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E-raamat: Protein Analysis using Mass Spectrometry: Accelerating Protein Biotherapeutics from Lab to Patient

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Protein Analysis using Mass Spectrometry: Accelerating Protein Biotherapeutics from Lab to PatientSuurem pilt
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This book illustrates the interdisciplinary advances of mass spectrometry (MS) and its applications for protein analysis. It focuses on studies that have contributed to the rapid progress and development of protein therapeutics to meet challenging medical needs. It brings together the most current advances in the mass spectrometry technology and related method in protein analysis including a variety of applications and their impact on accelerating discovery and development of protein biotherapeutics.

Split into four sections the book covers Principles, Instrumentation, Technologies (MS of peptides and proteins, instrumentation in protein analysis, and Chip technology in mass spectrometry protein analysis); Mass spectrometry protein analysis in understanding mechanism and functions in living cells; Mass spectrometry protein analysis in support development of protein therapeutic drugs (qualitative and quantitative aspects, protein analysis in process and product development, and for PK and TK studies); and finally Emerging areas from drug monitoring to patient care including MS in the analysis of protein, peptide and lipid biomarkers, biomarker discovery, regulatory perspectives, and new technologies.

List of Contributors xiii
Foreword xvii
Preface xix
1 Contemporary Protein Analysis by Ion Mobility Mass Spectrometry 1(10)
Johannes P.C. Vissers
James I. Langridge
1.1 Introduction
1(1)
1.2 Traveling-Wave Ion Mobility Mass Spectrometry
1(1)
1.3 IM-MS and LC-IM-MS Analysis of Simple and Complex Mixtures
2(5)
1.3.1 Cross Section and Structure
2(2)
1.3.2 Separation
4(1)
1.3.3 Sensitivity
5(2)
1.4 Outlook
7(1)
Acknowledgment
8(1)
References
8(3)
2 High-Resolution Accurate Mass Orbitrap and Its Application in Protein Therapeutics Bioanalysis 11(10)
Hongxia Wang
Patrick Bennett
2.1 Introduction
11(1)
2.2 Triple Quadrupole Mass Spectrometer and Its Challenges
11(1)
2.3 High-Resolution Mass Spectrometers
12(1)
2.4 Quantitation Modes on Q Exactive Hybrid Quadrupole Orbitrap
13(1)
2.5 Protein Quantitation Approaches Using Q Exactive Hybrid Quadrupole Orbitrap
14(2)
2.6 Data Processing
16(1)
2.7 Other Factors That Impact LC-MS-based Quantitation
16(2)
2.7.1 Sample Extraction to Reduce Matrices
16(1)
2.7.2 Internal Standard
17(1)
2.8 Conclusion and Perspectives of LC-HRMS in Regulated Bioanalysis
18(1)
References
18(3)
3 Current Methods for the Characterization of Posttranslational Modifications in Therapeutic Proteins Using Orbitrap Mass Spectrometry 21(14)
Zhiqi Hao
Qiuting Hong
Fan Zhang
Shiaw-Lin Wu
Patrick Bennett
3.1 Introduction
21(2)
3.2 Characterization of PTMs Using Higher-Energy Collision Dissociation
23(3)
3.2.1 Oxidation
24(1)
3.2.2 Deamidation
24(2)
