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MALDI MS: A Practical Guide to Instrumentation, Methods and Applications, 2nd Edition

ISBN: 978-3-527-33331-8
480 pages
December 2013, Wiley-Blackwell
MALDI MS: A Practical Guide to Instrumentation, Methods and Applications, 2nd Edition (3527333312) cover image
This authoritative book on MALDI MS, now finally available in its second edition and edited by one of its inventors, gives an in-depth description of the many different applications, along with a detailed discussion of the technology itself.
Thoroughly updated and expanded, with contributions from key players in the field, this unique book provides a comprehensive overview of MALDI MS along with its
possibilities and limitations.
The initial chapters deal with the technology and the instrumental setup, followed by chapters on the use of MALDI MS in protein research (including proteomics), genomics, glycomics and lipidomics. The option of MALDI-MS for the analysis of polymers and small molecules are also covered in separate chapters, while new to this edition is a section devoted to the interplay of MALDI MS and bioinformatics.
A much-needed practical and educational asset for individuals, academic institutions and companies in the field of bioanalytics.
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Preface to the Second Edition XI

List of Contributors XIII

1 The MALDI Process and Method 1
Franz Hillenkamp, Thorsten W. Jaskolla, and Michael Karas

1.1 Introduction 1

1.2 Analyte Incorporation 4

1.3 Absorption of the Laser Radiation 6

1.4 The Ablation/Desorption Process 9

1.5 Ionization 13

1.6 Fragmentation of MALDI Ions 17

1.7 MALDI of Noncovalent Complexes 21

1.8 The Optimal Choice of Matrix: Sample Preparation 24

1.8.1 Surface Preparation 27

1.8.2 Anchor Sample Plates 27

1.8.3 Matrix Additives and Influence of the Sample Plate Surface 29

Abbreviations 30

References 31

2 MALDI Mass Spectrometry Instrumentation 41
Peter B. O’Connor, Klaus Dreisewerd, Kerstin Strupat, and Franz Hillenkamp

2.1 Introduction 41

2.2 Lasers for MALDI-MS 42

2.3 Fragmentation of MALDI Ions 48

2.3.1 MALDI at Elevated Pressure 48

2.3.2 Tandem Mass Spectrometry of MALDI Ions 49

2.4 Mass Analyzers 52

2.4.1 Axial TOF Mass Spectrometers 53

2.4.2 Reflectron TOF Mass Spectrometers 55

2.4.3 Tandem TOF Mass Spectrometers 56

2.4.4 Orthogonal TOF Mass Analyzers 60

2.4.5 Tandem Mass Spectrometry in oTOF Mass Analyzers 61

2.4.6 Ion Detectors and Data Processing in MALDI-TOF Analyzers 62

2.5 Fourier Transform Ion Cyclotron Resonance Mass Spectrometers 64

2.5.1 Tandem Mass Spectrometry on FTICR Mass Spectrometers 70

2.6 Quadrupole Ion Trap Mass Spectrometers 72

2.6.1 RF-Only Ion Guides and LIT Mass Spectrometers 77

2.6.2 Tandem Mass Spectrometry on QIT Mass Spectrometers 77

2.7 Hybrid Mass Spectrometers 79

2.7.1 Quadrupole TOF Mass Spectrometers 79

2.7.2 Quadrupole FT Mass Spectrometers 80

2.7.3 QIT-TOF Mass Spectrometers 82

2.7.4 Ion Mobility oTOF Mass Spectrometers 83

2.7.5 Orbitrap 87

2.8 Future Directions 92

Definitions and Acronyms 93

References 96

3 MALDI-MS in Protein Chemistry and Proteomics 105
Karin Hjernø and Ole N. Jensen

3.1 Introduction 105

3.2 Sample Preparation for Protein and Peptide Analysis by MALDI-MS 108

3.3 Strategies for Using MALDI-MS in Protein Biochemistry 111

3.3.1 Peptide Mass Mapping of Purifi ed Proteins 113

3.3.2 Peptide Sequencing by MALDI-MS/MS 114

3.3.3 Analysis of Post-Translational Modifi cations 116

3.4 Applications of MALDI-MS in Proteomics 119

3.4.1 Protein Identifi cation by MALDI-MS Peptide Mass Mapping 119

3.4.2 Quantitation of Proteins by MALDI-MS 122

3.5 Computational Tools for Protein Analysis by MALDI-MS 123

3.6 Clinical Applications of MALDI-MS 124

3.7 Conclusions 125

Acknowledgments 125

References 126

4 MALDI-Mass Spectrometry Imaging 133
Bernhard Spengler

4.1 Introduction 133

4.2 History of Mass Spectrometry Imaging (MSI) and Microprobing Techniques 136

4.3 MALDI in Micro Dimensions: Instruments and Mechanistic Differences 137

4.4 Visualization of Mass Spectrometric Information 140

4.5 Data Processing and Data Exchange 143

4.6 Matrix Deposition for High-Resolution Imaging 144

4.7 Organisms, Organs, and Tissues: MALDI Imaging at Various Lateral Resolutions 148

4.7.1 Phospholipid Analysis 148

4.7.2 Peptide Analysis 150

4.7.3 Drug Monitoring 154

4.8 Whole-Cell and Single-Cell Analysis 154

4.8.1 Cellular Analysis 156

4.8.2 Individually Isolated Cells 156

4.8.3 Direct Cellular and Subcellular Imaging 157

4.9 Cell Sorting and Capturing 158

4.10 Direct Protein Identification and Localization 160

4.11 Identification and Characterization: Requirements for Mass Resolution and Accuracy 162

4.12 Conclusions 163

Acknowledgments 163

References 164

5 Analysis of Nucleic Acids, and Practical Implementations in Genomics and Genetics 169
Stefan Berkenkamp, Dirk van den Boom, and Daniele Fabris

