novel Protein:
The Example of Tumor Differentiation Factor (TDF) . . . . . . . . . . . . . . . . . . . . . . .417
Izabela Sokolowska, Armand G. Ngounou Wetie, Alisa G. Woods,
Madhuri Jayathirtha, and Costel C. Darie
25 M ass Spectrometry-Based Biomarkers in Drug Development . . . . . . . . . . . . . . . .435
Michelle R. Robinson, Ronald A. Miller, and Daniel S. Spellman
26 C ombinatorial Electrophoresis and Mass Spectrometry-Based
Proteomics in Breast Milk for Breast Cancer Biomarker Discovery . . . . . . . . . . .451
Roshanak Aslebagh, Devika Channaveerappa, Brian T. Pentecost,
Kathleen F. Arcaro, and Costel C. Darie
Contents xi
27 Proteomic Approaches to Dissect Neuronal Signalling Pathways . . . . . . . . . . . . .469
Heather L. Bowling, Shruti Nayak, and Katrin Deinhardt
28 Mass Spectrometry for the Study of Autism and Neurodevelopmental
Disorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .477
Kelly L. Wormwood, Armand G. Ngounou Wetie, Jeanne P. Ryan,
Costel C. Darie, and Alisa G. Woods
29 Simplifying the Proteome: Analytical Strategies for Improving
Peak Capacity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .501
Lee A. Gethings and Joanne B. Connolly
30 Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans
pAO1 by Microbial Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .515
Marius Mihăşan, Cornelia Babii, Roshanak Aslebagh, Devika Channaveerappa,
Emmalyn J. Dupree, and Costel C. Darie
31 Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)
for Quantitative Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .531
Esthelle Hoedt, Guoan Zhang, and Thomas A. Neubert
32 Mass Spectrometry Based Comparative Proteomics Using One
Dimensional and Two Dimensional SDS-PAGE of Rat Atria Induced
with Obstructive Sleep Apnea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .541
Devika Channaveerappa, Brian K. Panama, and Costel C. Darie
33 2D SDS PAGE in Combination with Western Blotting and Mass
Spectrometry Is a Robust Method for Protein Analysis
with Many Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .563
Nancy Kendrick, Costel C. Darie, Matt Hoelter, Ginny Powers,
and Jon Johansen
34 Pulse SILAC Approaches to the Measurement of Cellular Dynamics . . . . . . . . . .575
Justin Snider, Daifeng Wang, Daniel F. Bogenhagen, and John D. Haley
35 Protein Biomarkers in Major Depressive Disorder: An Update . . . . . . . . . . . . . .585
Alisa G. Woods, Kelly L. Wormwood, Dan V. Iosifescu, James Murrough,
and Costel C. Darie
36 A Pilot Exploratory Proteomics Investigation of Mental Fatigue
and Mental Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .601
Emmalyn J. Dupree, Aurora Goodwin, Costel C. Darie, and Ali Boolani
37 Metabolomics and Biomarker Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .613
Kathryn Sinclair and Ed Dudley
38 Analytical Methods for Mass Spectrometry-Based Metabolomics Studies . . . . . .635
Siyu Wang, Ian A. Blair, and Clementina Mesaros
39 Trends in Analysis of Cortisol and Its Derivatives . . . . . . . . . . . . . . . . . . . . . . . . . .649
Ali Boolani, Devika Channaveerappa, Emmalyn J. Dupree, Madhuri
Jayathirtha, Roshanak Aslebagh, Stephanie Grobe, Tyler Wilkinson, and Costel
C. Darie
40 Detection of Biomedically Relevant Stilbenes from Wines
by Mass Spectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .665
Veronica Andrei, Dana Copolovici, Florentina- Daniela Munteanu, Armand G.
Ngounou Wetie, Iuliana Mihai, Costel C. Darie, and Alina Vasilescu