Targeted Biomarker Quantitation by LC-MS

Naidong Weng, PhD, is Scientific Director, Janssen Fellow, and Head of Bioanalytical Chemistry and Pharmacokinetics within Department of Pharmacokinetics, Dynamics and Metabolism at US East Coast, Janssen Research & Development, Johnson and Johnson. He has over 25 years of experiences on quantitative bioanalysis. His research interest includes using HILIC-MS/MS for quantitation of highly polar analytes as well as chiral analysis. He has published more than 110 journal papers and book chapters. Wenying Jian, PhD, a Senior Principal Scientist of Bioanalytical Chemistry and Pharmacokinetics within Department of Pharmacokinetics, Dynamics and Metabolism at US East Coast, Janssen Research & Development, Johnson and Johnson. Her research experience and interest center on application of advanced LC-MS methodologies in detection, identification, and quantitation of endogenous molecules, drugs and their metabolites, including small and large molecules, and in complicated biological matrices. She has published more than 40 journal papers and book chapters.

List of Contributors xv

Preface xix

Abbreviations xxiii

Part I Overview 1

1 Overview of Targeted Quantitation of Biomarkers and Its Applications 3
Naidong Weng

1.1 Introduction 3

1.2 Biomarker Definition 4

1.3 Current Challenges of a Biomarker 5

1.4 Biomarker Validation Process 6

1.5 Current Regulatory Requirement for Target Biomarker Quantitation 6

1.6 Challenges of Biomarker Quantitation 7

1.7 Current Technologies for Biomarker Quantitation 8

1.8 Current Biomarker Quantitation Applications 9

1.9 Conclusion and Future Perspective 12

References 13

2 Translational Application of Biomarkers 17
Ray Bakhtiar

2.1 Introduction 17

2.2 Translational Medicine 17

2.3 Biomarkers 18

2.4 Biomarker Categories 18

2.5 Neurobiological Disorders 21

2.6 Cardiovascular Disorders 22

2.7 Chronic Obstructive Pulmonary Disease 23

2.8 Oncology 24

2.9 Biomarker Measurements and Regulatory Considerations 26

2.10 Conclusions 27

References 29

3 Current Regulatory Guidance Pertaining Biomarker Assay Establishment and Industrial Practice of Fit‐for‐Purpose and Tiered Approach 35
Naidong Weng

3.1 Introduction 35

3.2 Current Regulatory Guidance and Interpretation 36

3.3 Current Industrial Discussion and Recommendations 37

3.4 Considerations for Assay Validation and Sample Analysis 39

3.5 Examples of Fit‐for‐Purpose and Tiered Approach 41

3.6 Conclusion 42

References 42

4 Modern Liquid Chromatography and Mass Spectrometry for Targeted Biomarker Quantitation 45
Wenying Jian

4.1 Introduction 45

4.2 Liquid Chromatography 45

4.3 Mass Spectrometry 51

4.4 Summary and Future Perspectives 58

References 59

5 Comparison Between LC–MS and Ligand‐Binding Assay Approaches for Biomarker Quantification 65
QingQing Wang, Lili Guo, and Ian A. Blair

5.1 General Considerations: LBAs or LC–MS Assays 65

5.2 General Quantification Approaches 66

5.3 Analytical Issues Specifically Related to LBAs 67

5.4 Analytical Features Specifically Related to LC–MS Methods 68

5.5 Case Studies: Comparison Between ELISA and LC–MS 72

5.6 Summary and Future Perspective 74

References 74

6 Sample Preparation Methods for Targeted Biomarker Quantification by LC‐MS 79
Shichen Shen, Bo An, and Jun Qu

6.1 Introduction 79

6.2 Sample Preparation Strategies for Small Molecule Biomarkers 79

6.3 Sample Preparation Strategies for Macromolecule Biomarkers 86

6.4 Conclusive Remarks 94

References 95

7 Overcome the Endogenous Levels in Biomarker Quantitation Using LC–MS 107
Guowen Liu

7.1 Introduction 107

7.2 How Does Matrix Effect Affect Quantitation? 108

7.3 Commonly Used Strategies 109

7.4 Discussions and Future Perspectives 114

References 115

Part II Challenges and Approaches 119

8 Sample Collection for Targeted Biomarker Quantitation by LC–MS 121
Yuzhong Deng and Xiaorong Liang

8.1 Introduction 121

8.2 Timing of Biomarker Sample Collection 121

8.3 Matrix Type 122

8.4 Collection Methods 124

8.5 Sample Storage Stability 128

8.6 Summary 129

References 130

9 Nonspecific Binding in LC–MS Bioanalysis 137
Aimin Tan and John C. Fanaras

9.1 Introduction 137

9.2 Identification and Evaluation of NSB 137

9.3 Causes for NSB 140

9.4 Overcoming NSB Challenges 140

9.5 Conclusion 144

References 146

10 Strategies for Improving Sensitivity for Targeted Quantitation by LC–MS 149
Long Yuan and Qin C. Ji

10.1 Introduction 149

10.2 Sample Preparation Strategies for Improving Sensitivity 150

10.3 LC Separation Strategies for Improving Sensitivity 156

10.4 MS Detection Strategies for Improving Sensitivity 160

10.5 Conclusions 163

References 163

11 Strategies to Improve Specificity for Targeted Biomarker Quantitation by LC–MS 171
Yuan‐Qing Xia and Jeffrey D. Miller

