Spectrum analysis Books

Book SynopsisThe current state of practical ICP-MS and the latest developments in the field.Table of ContentsContents; Bio-analytical Applications; Metalloprotein Crosstalk; Quantifying Zinc Exchange Between Stable Isotopically Labeled Proteins Using Directly Coupled HPLC-ICP-MS; Speciation of Selenium Compounds by Capillary Electrophoresis ICP-MS - Evaluation of ICP-DRC-MS Detection and Different Quantification Methods; Application of ICPMS and Chromatography Based ICPMS to Studies of Metal-Protein Binding in Bioanalysis; Determination of Total Mercury in Urine By Inductively Coupled Plasma Mass Spectrometry (ICP-MS); Labile Arsenic Compounds in Biological Matrices, or Possible Problems Finding the Metal Species Present in Cells; Speciation Analysis with GC-ICP-MS: Organometal Detection in Tobacco Smoke; Reaction Cells and High Resolution; Determination of 44Ca-Isotope Markers for Parasitoid Studies Using Dynamic Reaction Cell ICPMS; Application of ICP-MS with a Hexapole Collision and Reaction Cell as an Element Selective Phosphorus Detector for Quality Control of Pharmaceuticals; Advantages of Dynamic Reaction Cell ICP-MS for Geological Analyses; Characterization and Production Ratio of Polyatomic Ion Interferences in Inductively Coupled Plasma Mass Spectrometry Using a High Resolution Mass Spectrometer; Measurement of Actinides at Ultra-Trace Level By Double-Focusing Sector-Field ICP-MS: Instrumental Performances and Analytical Difficulties; Trends in Instrumentation; Biomolecular and Atomic Mass Spectrometry: Good Friends or Uncaring Strangers?; Love Triangle: Trapping Fields, Ion Energy and Ion Molecule Reactions; Investigation of Vaporization of Laser Ablation Generated Aerosol and Monodisperse Particles in a Dry Ar ICP Using Time-Resolved Mass Spectrometry; Environmental Applications; Signal Smoothing Device for Improving Analytical Precision in LA-ICP-MS and Its Applications; Metrology in Chemistry: ICP-Analysis in Environmental Science; ICP-MS as Analytical Tool on Spent Nuclear Fuel Analogues Studies; Preliminary Work for the LA-ICP-MS Analysis of Carnelian Archaeological Artefacts; Selenium Speciation in Amphibian Larvae Developing in a Coal Fly Ash Settling Basin; Speciation of Cancerostatic Platinum Compounds in a Waste Water Pilot Plant; Multi-collectors Accurate Determination of Pt Concentrations at Ultra-low Levels (<<20Pg) in Clinical DNA Samples with High HF/PT Ratios Using the Thermo Finnigan Neptune Plasma Ionisation Multi-collector Mass Spectrometer (PIMMS); Novel Applications of MC-ICPMS for Isotope Dilution; Solution and Laser Ablation Analysis of Sulphur Isotopes with the Neptune High Resolution Multi-collector ICP-MS (MC-ICP-MS): Application to Diffusive Gradients in Thin Films; Accuracy and Precision in Plasma Ionisation Multi-collector Mass Spectrometry: Constraints from Neodymium and Hafnium Isotope Measurements; Semiconductors; Application of ICP-MS Technology to Semiconductor Manufacturing;