3.3 Application of Electron Transfer Dissociation to the Characterization of Labile PTMs
26(5)
3.3.1 Performing ETD Experiments in Orbitrap Instruments
27(1)
3.3.2 Structure Elucidation of Glycopeptides Using Multiple Fragmentation Mechanisms in Orbitrap Instruments
28(3)
3.4 Conclusion
31(1)
Acknowledgment
32(1)
References
32(3)
4 Macro-to Micromolecular Quantitation of Proteins and Peptides by Mass Spectrometry 35(10)
Suma Ramagiri
Brigitte Simons
Laura Baker
4.1 Introduction
35(1)
4.2 Key Challenges of Peptide Bioanalysis
36(2)
4.2.1 Key Benefits of the LC/MS/MS Peptide Quantitation Workflow
38(1)
4.3 Key Features of LC/MS/MS-Based Peptide Quantitation
38(3)
4.3.1 Sensitivity
39(1)
4.3.2 Selectivity
39(1)
4.3.2.1 MRM3
39(1)
4.3.2.2 Differential Mobility Spectrometry (DMS)
39(1)
4.3.3 High-Resolution Accurate-Mass Spectrometry
39(1)
4.3.4 Software
40(1)
4.4 Advantages of the Diversity of Mass Spectrometry Systems
41(1)
4.5 Perspectives for the Future
41(1)
References
42(3)
5 Peptide and Protein Bioanalysis Using Integrated Column-to-Source Technology for High-Flow Nanospray 45(10)
Shane R. Needham
Gary A. Valaskovic
5.1 Introduction-LC-MS Has Enabled the Field of Protein Biomarker Discovery
45(1)
5.2 Integration of Miniaturized LC with Nanospray ESI-MS Is a Key for Success
46(1)
5.3 Micro-and Nano-LC Are Well Suited for Quantitative Bioanalysis
47(2)
5.4 Demonstrating Packed-Emitter Columns Are Suitable for Bioanalysis
49(2)
5.5 Future Outlook
51(1)
References
52(3)
6 Targeting the Right Protein Isoform: Mass Spectrometry-Based Proteomic Characterization of Alternative Splice Variants 55(12)
Jiang Wu
6.1 Introduction
55(1)
6.2 Alternative Splicing and Human Diseases
55(1)
6.3 Identification of Splice Variant Proteins
56(8)
6.3.1 Global Profiling of Splicing Variant Proteins
56(1)
6.3.2 Characterization of Relative Expression of Protein Splice Variants
57(5)
6.3.3 Quantitation of Splice Variants by MRM-MS
62(2)
6.4 Conclusion
64(1)
References
64(3)
7 The Application of Immunoaffinity-Based Mass Spectrometry to Characterize Protein Biomarkers and Biotherapeutics 67(24)
Bradley L. Ackermann
Michael J. Berna
7.1 Introduction
67(2)
7.1.1 The Importance of Protein Measurement
67(1)
7.1.2 Ligand Binding Assays
68(1)
7.1.3 The Introduction of Hybrid IA-MS Methods
68(1)
7.2 Overview of IA-MS Methods
69(5)
7.2.1 Classification of IA-MS Methods
69(2)
7.2.2 Stable-Isotope-Labeled Internal Standards
71(1)
7.2.3 IA Capture Formats
71(1)
7.2.4 Liquid Chromatography
72(2)
7.2.5 MS Detection
74(1)
7.3 IA-MS Applications-Biomarkers
74(7)
7.3.1 Peptide Biomarkers
74(4)
7.3.2 Protein Biomarkers-Anti-Protein Capture
78(2)
7.3.3 Protein Biomarkers-Anti-Peptide Capture
80(1)
7.4 IA-MS Applications-Biotherapeutics
81(3)
7.4.1 Therapeutic Peptides
81(2)
7.4.2 Therapeutic Antibodies
83(1)
7.4.3 Antibody-Drug Conjugates
84(1)
7.5 Future Direction
84(1)
References
85(6)
8 Semiquantification and Isotyping of Antidrug Antibodies by lmmunocapture-LC/MS for Immunogenicity Assessment 91(8)
Jianing Zeng
Hao Jiang
Linlin Luo
8.1 Introduction
91(2)
