Analyzing Biomolecular Interactions by Mass Spectrometry (eBook)

Jeroen Kool, Wilfried M. A. Niessen (Herausgeber)

eBook Download: EPUB

2015
Wiley-VCH (Verlag)
978-3-527-67341-4 (ISBN)

Infos

This monograph reviews all relevant technologies based on mass spectrometry that are used to study or screen biological interactions in general.
Arranged in three parts, the text begins by reviewing techniques nowadays almost considered classical, such as affinity chromatography and ultrafiltration, as well as the latest techniques. The second part focusses on all MS-based methods for the study of interactions of proteins with all classes of biomolecules. Besides pull down-based approaches, this section also emphasizes the use of ion mobility MS, capture-compound approaches, chemical proteomics and interactomics. The third and final part discusses other important technologies frequently employed in interaction studies, such as biosensors and microarrays.
For pharmaceutical, analytical, protein, environmental and biochemists, as well as those working in pharmaceutical and analytical laboratories.


Jeroen Kool focused on the integration of chemical and biochemical detection after separation methodologies during his PhD study at the VU University Amsterdam. Following his PhD, he was responsible for target evaluation, hit screening and identification, and lead optimization processes at Kiadis Pharma. He continued his academic career in 2005 as a postdoc in the Biomolecular Mass Spectrometry group in Utrecht working on proteomics and biomarker discovery. From 2007 to present, he is responsible for the research line Bioanalytical Screening Methodologies at the VU University Amsterdam with a particular focus on hyphenated analytical techniques combining mass spectrometry and chromatography with novel bioassay techniques for bioactive mixture analysis. He published over 50 peer reviewed articles and one book chapter.

Wilfried M.A. Niessen studied chemistry at the VU University Amsterdam. After his PhD, he worked for 9 years as an analytical chemist within the Leiden/ Amsterdam Center for Drug Research at Leiden University. After leaving the university in 1996, he started the company hyphen MassSpec, providing independent consultancy and training in the field of analytical mass spectrometry. In parallel to this, he was extraordinary professor in bioanalytical mass spectrometry at the Faculty of Science of the VU University Amsterdam between 2002 and 2014. There, he was involved in high-resolution screening and the role of MS therein. His main research interests involve principles, instrumentation and applications of liquid chromatography-mass spectrometry as well as interpretation of small-molecule MS-MS mass spectra. He is (co)author of more than 200 peer reviewed publications in the field of LC-MS and more than 40 book chapters. Wilfried Niessen authored and edited five books, and was guest editor on several special journal issues.

Inhalt

Preface

INTRODUCTION TO MASS SPECTROMETRY, A TUTORIAL
Introduction
Figures of Merit
Analyte Ionization
Mass Analyzer Building Blocks
Tandem Mass Spectrometry
Data Interpretation and Analytical Strategies
Conclusion and Perspectives

PART I: Direct MS Based Affinity Techniques

STUDYING PROTEIN-PROTEIN INTERACTIONS BY COMBINING NATIVE MASS SPECTROMETRY AND CHEMICAL CROSS-LINKING
Introduction
Protein Analysis by Mass Spectrometry
Native MS
Chemical Cross-Linking MS
Value of Combining Native MS with Chemical Cross-Linking MS
Regulating the Giant
Capturing Transient Interactions
An Integrative Approach for Obtaining Low-Resolution Structures of Native Protein Complexes
Future Directions

NATIVE MASS SPECTROMETRY APPROACHES USING ION MOBILITY-MASS SPECTROMETRY
Introduction
Sample Preparation
Electrospray Ionization
Mass Analyzers and Tandem MS Approaches
Ion Mobility
Data Processing
Challenges and Future Perspectives

PART II: LC-MS Based with Indirect Assays

METHODOLOGIES FOR EFFECT-DIRECTED ANALYSIS: ENVIRONMENTAL APPLICATIONS, FOOD ANALYSIS, AND DRUG DISCOVERY
Introduction
Principle of Traditional Effect-Directed Analysis
Sample Preparation
Fractionation for Bioassay Testing
Miscellaneous Approaches
Identification of Confirmation Process
Conclusion and Perspectives

MS BINDING ASSAYS
Introduction
MS Binding Assays - Strategy
Application of MS Binding Assays
Summary and Perspectives