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Book SynopsisThe main aim of this unique book is to introduce the student to spectroscopy in a clear manner which avoids, as far as possible, the mathematical aspects of the subject. It is thus intended for first or second year undergraduates, particularly those with minimal mathematics qualifications. After explaining the theory behind spectroscopy, the book then goes on to look at the different techniques, such as rotational, vibrational and electronic spectroscopy. It encompasses both high resolution (structural) and low resolution (analytical) spectroscopy, demonstrating their close interrelationship. The many worked problems make this book particularly appealing for independent study. Ideal for the needs of undergraduate chemistry students, Tutorial Chemistry Texts is a major new series consisting of short, single topic or modular texts concentrating on the fundamental areas of chemistry taught in undergraduate science courses. Each book provides a concise account of the basic principles underTrade ReviewFills an important gap....clearly written and is pitched at just the right level for under-graduate chemistry students in the early years of their degree studies.An ideal introductory text for undergraduate students, and I hope that many students, and I hope that many students will use it to supplement their existing general text books of physical chemistry. * Angewandte Chemie, International Edition, 2004, 43, 5117-5118 (David Smith) *A useful companion to the undergraduate learning experience. The book will also provide a good recap in the subject for those who want to take their study on to postgraduate level. * Education in Chemistry, September 2004 issue (Matthew Ingram) *"... accessible to the average Advanced level student, and ... will greatly interest students intending to go on and study chemistry at university. * School Science Review, Issue No 308, 2003 *"This is an excellent book, and is great value-for-money. I will be prescribing Holla's text for my students. This ends a search for a suitable spectroscopy text, which has lasted several years. I highly recommend the book to you as a class text. It would also be a worthwhile addition to the departmental library or your personal reference library." * Physical Sciences Educational Reviews, No 6, June 2003 *Table of ContentsWhat is Spectroscopy?; The Electromagnetic Spectrum; Quantization and the Hydrogen Atom; Quantization in Polyelectronic Atoms; Electronic States of Diatomic and Polyatomic Molecules; Molecular Vibrations; Molecular Rotation; How Spectra are Obtained; Rotational Spectroscopy; Vibrational Spectroscopy; Electronic Spectroscopy; Answers to problems; Further Reading; Subject Index.

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Book SynopsisThe understanding of the principles of ICP-MS and its application as an analytical technique is continually evolving and this book provides a unique snapshot of the current state-of-the-art. Plasma Source Mass Spectrometry: The New Millennium covers a diverse range of topics including the fate of the sample as it passes through the sample introduction system, chemical resolution using reaction and collision cells, various methods of mass analysis, approaches to account for spectral interferences, hyphenation methods to enable speciation, and the results of analyses ranging from natural waters and archaeological isotope ratios to organometallic speciation in biological materials. Describing explicitly the analytical methods that deal with current analytical challenges, and offering a current perspective on elemental analysis by plasma source mass spectrometry that is not to be found elsewhere, this book will be welcomed by both academics and industrialists as containing the most up-to-dTrade Review"... many extremely interesting results are presented here, and the book is likely to be of interest to most workers in the area." * Aslib Book Guide, Vol 66, No 12, December 2001 *"... an excellent supplement to more traditional textbooks on plasma source mass spectrometry ..." * www.rsc.org/anlreview, January 2002 *"... an excellent supplement to more traditional textbooks on plasma source mass spectrometry ..." * Journal of Analytical Atomic Spectrometry, March 2002, 17 *"... modern, well organized, and is easy to read and comprehend ... highly recommended." * Journal of the American Society for Mass Spectrometry, 14, 171-172, 2003 *"... readers with a current interest in the technique of ICP-MS or those wishing to learn of its capabilities will find plenty to interest them." * International Journal of Environment and Pollution, Vol 18, No 4, 2002 *Table of ContentsSample Preparation and Introduction; Mass Analyser Instrumentation; Reaction Cells for ICP-MS; Applications; Isotope Ratio Measurement; Speciation; Author Index; Subject Index.

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Book SynopsisA practical manual for the microscopic analysis of paint, coatings, fibres and adhesives - materials found in works of art.Table of ContentsPart 1 History of infrared spectroscopy: additional reading. Part 2 Infrared absorption theory: electromagnetic radiation; absorption theory; infrared spectra; infrared regions; summary; additional reading. Part 3 Sample collection and preparation: sampling methodology; sampling implementation; sample collection and preparation procedures; summary; additional reading. Part 4 Infrared analysis methods: infrared transmission measurements; infrared reflection measurements; infrared microspectroscopy; summary; additional reading. Part 5 Spectral interpretation: infrared spectra; qualitative analysis; identification of materials used in art and art conservation; quantitative analysis; mathematical manipulations of spectra; summary; additional reading. Part 6 Case studies: identification and characterization of materials; deterioration studies; the case studies; case study 1 - ultramarine pigments; case study 2 - creosote lac resin; case study 3 - Chumash Indian paints; case study 4 - varnish on a desk; case study 5 - reflection versus transmission; case study 6 -painting cross sections; case study 7 - vikane; case study 8 -parylene; case study 9 - cellulose nitrate sculptures; 10 - Dead Sea scrolls; summary; appendices.

