Analyzing Biomolecular Interactions by Mass Spectrometry -- Contents -- List of Contributors -- Preface -- Abbreviations -- Chapter 1 Introduction to Mass Spectrometry, a Tutorial -- 1.1 Introduction -- 1.2 Figures of Merit -- 1.2.1 Introduction -- 1.2.2 Resolution -- 1.2.3 Mass Accuracy -- 1.2.4 General Data Acquisition in MS -- 1.3 Analyte Ionization -- 1.3.1 Introduction -- 1.3.2 Electrospray Ionization -- 1.3.3 Matrix-Assisted Laser Desorption Ionization -- 1.3.4 Other Ionization Methods -- 1.3.5 Solvent and Sample Compatibility Issues -- 1.4 Mass Analyzer Building Blocks -- 1.4.1 Introduction -- 1.4.2 Quadrupole Mass Analyzer -- 1.4.3 Ion-Trap Mass Analyzer -- 1.4.4 Time-of-Flight Mass Analyzer -- 1.4.5 Fourier Transform Ion Cyclotron Resonance Mass Spectrometer -- 1.4.6 Orbitrap Mass Analyzer -- 1.4.7 Ion Detection -- 1.5 Tandem Mass Spectrometry -- 1.5.1 Introduction: "Tandem-in-Time" and "Tandem-in-Space" -- 1.5.2 Ion Dissociation Techniques -- 1.5.3 Tandem Quadrupole MS-MS Instruments -- 1.5.4 Ion-Trap MS n Instruments -- 1.5.5 Tandem TOF (TOF-TOF) Instruments -- 1.5.6 Hybrid Instruments (Q-TOF, Q-LIT, IT-TOF) -- 1.5.7 MS-MS and MSn in FT-ICR-MS -- 1.5.8 Orbitrap-Based Hybrid Systems -- 1.5.9 Ion-Mobility Spectrometry-Mass Spectrometry -- 1.6 Data Interpretation and Analytical Strategies -- 1.6.1 Data Acquisition in MS Revisited -- 1.6.2 Quantitative Bioanalysis and Residue Analysis -- 1.6.3 Identification of Small-Molecule "Known Unknowns" -- 1.6.4 Identification of Drug Metabolites -- 1.6.5 Protein Molecular Weight Determination -- 1.6.6 Peptide Fragmentation and Sequencing -- 1.6.7 General Proteomics Strategies: Top-Down, Middle-Down, Bottom-Up -- 1.7 Conclusion and Perspectives -- References -- Part I Direct MS Based Affinity Techniques.

Chapter 2 Studying Protein-Protein Interactions by Combining Native Mass Spectrometry and Chemical Cross-Linking -- 2.1 Introduction -- 2.2 Protein Analysis by Mass Spectrometry -- 2.3 Native MS -- 2.3.1 Instrumentation for High-mass ion Detection -- 2.3.2 Defining the Exact Mass of the Composing Subunits -- 2.3.3 Analyzing the Intact Complex -- 2.4 Chemical Cross-linking MS -- 2.4.1 Types of Cross-linkers -- 2.4.2 MS/MS Cleavable Cross-linkers -- 2.4.3 Data Analysis -- 2.5 Value of Combining Native MS with Chemical Cross-linking MS -- 2.6 Regulating the Giant -- 2.7 Capturing Transient Interactions -- 2.8 An Integrative Approach for Obtaining Low-Resolution Structures of Native Protein Complexes -- 2.9 Future Directions -- References -- Chapter 3 Native Mass Spectrometry Approaches Using Ion Mobility-Mass Spectrometry -- 3.1 Introduction -- 3.2 Sample Preparation -- 3.3 Electrospray Ionization -- 3.4 Mass Analyzers and Tandem MS Approaches -- 3.5 Ion Mobility -- 3.6 Data Processing -- 3.7 Challenges and Future Perspectives -- References -- Part II LC-MS Based with Indirect Assays -- Chapter 4 Methodologies for Effect-Directed Analysis: Environmental Applications, Food Analysis, and Drug Discovery -- 4.1 Introduction -- 4.2 Principle of Traditional Effect-Directed Analysis -- 4.3 Sample Preparation -- 4.3.1 Environmental Analysis -- 4.3.1.1 Aqueous Samples -- 4.3.1.2 Biological Samples -- 4.3.1.3 Sediment, Soil, Suspended Matter -- 4.3.2 Food Analysis -- 4.3.2.1 Chromatography-Olfactometry -- 4.3.2.2 Functional Foods -- 4.3.3 Drug Discovery -- 4.3.3.1 Combinatorial Libraries and Natural Extracts -- 4.4 Fractionation for Bioassay Testing -- 4.4.1 Environmental Analysis -- 4.4.2 Food Analysis -- 4.4.3 Drug Discovery -- 4.5 Miscellaneous Approaches -- 4.6 Bioassay Testing -- 4.6.1 Environmental Analysis -- 4.6.2 Food Analysis.