METABOLIC PROFILING APPROACHES FOR THE IDENTIFICATION OF BIOACTIVE METABOLITES IN PLANTS
Introduction to Plant Metabolic Profiling
Sample Collection and Processing
Hyphenated Techniques
Mass Spectrometry
Mass Spectrometric Imaging
Data Analysis
Future Perspectives

ANTIVENOMICS: A PROTEOMICS TOOL FOR STUDYING THE IMMUNOREACTIVITY OF ANTIVENOMS
Introduction
Challenge of Fighting Human Envenoming by Snakebites
Toolbox for Studying the Immunological Profile of Antivenoms
First-Generation Antivenomics
Snake Venomics
Second-Generation Antivenomics
Concluding Remarks

PART III: Direct Pre- and On-Column Coupled Techniques

FRONTAL AND ZONAL AFFINITY CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY
Introduction
Frontal Affinity Chromatography
Staircase Method
Simultaneous Frontal Analysis of a Complex Mixture
Multiprotein Stationary Phase
Zonal Chromatography
Nonlinear Chromatography

ONLINE AFFINITY ASSESSMENT AND IMMUNOAFFINITY SAMPLE PRETREATMENT IN CAPILLARY ELECTROPHORESIS-MASS SPECTROMETRY
Introduction
Capillary Electrophoresis
Affinity Capillary Electrophoresis
Immunoaffinity Capillary Electrophoresis
Capillary Electrophoresis-Mass Spectrometry
Application of ACE-MS
Applications of IA-CE-MS
Conclusions

LABEL-FREE BIOSENSOR AFFINITY ANALYSIS COUPLED TO MASS SPECTROMETRY
Introduction to MS-Coupled Biosensor Platforms
Strategies for Coupling Label-Free Analysis with Mass Spectrometry
New Sensor and MS Platforms, Opportunities for Integration

PART IV: Direct Post Column Coupled Affinity Techniques

HIGH-RESOLUTION SCREENING: POST-COLUMN CONTINUOUS-FLOW BIOASSAYS
Introduction
The High-Resolution Screening Platform
Data Analysis
Conclusions and Perspectives

