Contents. Preface to the Second Edition List of Contributors XIII

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1 Contents Preface to the Second Edition List of Contributors XIII XI 1 The MALDI Process and Method 1 Franz Hillenkamp, Thorsten W. Jaskolla, and Michael Karas 1.1 Introduction Analyte Incorporation Absorption of the Laser Radiation The Ablation/Desorption Process Ionization Fragmentation of MALDI Ions MALDI of Noncovalent Complexes The Optimal Choice of Matrix: Sample Preparation Surface Preparation Anchor Sample Plates 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 Drehewerd, Kerstin Strupat, and Franz Hillenkamp 2.1 Introduction Lasers for MALDI-MS Fragmentation of MALDI Ions MALDI at Elevated Pressure Tandem Mass Spectrometry of MALDI Ions Mass Analyzers Axial TOF Mass Spectrometers Reflectron TOF Mass Spectrometers Tandem TOF Mass Spectrometers 56

2 VII Contents Orthogonal TOF Mass Analyzers Tandem Mass Spectrometry in otof Mass Analyzers Ion Detectors and Data Processing in MALDI-TOF Analyzers Fourier Transform Ion Cyclotron Resonance Mass Spectrometers Tandem Mass Spectrometry on FTICR Mass Spectrometers Quadrupole Ion Trap Mass Spectrometers RF-Only Ion Guides and LIT Mass Spectrometers Tandem Mass Spectrometry on QIT Mass Spectrometers Hybrid Mass Spectrometers Quadrupole TOF Mass Spectrometers Quadrupole FT Mass Spectrometers QIT-TOF Mass Spectrometers Ion Mobility otof Mass Spectrometers Orbitrap Future Directions 92 Definitions and Acronyms 93 References 96 3 MALDI-MS in Protein Chemistry and Proteomics 105 Karin Hjema and Ole N. Jensen 3.1 Introduction Sample Preparation for Protein and Peptide Analysis by MALDI-MS Strategies for Using MALDI-MS in Protein Biochemistry Peptide Mass Mapping of Purified Proteins Peptide Sequencing by MALDI-MS/MS Analysis of Post-Translational Modifications Applications of MALDI-MS in Proteomics Protein Identification by MALDI-MS Peptide Mass Mapping Quantitation of Proteins by MALDI-MS Computational Tools for Protein Analysis by MALDI-MS Clinical Applications of MALDI-MS Conclusions 125 Acknowledgments 125 References MALDI-Mass Spectrometry Imaging 133 Bernhardt Spengler 4.1 Introduction History of Mass Spectrometry Imaging (MSI) and Microprobing Techniques MALDI in Micro Dimensions: Instruments and Mechanistic Differences Visualization of Mass Spectrometric Information Data Processing and Data Exchange Matrix Deposition for High-Resolution Imaging 144

3 Contents VII 4.7 Organisms, Organs, and Tissues: MALDI Imaging at Various Lateral Resolutions Phospholipid Analysis Peptide Analysis Drug Monitoring Whole-Cell and Single-Cell Analysis Cellular Analysis Individually Isolated Cells Direct Cellular and Subcellular Imaging Cell Sorting and Capturing Direct Protein Identification and Localization Identification and Characterization: Requirements for Mass Resolution and Accuracy Conclusions 163 Acknowledgments 163 References 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 Genetic Markers Restriction Fragment Length Polymorphisms (RFLPs) Microsatellites/Short Tandem Repeats (STRs) Single Nucleotide Polymorphisms (SNPs) Characterization of Base Modifications and Covalent Adducts Detection of Noncovalent Complexes of Nucleic Acids Assay Formats for Nucleic Acid Analysis by MALDI-MS Applications in Genotyping MALDI-TOF-MS SNP and Mutation Analysis The PinPoint Assay The PROBE Assay The MassEXTEND Assay The GOOD Assay The Invader Assay The Incorporation and Complete Chemical Cleavage Assay The Restriction Fragment Mass Polymorphism Assay MALDI-TOF MS for Haplotyping Applications in Comparative Sequence Analysis Applications in Quantitation of Nucleic Acids for Analysis of Gene Expression and Gene Amplification Analysis of DNA Mixtures and Allele Frequency Determinations in DNA Pools Analysis of Gene Expression Future Perspectives for the MALDI-MS Analysis of Nucleic Acids 222