8.2 Multiplexing Direct Measurement of ADAs by Immunocapture-LC/MS for Immunogenicity Screening, Titering, and Isotyping
93(2)
8.3 Indirect Measurement of ADAs by Quantifying ADA Binding Components
95(1)
8.4 Use of LC-MS to Assist in Method Development of Cell-Based Neutralizing Antibody Assays
96(1)
8.5 Conclusion and Future Perspectives
97(1)
References
97(2)
9 Mass Spectrometry-Based Assay for High-Throughput and High-Sensitivity Biomarker Verification 99(8)
Xuejiang Guo
Keqi Tang
9.1 Background
99(1)
9.2 Sample Processing Strategies
100(2)
9.3 Advanced Electrospray Ionization Mass Spectrometry Instrumentation
102(3)
9.4 Conclusion
105(1)
References
105(2)
10 Monitoring Quality of Critical Reagents Used in Ligand Binding Assays with Liquid Chromatography Mass Spectrometry (LC-MS) 107(22)
Brian Geist
Adrienne Clements-Egan
Tong-Yuan Yang
10.1 Introduction
107(7)
10.2 Case Study Examples
114(8)
10.2.1 Case Study #1: Confirmation of Correct Reagent Construct Prior to Use in Development of an LBA Method
114(2)
10.2.2 Case Study #2: Monitoring the Integrity of the Reagent Cell Line Production System
116(1)
10.2.3 Case Study #3: Investigation of the Loss of LBA Specificity During Clinical Development
116(6)
10.2.3.1 Prestudy Investigation
116(3)
10.2.3.2 In-Study Investigation
119(3)
10.2.4 Case Study #4: Monitoring the Incorporation Ratio of Conjugated Critical Reagent Used in LBAs
122(1)
10.3 Discussion
122(4)
10.3.1 Keys to Reagent Management
122(1)
10.3.2 Importance of LC-MS Characterization
123(2)
10.3.3 The Analytical Toolbox and a "Fit-for-Purpose" Approach for Reagent Management
125(1)
Acknowledgment
126(1)
References
126(3)
11 Application of Liquid Chromatography-High Resolution Mass Spectrometry in the Quantification of Intact Proteins in Biological Fluids 129(16)
Stanley Zhang
Jonathan Crowther
Wenying Jian
11.1 Introduction
129(2)
11.2 Workflows for Quantification of Proteins Using Full-Scan LC-HRMS
131(2)
11.2.1 Sample Preparation
131(1)
11.2.1.1 Solid-Phase Extraction (SPE)
131(1)
11.2.1.2 Affinity Enrichment
131(1)
11.2.1.3 Depletion of High-Abundant Proteins
131(1)
11.2.1.4 Solution Fractionation
132(1)
11.2.1.5 Protein Precipitation for PEGylated Proteins
132(1)
11.2.2 LC-HRMS
132(1)
11.2.2.1 HPLC
132(1)
11.2.2.2 Full-Scan HRMS Data Acquisition and Analysis
133(1)
11.3 Internal Standard Strategy
133(2)
11.3.1 Stable Isotope Labeled Protein
134(1)
11.3.2 Protein Analog
135(1)
11.4 Calibration and Quality Control (QC) Sample Strategy
135(1)
11.5 Common Issues in Quantification of Proteins Using LC-HRMS
135(2)
11.5.1 Stability
135(1)
11.5.2 Adsorption
136(1)
11.5.3 Specific Protein Binding
136(1)
11.5.4 Posttranslational Modifications (PTMs)
136(1)
11.6 Examples of LC-HRMS-Based Intact Protein Quantification
137(1)
11.7 Conclusion and Future Perspectives
138(2)
Acknowledgment
140(1)
References
140(5)
12 LC-MS/MS Bioanalytical Method Development Strategy for Therapeutic Monoclonal Antibodies in Preclinical Studies 145(16)
Hongyan Li
Timothy Heath
Christopher A. James
12.1 Introduction: LC-MS/MS Bioanalysis of Therapeutic Monoclonal Antibodies
145(1)