CONCLUSIONS

Index

Textauszug

Abbreviations

μ	Electrophoretic mobility

2DE	Two-dimensional electrophoresis

5-HT	5-Hydroxytryptamine, serotonin

5-HT2A

5-Hydroxytryptamine (serotonin) receptor subtype 2A

Ab

Antibody

ACE	Affinity capillary electrophoresis

ACE	Angiotensin converting enzyme

AChBP

Acetyl choline binding protein

Ag

Antigen

Ag–Ab

Antigen–antibody complex

AhR	Aryl hydrocarbon receptor

AMAC	Accelerated membrane assisted clean-up

APCI	Atmospheric pressure chemical ionization

API	Atmospheric pressure ionization

AR-CALUX

Androgen chemically activated luciferase expression

BGE	Background electrolyte

BGF	Bioassay guided fractionation

BGT1	Betaine-GABA transporter

BLAST

Basic local alignment search tool

BS2G	Bis(sulfosuccinimidyl)suberate

CCT	Chaperonin containing Tcp1

CDER	Center for drug evaluation and research

CE	Capillary electrophoresis

CECs	Chemicals of emerging concern

CHCA	α-Cyano-4-hydroxy cinnamic acid

CI	Chemical ionization

CID	Collision-induced dissociation

CID-MS/MS

Collision-induced dissociation tandem mass spectrometry

CRISPR

Clustered regularly interspaced short palindromic repeat

CZE	Capillary zone electrophoresis

D1–5	Dopamine receptor subtypes D1 to D5

DAD	Diode array detector

DCC	Dynamic combinatorial chemistry

DCL	Dynamic combinatorial library

DDA	Data dependent acquisition

DVB/CAR/PDMS

Divinyl-benzene/carboxen/polydimethylsiloxane

EC	Electrochemical conversion

ECD	Electron-capture dissociation

EDA	Effect-directed analysis

EI	Electron ionization

EIC	Extracted ion chromatograms

EICs	Extracted ion currents

ELSD	Evaporative light scattering detection

EOF	Electroosmotic flow

ER	Estrogen receptor

EROD	Ethoxyresorufin-O-deethylase

ESI	Electron spray ionization

ESI	Electrospray ionization

ESI-MS

Electrospray-ionization mass spectrometry

ETD	Electron-transfer dissociation

FA	Formic acid

FA	Frontal analysis

Fab	Fragment antigen-binding

FACCE

Frontal analysis continuous capillary electrophoresis

FDA	US Food and Drug Administration

FIA	Flow-injection analysis

FLD	Fluorescence detection

FRAP	Ferric reducing antioxidant power

FRET	Fluorescence resonance energy transfer

FWHM	Full width at half maximum

GABA	γ-Aminobutyric acid

GAT1–3

GABA transporter subtypes 1–3 (according to HUGO)

GC–MS

Gas chromatography mass spectrometry

GC-O	Gas chromatography olfactometry

GCxGC

Comprehensive two dimensional gas chromatography

GPC	Gel permeation chromatography

GPCR	G protein-coupled receptor

GSI	Global snakebite initiative

GST	Glutathione-S-transferase

HBH	Histidine–biotin–histidine

HDX	Hydrogen–deuterium exchange

HEK	Human embryonic kidney cells

HPLC	High performance liquid chromatography

HRS	High-resolution screening

HTLC	High-temperature liquid chromatography

HTS	High throughput screening

I.D.	Inner diameter

IA-CE

Immunoaffinity capillary electrophoresis

IC50	Half maximal inhibitory concentration

ICP	Inductively coupled plasma

ICP-MS

Inductively coupled plasma MS

ID	Inner diameter

IMS	Ion mobility spectrometry

ISD	In-source decay

IT	Ion-trap MS

IT-TOF

Tandem ion-trap – time-of-flight MS

Ka	Association constant

Kd	Dissociation constant

Kd	Equilibrium dissociation constant

kDa	kilodalton (103 Da)

Ki	Affinity constant

koff	Rate constant of complex dissociation

kon	Rate constant of complex formation

L

Ligand

LC	Liquid chromatography

LC–MS

Liquid chromatography mass spectrometry

LC–MSE

Liquid chromatography mass spectrometry in an alternating energy mode

LIF	Laser induced fluorescence

LLE	Liquid liquid extraction

LLOQ	Lower limit of quantification

MALDI

Matrix assisted laser desorption ionization

MS	Mass spectrometry/mass spectrometer

MS/MS

Tandem mass spectrometry

MTS	3-(4,5-Dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium

MTT	3-(4,5-Dimethyldiazol-2-yl)-2,5 diphenyl tetrazolium bromid

nAChR

Nicotinic acetylcholine receptor

NECEEM

Non-equilibrium capillary electrophoresis of equilibrium mixtures

NHS	N-Hydroxysuccinimide

NMR	Nuclear magnetic resonance

NMR	Nuclear magnetic resonance spectrometry

np-HPLC

Normal phase high performance liquid chromatography

p38	p38 mitogen-activated protein kinase

PAHs	Poly aromatic hydrocarbons

PDE	Phosphodiesterase

PEEK	Polyether ether ketone

PEG	Polyethylene glycol

PLE	Pressurized liquid extraction

POCIS

Polar organic chemical integrative sampler

PTFE	Polytetrafluoroethylene

QSAR	Quantitative structure–activity relationships

QTAX	Quantitative analysis of tandem affinity purified in vivo cross-linked protein complexes

Q-TOF

Quadrupole time-of-flight

q-TOF

Tandem quadropule – time-of-flight MS

R

Receptor

rhSHBG

Recombinant human sex hormone binding...

Produkt-Details

• Erscheint lt. Verlag: 9.2.2015
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Chemie
• Themenwelt: Technik
• Schlagworte: Analytische Chemie • Biopolymere • biopolymers • Biowissenschaften • Chemie • Chemistry • crosslinking ion-mobility affinity biosensors proteomics metabolomics • Genomforschung u. Proteomik • Genomics & Proteomics • Life Sciences • Massenspektrometrie • Mass Spectrometry • Pharmaceutical & Medicinal Chemistry • Pharmazeutische u. Medizinische Chemie • Polymer Science & Technology • Polymerwissenschaft u. -technologie
• ISBN-10: 3-527-67341-5 / 3527673415
• ISBN-13: 978-3-527-67341-4 / 9783527673414