4.6.3 Drug Discovery -- 4.7 Identification and Confirmation Process -- 4.7.1 Instrumentation -- 4.7.1.1 Gas Chromatography-Mass Spectrometry -- 4.7.1.2 Liquid Chromatography-Mass Spectrometry -- 4.7.2 Data Analysis -- 4.7.2.1 Deconvolution -- 4.7.2.2 Database Spectrum Searching -- 4.7.2.3 Database Searching on Molecular Formula -- 4.7.2.4 In Silico Tools -- 4.7.2.5 Use of Physicochemical Properties -- 4.7.2.6 Applications in Nontarget Screening and EDA -- 4.8 Conclusion and Perspectives -- References -- Chapter 5 MS Binding Assays -- 5.1 Introduction -- 5.2 MS Binding Assays - Strategy -- 5.2.1 Analogies and Differences Compared to Radioligand Binding Assays -- 5.2.2 Fundamental Assay Considerations -- 5.2.3 Fundamental Analytical Considerations -- 5.3 Application of MS Binding Assays -- 5.3.1 MS Binding Assays for the GABA Transporter GAT1 -- 5.3.1.1 GABA Transporters -- 5.3.1.2 MS Binding Assays for GAT1 - General Setup -- 5.3.1.3 MS Binding Assays for GAT1 - Speeding up Chromatography -- 5.3.1.4 MS Binding Assays for GAT1 with MALDI-MS/MS for Quantitation -- 5.3.1.5 Library Screening by Means of MS Binding Assays -- 5.3.2 MS Binding Assays for the Serotonin Transporter -- 5.3.2.1 Serotonin Transporter -- 5.3.2.2 MS Binding Assays for SERT - General Setup -- 5.3.3 MS Binding Assays Based on the Quantitation of the Nonbound Marker -- 5.3.3.1 Competitive MS Binding Assays for Dopamine D1 and D2 Receptors -- 5.3.4 Other Examples Following the Concept of MS Binding Assays -- 5.4 Summary and Perspectives -- Acknowledgments -- References -- Chapter 6 Metabolic Profiling Approaches for the Identification of Bioactive Metabolites in Plants -- 6.1 Introduction to Plant Metabolic Profiling -- 6.2 Sample Collection and Processing -- 6.3 Hyphenated Techniques -- 6.3.1 Liquid Chromatography-Mass Spectrometry.