5.1 Challenges in Nucleic Acid Analysis by MALDI-MS 169

5.2 Genetic Markers 175

5.2.1 Restriction Fragment Length Polymorphisms (RFLPs) 177

5.2.2 Microsatellites/Short Tandem Repeats (STRs) 177

5.2.3 Single Nucleotide Polymorphisms (SNPs) 178

5.2.4 Characterization of Base Modifi cations and Covalent Adducts 180

5.2.5 Detection of Noncovalent Complexes of Nucleic Acids 186

5.3 Assay Formats for Nucleic Acid Analysis by MALDI-MS 190

5.4 Applications in Genotyping 192

5.4.1 MALDI-TOF-MS SNP and Mutation Analysis 192

5.4.1.1 The PinPoint Assay 193

5.4.1.2 The PROBE Assay 195

5.4.1.3 The MassEXTEND Assay 196

5.4.1.4 The GOOD Assay 198

5.4.1.5 The Invader Assay 200

5.4.1.6 The Incorporation and Complete Chemical Cleavage Assay 202

5.4.1.7 The Restriction Fragment Mass Polymorphism Assay 203

5.4.2 MALDI-TOF MS for Haplotyping 203

5.5 Applications in Comparative Sequence Analysis 205

5.6 Applications in Quantitation of Nucleic Acids for Analysis of Gene Expression and Gene Amplification 215

5.6.1 Analysis of DNA Mixtures and Allele Frequency Determinations in DNA Pools 215

5.6.2 Analysis of Gene Expression 219

5.7 Future Perspectives for the MALDI-MS Analysis of Nucleic Acids 222

Acknowledgments 223

References 223

6 MALDI-MS of Glycans and Glycoconjugates 239
Hélène Perreault, Erika Lattová, Dijana Šagi, and Jasna Peter-Katalinic

6.1 Introduction 239

6.1.1 Glycans in Glycoproteins: Types and Importance 239

6.1.2 Glycosphingolipids 241

6.2 Profiling of Glycans and Glycosphingolipids 242

6.2.1 Importance of Glycan Profiling and Techniques Used for This Purpose 242

6.2.2 Importance of Glycosphingolipid Profi ling and Characterization; Techniques Used 243

6.2.3 MALDI-MS of Glycans and Glycoprotein Components 243

6.2.4 N- and O-Glycan Release 248

6.2.5 Preparation of Glycans for MALDI-MS Analysis 250

6.2.6 Preparation of Glycosphingolipids for MALDI-MS Analysis 253

6.3 Structural Determination 255

6.3.1 MS and MS/MS of N-Glycans 255

6.3.2 O-Glycosylation by MS and MS/MS 260

6.3.3 Exoglycosidase Arrays 262

6.3.4 Characterization of Glycopeptides 263

6.4 Quantitative Analysis 265

6.4.1 Quantitative Analysis of Glycans 265

6.4.2 Quantitative Analysis of Glycopeptides (e.g., i-Tag, i-Traq) 266

6.5 Conclusions 267

References 267

7 Lipids 273
Jürgen Schiller and Beate Fuchs

7.1 Introduction 273

7.1.1 Why Are Lipids of Such Great Interest? 273

7.1.2 Problems in Lipid Analysis: A Short Comparison of the Different Methods 276

7.1.3 Analysis of Lipids by Mass Spectrometry 277

7.1.4 Capabilities and Limitations of MALDI-TOF-MS in the Field of Lipid Analysis 278

7.1.5 Choosing an Appropriate Matrix 278

7.1.6 Sample Preparation, Extraction, and Purification 279

7.2 Analysis of Individual Lipid Classes and Their Characteristics 281

7.2.1 The Apolar Lipids: Diacylglycerols, Triacylglycerols, Cholesterol, and Cholesteryl Esters 281

7.2.1.1 Triacylglycerol Mixtures and Vegetable Oil Analyses 285

7.2.2 Zwitterionic Phospholipids: Sphingomyelin, Phosphatidylcholine, and Phosphatidylethanolamine 285

7.2.3 Acidic Phospholipids: Phosphatidic Acid, Cardiolipin, Phosphatidylglycerol, Phosphatidylserine, Phosphatidylinositol, and Phosphorylated Phosphoinositides 289