12.2 Highlights of Recent Method Development Strategies
146(8)
12.2.1 Strategy for Surrogate Peptide Selection and Optimization
146(2)
12.2.2 Sample Preparation
148(4)
12.2.2.1 Immunoaffinity-Based Sample Preparation
148(3)
12.2.2.2 Nonimmunoaffinity-Based Sample Preparation
151(1)
12.2.3 Accelerated Trypsin Digestion
152(1)
12.2.4 Internal Standard Selection
153(1)
12.2.4.1 SIL-Peptide IS
154(1)
12.2.4.2 Cleavable Flanking SIL-Peptide IS
154(1)
12.2.4.3 SIL-mAb IS
154(1)
12.3 Case Studies of Preclinical Applications of LC-MS/MS for Monoclonal Antibody Bioanalysis
154(2)
12.3.1 Case Study #1
154(1)
12.3.1.1 Key Analytical Method Features
154(1)
12.3.2 Case Study #2
155(6)
12.3.2.1 Key Analytical Method Features
155(1)
12.4 Conclusion and Future Perspectives
156(2)
References
158(3)
13 Generic Peptide Strategies for LC-MS/MS Bioanalysis of Human Monoclonal Antibody Drugs and Drug Candidates 161(22)
Michael T. Furlong
13.1 Introduction
161(1)
13.2 A Universal Peptide LC-MS/MS Assay for Bioanalysis of a Diversity of Human Monoclonal Antibodies and Fc Fusion Proteins in Animal Studies
161(4)
13.2.1 Identification of a Candidate Universal Surrogate Peptide to Enable Quantification of Human mAb and Fc Fusion Protein Drug Candidates
161(1)
13.2.2 Application of an Exploratory Universal (Peptide 1) LC-MS/MS Assay to a Monkey Pharmacokinetic Study
162(1)
13.2.3 Potential Applicability of a Peptide 1 Variant to Bioanalysis of Human IgG2-Based mAbs and Fc Fusion Proteins
163(1)
13.2.4 Impact of Peptide 1 Asparagine Deamidation on Human mAb Quantification Can Be Mitigated
164(1)
13.3 An Improved "Dual" Universal Peptide LC-MS/MS Assay for Bioanalysis of Human mAb Drug Candidates in Animal Studies
165(5)
13.3.1 Identification and Evaluation of "Dual" Universal Peptide LC-MS/MS Assay Candidates
165(2)
13.3.2 Quantitative Evaluation and Comparison of Light and Heavy Chain Dual Universal Peptide Candidates
167(1)
13.3.3 Assessing the Level of Quantitative Agreement Between Peptide 1 and Peptide 2 in Assay Performance Evaluation Runs
167(1)
13.3.4 Deployment of the Exploratory Dual Universal Peptide Assay in Support of a Monkey Pharmacokinetic Study
168(1)
13.3.5 Considerations for Calibration Curve/QC Replicate Acceptance Criteria When a Dual Peptide Assay Is Employed
168(1)
13.3.6 Interpreting and Reporting Study Sample Concentration Data Generated with a Dual Peptide Assay
168(1)
13.3.7 Related Studies: Generic LC-MS/MS Assays for Human mAb Bioanalysis in Animal Studies
169(1)
13.4 Extending the Universal Peptide Assay Concept to Human mAb Bioanalysis in Human Studies
170(3)
13.4.1 Potential Expansion of the Universal LC-MS/MS Assay Concept into Human Studies
170(1)
13.4.2 Development and Evaluation of an Exploratory Universal IgG4 Clinical LC-MS/MS Assay
171(2)
13.4.3 Evaluation of the Impact of Anti-mAb Antibodies on Exploratory Universal IgG4 LC-MS/MS Assay Performance
173(1)
13.5 Internal Standard Options for Generic Peptide LC-MS/MS Assays
173(2)
13.5.1 Stable Isotopically Labeled Peptide Internal Standards
173(1)
13.5.2 Stable Isotopically Labeled Protein Internal Standards