11.1 Introduction 171

11.2 Differential Mobility Spectrometry 171

11.3 High‐Resolution Mass Spectrometry 175

11.4 Conclusions 180

References 180

12 Biomarker Quantitation Using Relative Approaches 183
Shane M. Lamos and Katrina E. Wiesner

12.1 Introduction 183

12.2 Relative Quantitation Isotope Labeling Approaches 183

12.3 Conclusions 191

References 192

Part III Applications 195

13 Targeted Quantification of Amino Acid Biomarkers Using LC‐MS 197
Barry R. Jones, Raymond F. Biondolillo, and John E. Buckholz

13.1 Introduction 197

13.2 Amino Acids as Biomarkers 198

13.3 Methods of Measurement 201

13.4 Accuracy, Precision, Selectivity, and Stability Considerations 203

13.5 Assay Design 207

13.6 Conclusion 207

References 208

14 Targeted Quantification of Peptide Biomarkers: A Case Study of Amyloid Peptides 211
Lieve Dillen, Marc De Meulder, and Tom Verhaeghe

14.1 Overview 211

14.2 Challenges and Approaches 212

14.3 Application to the Quantification of Alzheimer’s Disease Biomarkers 216

14.4 Conclusion 222

References 222

15 Targeted Protein Biomarker Quantitation by LC‐MS 227
Yongle Pang, Chuan Shi, and Wenying Jian

15.1 Introduction 227

15.2 Sample Preparation for Targeted Protein Biomarker Quantitation 231

15.3 “Bottom‐Up” Approach for Targeted Protein Biomarker Quantitation Using LC‐MS 233

15.4 “Top Down” Approach for Targeted Protein Biomarker Quantitation Using LC‐MS 235

15.5 Key Considerations in Targeted Protein Biomarker Quantitation Using LC‐MS 236

15.6 Summary and Future Perspectives 239

References 240

16 Glycoprotein Biomarkers 245
Shuwei Li, Stefani N. Thomas, and Shuang Yang

16.1 Introduction 245

16.2 Technologies for Glycoprotein Analysis 246

16.3 Glycoprotein Biomarker Quantification Using LC‐MS 255

16.4 Protein Biomarkers for Clinical Applications 259

16.5 Summary and Future Direction 264

References 265

17 Targeted Lipid Biomarker Quantitation Using Liquid Chromatography–Mass Spectrometry (LC–MS) 273
Ashkan Salamatipour, Ian A. Blair, and Clementina Mesaros

17.1 Introduction of Lipids 273

17.2 LC–MS Analysis of Lipids 276

17.3 Examples of LC–MS Analysis of Lipids 278

17.4 Summary and Future Directions 283

References 283

18 Targeted LC–MS Quantification of Androgens and Estrogens for Biomarker Development 289
Daniel Tamae

18.1 Introduction 289

18.2 Current Considerations in Biomarker Validation 292

18.3 Current Considerations in LC–MS Method Development 293

18.4 Clinical Application of LC–MS Quantification of Estrogens and Androgens 296

18.5 Conclusion and Perspective 301

References 301

19 Steroid Biomarkers 307
Mike (Qingtao) Huang, Shefali Patel, and Zhongping (John) Lin

19.1 Introduction 307

19.2 Sterols as Endogenous Biomarkers and Their Quantitation 307

19.3 Cortisol and 6 β‐Hydroxycortisol (6β‐HC) as Biomarkers and Their Quantitation 312

19.4 Summary 316

References 316

20 Bile Acids as Biomarkers 321
Clara John, Philipp Werner, Joerg Heeren, and Markus Fischer

20.1 Introduction 321

20.2 Analytical Platform for Bile Acids 323

20.3 Summary 327

References 327

21 Biomarkers for Vitamin Status and Deficiency: LC‐MS Based Approach 331
Stanley (Weihua) Zhang and Jonathan Crowther

21.1 Introduction to Vitamin and Vitamin Deficiency 331

21.2 Detection of Vitamin D by LC‐MS/MS and Comparison with Other Methods 332

21.3 Other Vitamin Biomarkers 338

21.4 Conclusions and Perspectives 340

References 341

22 Quantitation of Acyl‐Coenzyme A Thioesters as Metabolic Biomarkers 347
Nathaniel Snyder

22.1 Introduction 347

22.2 Structure and Function of Acyl‐CoAs 347

22.3 Detection and Quantitation of Acyl‐CoAs 349

22.4 Acyl‐CoA Analysis for Current Drug Targets 352

22.5 Acyl‐CoAs as Biomarkers in Metabolic Disease 352

22.6 The Involvement of Acyl‐CoAs in Drug Metabolism 353

References 353

23 Neurotransmitter Biomarkers 357
Guodong Zhang

23.1 Introduction 357

23.2 Chromatographic Platforms of Biological Measurement for Neurotransmitters 358

23.3 Bioanalytical Methodologies 359

23.4 Conclusion 367

References 367

24 Targeted Quantification of Carbohydrate Biomarkers Using LC–MS 371
Cong Wei and Hong Gao

24.1 Introduction 371

24.2 Overview 371

24.3 Bioanalytical Method Development for Carbohydrate Biomarkers 374

24.4 Conclusions 384

References 384

25 Nucleoside/Nucleotide Biomarkers 389
Guodong Zhang

25.1 Introduction 389

25.2 Chromatographic Platforms for Nucleosides/Nucleotides 390

25.3 Bioanalytical Methodologies 391

25.4 Nucleoside/Nucleotide Biomarkers and Case Studies 398

25.5 Conclusion 399

References 402

26 LC–MS of RNA Biomarkers 407
Michael G. Bartlett, Babak Basiri, and Ning li

26.1 Introduction 407

26.2 Role in Disease and Therapeutics 408

26.3 Role of Mass Spectrometry in RNA Biomarkers 409

26.4 LC–MS Approaches for RNA Determination 411

26.5 Case Studies 415

References 418

Index 425