Note: Cover -- Related Titles -- Title page -- Copyright page -- Contents -- Preface to the Second Edition -- List of Contributors -- 1: The MALDI Process and Method -- 1.1 Introduction -- 1.2 Analyte Incorporation -- 1.3 Absorption of the Laser Radiation -- 1.4 The Ablation/Desorption Process -- 1.5 Ionization -- 1.6 Fragmentation of MALDI Ions -- 1.7 MALDI of Noncovalent Complexes -- 1.8 The Optimal Choice of Matrix: Sample Preparation -- 1.8.1 Surface Preparation -- 1.8.2 Anchor Sample Plates -- 1.8.3 Matrix Additives and Influence of the Sample Plate Surface -- Abbreviations -- References -- 2: MALDI Mass Spectrometry Instrumentation -- 2.1 Introduction -- 2.2 Lasers for MALDI-MS -- 2.3 Fragmentation of MALDI Ions -- 2.3.1 MALDI at Elevated Pressure -- 2.3.2 Tandem Mass Spectrometry of MALDI Ions -- 2.4 Mass Analyzers -- 2.4.1 Axial TOF Mass Spectrometers -- 2.4.2 Reflectron TOF Mass Spectrometers -- 2.4.3 Tandem TOF Mass Spectrometers -- 2.4.4 Orthogonal TOF Mass Analyzers -- 2.4.5 Tandem Mass Spectrometry in oTOF Mass Analyzers -- 2.4.6 Ion Detectors and Data Processing in MALDI-TOF Analyzers -- 2.5 Fourier Transform Ion Cyclotron Resonance Mass Spectrometers -- 2.5.1 Tandem Mass Spectrometry on FTICR Mass Spectrometers -- 2.6 Quadrupole Ion Trap Mass Spectrometers -- 2.6.1 RF-Only Ion Guides and LIT Mass Spectrometers -- 2.6.2 Tandem Mass Spectrometry on QIT Mass Spectrometers -- 2.7 Hybrid Mass Spectrometers -- 2.7.1 Quadrupole TOF Mass Spectrometers -- 2.7.2 Quadrupole FT Mass Spectrometers -- 2.7.3 QIT-TOF Mass Spectrometers -- 2.7.4 Ion Mobility oTOF Mass Spectrometers -- 2.7.5 Orbitrap -- 2.8 Future Directions -- Definitions and Acronyms -- References -- 3: MALDI-MS in Protein Chemistry and Proteomics -- 3.1 Introduction -- 3.2 Sample Preparation for Protein and Peptide Analysis by MALDI-MS. , 3.3 Strategies for Using MALDI-MS in Protein Biochemistry -- 3.3.1 Peptide Mass Mapping of Purified Proteins -- 3.3.2 Peptide Sequencing by MALDI-MS/MS -- 3.3.3 Analysis of Post-Translational Modifications -- 3.4 Applications of MALDI-MS in Proteomics -- 3.4.1 Protein Identification by MALDI-MS Peptide Mass Mapping -- 3.4.2 Quantitation of Proteins by MALDI-MS -- 3.5 Computational Tools for Protein Analysis by MALDI-MS -- 3.6 Clinical Applications of MALDI-MS -- 3.7 Conclusions -- Acknowledgments -- References -- 4: MALDI-Mass Spectrometry Imaging -- 4.1 Introduction -- 4.2 History of Mass Spectrometry Imaging (MSI) and Microprobing Techniques -- 4.3 MALDI in Micro Dimensions: Instruments and Mechanistic Differences -- 4.4 Visualization of Mass Spectrometric Information -- 4.5 Data Processing and Data Exchange -- 4.6 Matrix Deposition for High-Resolution Imaging -- 4.7 Organisms, Organs, and Tissues: MALDI Imaging at Various Lateral Resolutions -- 4.7.1 Phospholipid Analysis -- 4.7.2 Peptide Analysis -- 4.7.3 Drug Monitoring -- 4.8 Whole-Cell and Single-Cell Analysis -- 4.8.1 Cellular Analysis -- 4.8.2 Individually Isolated Cells -- 4.8.3 Direct Cellular and Subcellular Imaging -- 4.9 Cell Sorting and Capturing -- 4.10 Direct Protein Identification and Localization -- 4.11 Identification and Characterization: Requirements for Mass Resolution and Accuracy -- 4.12 Conclusions -- Acknowledgments -- References -- 5: Analysis of Nucleic Acids, and Practical Implementations in Genomics and Genetics -- 5.1 Challenges in Nucleic Acid Analysis by MALDI-MS -- 5.2 Genetic Markers -- 5.2.1 Restriction Fragment Length Polymorphisms (RFLPs) -- 5.2.2 Microsatellites/Short Tandem Repeats (STRs) -- 5.2.3 Single Nucleotide Polymorphisms (SNPs) -- 5.2.4 Characterization of Base Modifications and Covalent Adducts. , 5.2.5 Detection of Noncovalent Complexes of Nucleic Acids -- 5.3 Assay Formats for Nucleic Acid Analysis by MALDI-MS -- 5.4 Applications in Genotyping -- 5.4.1 MALDI-TOF-MS SNP and Mutation Analysis -- 5.4.2 MALDI-TOF MS for Haplotyping -- 5.5 Applications in Comparative Sequence Analysis -- 5.6 Applications in Quantitation of Nucleic Acids for Analysis of Gene Expression and Gene Amplification -- 5.6.1 Analysis of DNA Mixtures and Allele Frequency Determinations in DNA Pools -- 5.6.2 Analysis of Gene Expression -- 5.7 Future