174(1)
13.5.3 "Flanked" Stable Isotopically Labeled Peptide Internal Standards
175(1)
13.6 Sample Preparation Strategies for Generic Peptide LC-MS/MS Assays
175(2)
13.6.1 Direct Digestion, Pellet Digestion, and Solid-Phase Extraction
175(1)
13.6.2 Affinity Capture
176(1)
13.6.3 Additional Sample Preparation Approaches for Generic Peptide LC-MS/MS Assays
176(1)
13.7 Limitations of Generic Peptide LC-MS/MS Assays
177(1)
13.8 Conclusion
178(1)
Acknowledgments
178(1)
References
178(5)
14 Mass Spectrometry-Based Methodologies for Pharmacokinetic Characterization of Antibody Drug Conjugate Candidates During Drug Development 183(20)
Yongjun Xue
Priya Sriraman
Matthew V. Myers
Xiaomin Wang
Jian Chen
Brian Melo
Martha Vallejo
Stephen E. Maxwell
Sekhar Surapaneni
14.1 Introduction
183(1)
14.2 Mechanism of Action
183(3)
14.2.1 Linker Chemistry
185(1)
14.2.2 Toxins
185(1)
14.2.3 ADME
185(1)
14.2.4 Unique Bioanalytical Challenges
185(1)
14.3 Mass Spectrometry Measurement for DAR Distribution of Circulating ADCs
186(3)
14.3.1 Immunocapture of ADCs from Plasma or Serum
186(1)
14.3.2 Deglycosylation for Captured ADCs
187(1)
14.3.3 Mass Spectrometry Measurement for DAR Distribution of Circulating ADCs
188(1)
14.4 Total Antibody Quantitation by Ligand Binding or LC-MS/MS
189(4)
14.4.1 Ligand Binding Assay
189(1)
14.4.2 LC-MS/MS Assay for Total Antibody Quantitation
190(2)
14.4.2.1 Predigestion Treatment
190(1)
14.4.2.2 Enzymatic Digestion
191(1)
14.4.2.3 Postdigestion Treatment
191(1)
14.4.2.4 LC-MS/MS Analysis
191(1)
14.4.3 Ligand Binding versus LC-MS/MS Assays
192(1)
14.5 Total Conjugated Drug Quantitation by Ligand Binding or LC-MS/MS
193(3)
14.5.1 Ligand Binding Assays for ADC Quantitation
193(1)
14.5.1.1 DAR-Sensitive Total Conjugated Drug Assay
193(1)
14.5.1.2 DAR-Insensitive Total Conjugated Antibody Assay
193(1)
14.5.2 LC-MS/MS for the Total Conjugated Drug Quantitation
194(1)
14.5.2.1 Predigestion Treatment
194(1)
14.5.2.2 Enzymatic or Chemical Digestion
194(1)
14.5.2.3 Postdigestion Treatment
195(1)
14.5.2.4 LC-MS/MS Analysis
195(1)
14.5.3 Ligand Binding versus LC-MS/MS
195(1)
14.6 Catabolite Quantitation by LC-MS/MS
196(1)
14.6.1 Sample Preparation
196(1)
14.6.2 LC-MS/MS Analysis
197(1)
14.7 Preclinical and Clinical Pharmacokinetic Support
197(1)
14.8 Conclusion and Future Perspectives
198(1)
References
198(5)
15 Sample Preparation Strategies for LC-MS Bioanalysis of Proteins 203(18)
Long Yuan
Qin C. Ji
15.1 Introduction
203(2)
15.2 Sample Preparation Strategies to Improve Assay Sensitivity
205(8)
15.2.1 Protein Precipitation
205(1)
15.2.2 Solid-Phase Extraction
205(1)
15.2.3 Derivatization
206(1)
15.2.4 Depletion of High-Abundance Proteins
207(1)
15.2.5 Immunoaffinity Purification
208(3)
15.2.5.1 Immunocapture of a Specific Peptide
208(1)
15.2.5.2 Immunocapture of a Specific Protein
208(2)
15.2.5.3 Generic Immunocapture
210(1)
15.2.6 Online Sample Preparation
211(2)
15.3 Sample Preparation Strategies to Differentiate Free, Total, and ADA-Bound Proteins
213(1)
15.4 Sample Preparation Strategies to Overcome Interference from Antidrug Antibodies or Soluble Target