4 VIIII Contents Acknowledgments 223 References MALDI-MS of Glycans and Glycoconjugates 239 Htline Perreault, Erika Lattovd, Dijana Sag/, and Jasna Peter-Katalinic 6.1 Introduction Glycans in Glycoproteins: Types and Importance Glycosphingolipids Profiling of Glycans and Glycosphingolipids Importance of Glycan Profiling and Techniques Used for This Purpose Importance of Glycosphingolipid Profiling and Characterization; Techniques Used MALDI-MS of Glycans and Glycoprotein Components N- and O-Glycan Release Preparation of Glycans for MALDI-MS Analysis Preparation of Glycosphingolipids for MALDI-MS Analysis Structural Determination MS and MS/MS of N-Glycans O-Glycosylation by MS and MS/MS Exoglycosidase Arrays Characterization of Glycopeptides Quantitative Analysis Quantitative Analysis of Glycans Quantitative Analysis of Glycopeptides (e.g., i-tag, i-traq) Conclusions 267 References Lipids 273 Jiirgen Schiller and Beate Fuchs 7.1 Introduction Why Are Lipids of Such Great Interest? Problems in Lipid Analysis: A Short Comparison of the Different Methods Analysis of Lipids by Mass Spectrometry Capabilities and Limitations of MALDI-TOF-MS in the Field of Lipid Analysis Choosing an Appropriate Matrix Sample Preparation, Extraction, and Purification Analysis of Individual Lipid Classes and Their Characteristics The Apolar Lipids: Diacylglycerols, Triacylglycerols, Cholesterol, and Cholesteryl Esters Triacylglycerol Mixtures and Vegetable Oil Analyses Zwitterionic Phospholipids: Sphingomyelin, Phosphatidylcholine, and Phosphatidylethanolamine 285

5 7.2.3 Acidic Phospholipids: Phosphatide Acid, Cardiolipin, Phosphatidylglycerol, Phosphatidylserine, Phosphatidylinositol, and Phosphorylated Phosphoinositides Free Fatty Acids MALDI-TOF-MS of Typical Lipid Mixtures Brain lipids Characterization of Typical Oxidation Products of Lipids MALDI-MS Imaging Combining TLC and MALDI for Lipid Analysis Summary and Outlook 303 Acknowledgments 304 Abbreviations 305 References 306 Contents IX 8 MALDI-MS for Polymer Characterization 313 Liang Li 8.1 Introduction Technical Aspects of MALDI-MS Sample Preparation Issues Matrix Cationization Reagent Solvent Solvent-Free Sample Preparation Instrumental and Measurement Issues Mass Resolution and Accuracy Sensitivity and Dynamic Range Mass Range MS/MS Capability Data Processing Issues Attributes and Limitations of MALDI-MS Conclusions and Perspectives 352 References Small-Molecule Desorption/lonization Mass Analysis 367 Lucinda H. Cohen, Fangbiao Li, Eden P. Co, and Gary Siuzdak 9.1 Introduction Matrix Choices for Small-Molecule MALDI Organic Matrices Inorganic Matrices Liquid Matrices Matrix-Free Approaches Sample Preparation Electrospray Sample Deposition Analyte Derivatization Analyte Pre-Concentration 380

6 X Contents Prestructured Sample Supports DIOS with Solid Liquid Extraction Matrix Suppression Qualitative Characterization of LMM Molecules Analyte Quantitation by MALDI Selection of IS Methods for Improving Quantitative Performance Quantitation of Pharmaceutical Compounds Enzyme Activity and Inhibition Studies Quantitative Analysis of Samples from Complex Biological Matrices Environmental Applications of Quantitative MALDI Separation Methods Coupled with MALDI and DIOS TLC-MALDI Capillary and Frontal Affinity Liquid Chromatography Conclusions 402 Acknowledgments 402 Abbreviations/Acronyms 402 References Computational Analysis of High-Throughput MALDI-TOF-MS-Based Peptide Profiling 411 Thang V. Pham and Connie R. Jimenez 10.1 Introduction MALDI-MS Data Preprocessing A Workflow for Data Acquired on a 4800 MALDI-TOF/TOF Mass Spectrometer Identification of Peptide Ion Peaks Statistical Analysis of Preprocessed Data Unsupervised Methods Supervised Methods Concluding Remarks 426 References Biotyping of Microorganisms 431 Markus Kostrzewa 11.1 The Technique Standard Identification of Bacteria and Other Microorganisms Applicability and Performance in Routine Laboratories Direct Specimen Analysis Subtyping Resistance Testing Outlook 436 References 437 Index 445

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