Perspectives for the MALDI-MS Analysis of Nucleic Acids -- Acknowledgments -- References -- 6: MALDI-MS of Glycans and Glycoconjugates -- 6.1 Introduction -- 6.1.1 Glycans in Glycoproteins: Types and Importance -- 6.1.2 Glycosphingolipids -- 6.2 Profiling of Glycans and Glycosphingolipids -- 6.2.1 Importance of Glycan Profiling and Techniques Used for This Purpose -- 6.2.2 Importance of Glycosphingolipid Profiling and Characterization -- Techniques Used -- 6.2.3 MALDI-MS of Glycans and Glycoprotein Components -- 6.2.4 N- and O-Glycan Release -- 6.2.5 Preparation of Glycans for MALDI-MS Analysis -- 6.2.6 Preparation of Glycosphingolipids for MALDI-MS Analysis -- 6.3 Structural Determination -- 6.3.1 MS and MS/MS of N-Glycans -- 6.3.2 O-Glycosylation by MS and MS/MS -- 6.3.3 Exoglycosidase Arrays -- 6.3.4 Characterization of Glycopeptides -- 6.4 Quantitative Analysis -- 6.4.1 Quantitative Analysis of Glycans -- 6.4.2 Quantitative Analysis of Glycopeptides (e.g., i-Tag, i-Traq) -- 6.5 Conclusions -- References -- 7: Lipids -- 7.1 Introduction -- 7.1.1 Why Are Lipids of Such Great Interest? -- 7.1.2 Problems in Lipid Analysis: A Short Comparison of the Different Methods -- 7.1.3 Analysis of Lipids by Mass Spectrometry -- 7.1.4 Capabilities and Limitations of MALDI-TOF-MS in the Field of Lipid Analysis. , 7.1.5 Choosing an Appropriate Matrix -- 7.1.6 Sample Preparation, Extraction, and Purification -- 7.2 Analysis of Individual Lipid Classes and Their Characteristics -- 7.2.1 The Apolar Lipids: Diacylglycerols, Triacylglycerols, Cholesterol, and Cholesteryl Esters -- 7.2.2 Zwitterionic Phospholipids: Sphingomyelin, Phosphatidylcholine, and Phosphatidylethanolamine -- 7.2.3 Acidic Phospholipids: Phosphatidic Acid, Cardiolipin, Phosphatidylglycerol, Phosphatidylserine, Phosphatidylinositol, and Phosphorylated Phosphoinositides -- 7.2.4 Free Fatty Acids -- 7.3 MALDI-TOF-MS of Typical Lipid Mixtures -- 7.3.1 Brain Lipids -- 7.4 Characterization of Typical Oxidation Products of Lipids -- 7.5 MALDI-MS Imaging -- 7.6 Combining TLC and MALDI for Lipid Analysis -- 7.7 Summary and Outlook -- Acknowledgments -- Abbreviations -- References -- 8: MALDI-MS for Polymer Characterization -- 8.1 Introduction -- 8.2 Technical Aspects of MALDI-MS -- 8.2.1 Sample Preparation Issues -- 8.2.2 Instrumental and Measurement Issues -- 8.2.3 Data Processing Issues -- 8.3 Attributes and Limitations of MALDI-MS -- 8.4 Conclusions and Perspectives -- References -- 9: Small-Molecule Desorption/Ionization Mass Analysis -- 9.1 Introduction -- 9.2 Matrix Choices for Small-Molecule MALDI -- 9.2.1 Organic Matrices -- 9.2.2 Inorganic Matrices -- 9.2.3 Liquid Matrices -- 9.2.4 Matrix-Free Approaches -- 9.3 Sample Preparation -- 9.3.1 Electrospray Sample Deposition -- 9.3.2 Analyte Derivatization -- 9.3.3 Analyte Pre-Concentration -- 9.3.4 Matrix Suppression -- 9.4 Qualitative Characterization of LMM Molecules -- 9.5 Analyte Quantitation by MALDI -- 9.5.1 Selection of IS -- 9.5.2 Methods for Improving Quantitative Performance -- 9.5.3 Quantitation of Pharmaceutical Compounds -- 9.5.4 Enzyme Activity and Inhibition Studies. , 9.5.5 Quantitative Analysis of Samples from Complex Biological Matrices -- 9.5.6 Environmental Applications of Quantitative MALDI -- 9.5.7 Separation Methods Coupled with MALDI and DIOS -- 9.5.8 TLC-MALDI -- 9.5.9 Capillary and Frontal Affinity Liquid Chromatography -- 9.6 Conclusions -- Acknowledgments -- Abbreviations/Acronyms -- References -- 10: Computational Analysis of High-Throughput MALDI-TOF-MS-Based Peptide Profiling -- 10.1 Introduction -- 10.2 MALDI-MS Data Preprocessing -- 10.2.1 A Workflow for Data Acquired on a 4800 MALDI-TOF/TOF Mass Spectrometer -- 10.2.2 Identification of Peptide Ion Peaks -- 10.3 Statistical Analysis of Preprocessed Data -- 10.3.1 Unsupervised Methods -- 10.3.2 Supervised Methods -- 10.4 Concluding Remarks -- References -- 11: Biotyping of Microorganisms -- 11.1 The Technique -- 11.2 Standard Identification of Bacteria and Other Microorganisms -- 11.3 Applicability and Performance in Routine Laboratories -- 11.4 Direct Specimen Analysis -- 11.5 Subtyping -- 11.6 Resistance Testing -- 11.7 Outlook -- References -- Index.