6.3.2 Gas Chromatography-Mass Spectrometry -- 6.3.3 Capillary Electrophoresis-Mass Spectrometry -- 6.4 Mass Spectrometry -- 6.4.1 Time of Flight -- 6.4.2 Quadrupole Mass Filter -- 6.4.3 Ion Traps (Orbitrap and Linear Quadrupole (LTQ)) -- 6.4.4 Fourier Transform Mass Spectrometry -- 6.4.5 Ion Mobility Mass Spectrometry -- 6.5 Mass Spectrometric Imaging -- 6.5.1 MALDI-MS -- 6.5.2 SIMS-MS -- 6.5.3 DESI-MS -- 6.5.4 LAESI-MS -- 6.5.5 LDI-MS and Others for Imaging -- 6.6 Data Analysis -- 6.6.1 Data Processing -- 6.6.2 Data Analysis Methods -- 6.6.3 Databases -- 6.7 Future Perspectives -- References -- Chapter 7 Antivenomics: A Proteomics Tool for Studying the Immunoreactivity of Antivenoms -- 7.1 Introduction -- 7.2 Challenge of Fighting Human Envenoming by Snakebites -- 7.3 Toolbox for Studying the Immunological Profile of Antivenoms -- 7.4 First-Generation Antivenomics -- 7.5 Snake Venomics -- 7.6 Second-Generation Antivenomics -- 7.7 Concluding Remarks -- Acknowledgments -- References -- Part III Direct Pre- and On-Column Coupled Techniques -- Chapter 8 Frontal and Zonal Affinity Chromatography Coupled to Mass Spectrometry -- 8.1 Introduction -- 8.2 Frontal Affinity Chromatography -- 8.3 Staircase Method -- 8.4 Simultaneous Frontal Analysis of a Complex Mixture -- 8.5 Multiprotein Stationary Phase -- 8.6 Zonal Chromatography -- 8.7 Nonlinear Chromatography -- Acknowledgments -- References -- Chapter 9 Online Affinity Assessment and Immunoaffinity Sample Pretreatment in Capillary Electrophoresis-Mass Spectrometry -- 9.1 Introduction -- 9.2 Capillary Electrophoresis -- 9.3 Affinity Capillary Electrophoresis -- 9.3.1 Dynamic Equilibrium ACE (Fast Complexation Kinetics) -- 9.3.2 Pre-Equilibrium ACE (Slow Complexation Kinetics) -- 9.3.3 Kinetic ACE (Intermediate Complexation Kinetics).

9.4 Immunoaffinity Capillary Electrophoresis -- 9.5 Capillary Electrophoresis-Mass Spectrometry -- 9.5.1 General Requirements for Effective CE-MS Coupling -- 9.5.2 Specific Requirements for ACE-MS and IA-CE-MS -- 9.6 Application of ACE-MS -- 9.7 Applications of IA-CE-MS -- 9.8 Conclusions -- References -- Chapter 10 Label-Free Biosensor Affinity Analysis Coupled to Mass Spectrometry -- 10.1 Introduction to MS-Coupled Biosensor Platforms -- 10.2 Strategies for Coupling Label-Free Analysis with Mass Spectrometry -- 10.2.1 On-Chip Approaches -- 10.2.1.1 SPR-MALDI-MS -- 10.2.1.2 SPR-LDI-MS -- 10.2.2 Off-Chip Configurations -- 10.2.2.1 ESI-MS -- 10.2.2.2 In Parallel Approach -- 10.2.3 Chip Capture and Release Chromatography - Electrospray-MS -- 10.3 New Sensor and MS Platforms, Opportunities for Integration -- 10.3.1 Imaging Nanoplasmonics -- 10.3.2 Evanescent Wave Silicon Waveguides -- 10.3.3 New Trends in MS Matrix-Free Ion Sources -- 10.3.4 Tag-Mass -- 10.3.5 Integration -- References -- Part IV Direct Post Column Coupled Affinity Techniques -- Chapter 11 High-Resolution Screening: Post-Column Continuous-Flow Bioassays -- 11.1 Introduction -- 11.1.1 Variants of On-line Post-Column Assays Using Mass Spectrometry -- 11.1.1.1 Mass Spectrometry as Readout for Biological Assays -- 11.1.1.2 Structure Elucidation by Mass Spectrometry -- 11.1.2 Targets and Analytes -- 11.1.2.1 Targets -- 11.1.2.2 Analytes and Samples -- 11.2 The High-Resolution Screening Platform -- 11.2.1 Separation -- 11.2.2 Flow Splitting -- 11.2.3 Bioassay -- 11.2.4 MS Detection -- 11.3 Data Analysis -- 11.3.1 Differences between HRS and HTS -- 11.3.1.1 Influence of Shorter Incubation Times -- 11.3.1.2 The Assay Signal -- 11.3.1.3 Dilution Calculations -- 11.3.1.4 MS Structure Elucidation -- 11.3.1.5 Structure-Affinity Matching -- 11.3.2 Validation.

11.4 Conclusions and Perspectives.