214(1)
15.5 Protein Digestion Strategies
214(1)
15.6 Conclusion
215(1)
Acknowledgment
216(1)
References
216(5)
16 Characterization of Protein Therapeutics by Mass Spectrometry 221(19)
Wei Wu
Hangtian Song
Thomas Slaney
Richard Ludwig
Li Tao
Tapan Das
16.1 Introduction
221(1)
16.2 Variants Associated with Cysteine/Disulfide Bonds in Protein Therapeutics
221(4)
16.2.1 Thiolation Isoforms
222(1)
16.2.2 Disulfide Isoforms
222(2)
16.2.3 Free Sulfhydryl
224(1)
16.2.4 Thioether/Trisulfide Bond
224(1)
16.2.5 Disulfide Bond in Antibody Drug Conjugates
224(1)
16.3 N-C-Terminal Variants
225(1)
16.4 Glycation
226(1)
16.5 Oxidation
226(2)
16.5.1 Methionine Oxidation
227(1)
16.5.2 Metal-Catalyzed Oxidation (MCO)
227(1)
16.5.3 Photooxidation
227(1)
16.5.4 Deamidation
228(1)
16.5.5 Effect of Sequence and Structure on Deamidation
228(1)
16.6 Discoloration
228(2)
16.7 Sequence Variants
230(2)
16.8 Glycosylation
232(8)
16.8.1 Glycoprotein Structure
232(3)
16.8.2 Intact Glycoprotein Analysis
235(2)
16.8.3 Glycopeptide Analysis
237(1)
16.8.4 Tandem MS of Glycopeptides
237(1)
16.8.5 Free Glycan Analysis
238(1)
16.8.6 Release of Glycans from Glycoproteins
238(1)
16.8.7 Detailed Sequence and Linkage Analysis of Glycans
239(1)
16.9 Conclusion
240(1)
References 240(11)
Index 251
Dr. Mike S. Lee is a biotechnology entrepreneur and Founder and President of Milestone Development Services. He actively participates in the development of new technologies and their integration into industrial settings.  Dr. Lee is a founder of the Annual Symposium on Clinical and Pharmaceutical Solutions through Analysis (CPSA). These unique events, held in the US, China and Brazil, highlight industry-related applications and feature sessions promoting discussion on real-world experiences with the latest analytical technology and industry initiatives. Dr. Lee is the author or co-author of over 50 scientific papers and patents. He received his BS degree in Chemistry at the University of Maryland in 1982. In 1985 and 1987, he completed his MS and PhD, respectively, in Analytical Chemistry from the University of Florida under the direction of Professor Richard A. Yost.

Dr. Qin C. Ji is a Research Fellow in the Department of Bioanalytical Sciences at Bristol-Myers Squibb, Princeton, New Jersey. His current job responsibilities include regulated bioanalytical support (with LC-MS/MS and ligand binding assays) for the development of biologic, new modality, and small molecule drugs in preclinical and clinical stages. He has authored and co-authored more than 60 peer reviewed articles and book chapters.  Prior to his current position, he held scientific and management positions at Abbott and Covance. Dr. Ji obtained his Ph.D. from Michigan State University and has completed Postdoctoral training at Mayo Clinic. He was awarded two President Awards and was an Associate Research Fellow in the prestigious Volwiler scientific society at Abbott Laboratories. He was also awarded a Chemistry Leadership Award at Bristol-Myers Squibb.
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