7.2.4 Free Fatty Acids 291

7.3 MALDI-TOF-MS of Typical Lipid Mixtures 292

7.3.1 Brain Lipids 296

7.4 Characterization of Typical Oxidation Products of Lipids 297

7.5 MALDI-MS Imaging 299

7.6 Combining TLC and MALDI for Lipid Analysis 301

7.7 Summary and Outlook 303

Acknowledgments 304

Abbreviations 305

References 306

8 MALDI-MS for Polymer Characterization 313
Liang Li

8.1 Introduction 313

8.2 Technical Aspects of MALDI-MS 314

8.2.1 Sample Preparation Issues 314

8.2.1.1 Matrix 315

8.2.1.2 Cationization Reagent 317

8.2.1.3 Solvent 320

8.2.1.4 Solvent-Free Sample Preparation 325

8.2.2 Instrumental and Measurement Issues 326

8.2.2.1 Mass Resolution and Accuracy 326

8.2.2.2 Sensitivity and Dynamic Range 331

8.2.2.3 Mass Range 335

8.2.2.4 MS/MS Capability 338

8.2.3 Data Processing Issues 341

8.3 Attributes and Limitations of MALDI-MS 344

8.4 Conclusions and Perspectives 352

References 354

9 Small-Molecule Desorption/Ionization Mass Analysis 367
Lucinda H. Cohen, Fangbiao Li, Eden P. Go, and Gary Siuzdak

9.1 Introduction 367

9.2 Matrix Choices for Small-Molecule MALDI 368

9.2.1 Organic Matrices 368

9.2.2 Inorganic Matrices 370

9.2.3 Liquid Matrices 374

9.2.4 Matrix-Free Approaches 374

9.3 Sample Preparation 377

9.3.1 Electrospray Sample Deposition 379

9.3.2 Analyte Derivatization 379

9.3.3 Analyte Pre-Concentration 380

9.3.3.1 Prestructured Sample Supports 380

9.3.3.2 DIOS with Solid Liquid Extraction 381

9.3.4 Matrix Suppression 383

9.4 Qualitative Characterization of LMM Molecules 383

9.5 Analyte Quantitation by MALDI 388

9.5.1 Selection of IS 388

9.5.2 Methods for Improving Quantitative Performance 389

9.5.3 Quantitation of Pharmaceutical Compounds 389

9.5.4 Enzyme Activity and Inhibition Studies 391

9.5.5 Quantitative Analysis of Samples from Complex Biological Matrices 393

9.5.6 Environmental Applications of Quantitative MALDI 394

9.5.7 Separation Methods Coupled with MALDI and DIOS 397

9.5.8 TLC-MALDI 397

9.5.9 Capillary and Frontal Affi nity Liquid Chromatography 399

9.6 Conclusions 402

Acknowledgments 402

Abbreviations/Acronyms 402

References 404

10 Computational Analysis of High-Throughput MALDI-TOF-MS-Based Peptide Profiling 411
Thang V. Pham and Connie R. Jimenez

10.1 Introduction 411

10.2 MALDI-MS Data Preprocessing 413

10.2.1 A Workflow for Data Acquired on a 4800 MALDI-TOF/TOF Mass Spectrometer 416

10.2.2 Identification of Peptide Ion Peaks 417

10.3 Statistical Analysis of Preprocessed Data 418

10.3.1 Unsupervised Methods 421

10.3.2 Supervised Methods 422

10.4 Concluding Remarks 426

References 426

11 Biotyping of Microorganisms 431
Markus Kostrzewa

11.1 The Technique 431

11.2 Standard Identification of Bacteria and Other Microorganisms 432

11.3 Applicability and Performance in Routine Laboratories 433

11.4 Direct Specimen Analysis 434

11.5 Subtyping 435

11.6 Resistance Testing 435

11.7 Outlook 436

References 437

Index 445

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Franz Hillenkamp is Professor Emeritus at the University of Münster, Germany. He holds a MS degree in electrical engineering from Purdue University, USA, and a PhD from the Technical University of Munich, Germany. Before he was appointed Professor of Biophysics and Medical Physics at Münster in 1986, he held a professorship at the University of Frankfurt, Germany. During the 1980s,
he developed the now world famous MALDI technique that was later on shown to be highly useful for the analysis of biomolecules. For his ground-breaking work on mass spectrometry methods, Professor Hillenkamp has received numerous awards, among them the Thomson Medal of the Mass Spectrometry Society, the Fresenius Medal of the German Chemical Society, and the Bergman Medal of the
Swedish Chemical Society.

Jasna Peter-Katalinic is Professor at the University of Rijeka, Croatia, and former Associate Professor of Biophysics at the University of Münster, Germany. She was
born and educated in Zagreb, Croatia, and obtained her PhD in chemistry at the University of Zürich, Switzerland. After the postdoc time at the Texas A+M University, USA, she obtained the habilitation in physiological chemistry from the University of Bonn, Germany. She pioneered the introduction of modern mass
spectrometric methods to structural glycobiology/ glycomics, as described in more than 250 publications. Her current interests are in the Human Glycoproteome Initiative and Nanobioanalytics. She was the first recipient of the Life Science Award from the German Society of Mass Spectrometry in 2002.
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