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Book SynopsisFocusing on the organic inventory of regions of star and planet formation in the interstellar medium of galaxies, this comprehensive overview of the molecular universe is an invaluable reference source for advanced undergraduates through to entry-level researchers. It includes an extensive discussion of microscopic physical and chemical processes in the universe; these play a role in the excitation, spectral characteristics, formation, and evolution of molecules in the gas phase and on grain surfaces. In addition, the latest developments in this area of molecular astrophysics provide a firm foundation for an in-depth understanding of the molecular phases of the interstellar medium. The physical and chemical properties of gaseous molecules, mixed molecular ices, and large polycyclic aromatic hydrocarbon molecules and fullerenes and their role in the interstellar medium are highlighted. For those with an interest in the molecular universe, this advanced textbook bridges the gap between mTrade Review'I am confident that this book will become an essential standard reference book for researchers in molecular astrophysics. I recommend it to all molecular astrophysicists.' David A. Williams, The Observatory MagazineTable of ContentsPreface; 1. Introduction; 2. Introduction to chemistry; 3. Molecular spectroscopy; 4. Molecular emission and absorption; 5. Chemical thermodynamics; 6. Gas phase chemical processes; 7. Chemistry on interstellar grain surfaces; 8. Physics and chemistry of large molecules; 9. Diffuse clouds; 10. Molecular clouds; 11. Star formation; 12. The aromatic universe.

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Book SynopsisPhosphorylation is the addition of a phosphate (PO 4) group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes, causing or preventing the mechanisms of diseases such as cancer and diabetes.Table of ContentsPreface xvii Acknowledgments xxi About the Author xxiii 1 Posttranslational Modification (PTM) of Proteins 1 1.1 Over 200 Forms of PTM of Proteins 1 1.2 Three Main Types of PTM Studied by MS 2 1.3 Overview of Nano-Electrospray/Nanofl ow LC-MS 2 1.3.1 Defi nition and Description of MS 2 1.3.2 Basic Design of Mass Analyzer Instrumentation 3 1.3.3 ESI 7 1.3.4 Nano-ESI 11 1.4 Overview of Nucleic Acids 15 1.5 Proteins and Proteomics 20 1.5.1 Introduction to Proteomics 20 1.5.2 Protein Structure and Chemistry 22 1.5.3 Bottom-Up Proteomics: MS of Peptides 27 1.5.3.1 History and Strategy 27 1.5.3.2 Protein Identifi cation through Product Ion Spectra 30 1.5.3.3 High-Energy Product Ions 36 1.5.3.4 De Novo Sequencing 37 1.5.3.5 Electron Capture Dissociation (ECD) 40 1.5.4 Top-Down Proteomics: MS of Intact Proteins 42 1.5.4.1 Background 42 1.5.4.2 GP Basicity and Protein Charging 42 1.5.4.3 Calculation of Charge State and Molecular Weight 44 1.5.4.4 Top-Down Protein Sequencing 46 1.5.5 Systems Biology and Bioinformatics 48 1.5.6 Biomarkers in Cancer 52 Reference 56 2 Glycosylation of Proteins 59 2.1 Production of a Glycoprotein 59 2.2 Biological Processes of Protein Glycosylation 59 2.3 N-Linked and O-Linked Glycosylation 60 2.4 Carbohydrates 60 2.4.1 Ionization of Oligosaccharides 64 2.4.2 Carbohydrate Fragmentation 65 2.4.3 Complex Oligosaccharide Structural Elucidation 70 2.5 Three Objectives in Studying Glycoproteins 72 2.6 Glycosylation Study Approaches 72 2.6.1 MS of Glycopeptides 73 2.6.2 Mass Pattern Recognition 75 2.6.2.1 High Galactose Glycosylation Pattern 75 2.6.3 Charge State Determination 76 2.6.4 Diagnostic Fragment Ions 76 2.6.5 High-Resolution/High-Mass Accuracy Measurement and Identification 76 2.6.6 Digested Bovine Fetuin 78 Reference 79 3 Sulfation of Proteins as Posttranslational Modification 81 3.1 Glycosaminoglycan Sulfation 81 3.2 Cellular Processes Involved in Sulfation 81 3.3 Brief Example of Phosphorylation 82 3.4 Sulfotransferase Class of Enzymes 82 3.5 Fragmentation Nomenclature for Carbohydrates 82 3.6 Sulfated Mucin Oligosaccharides 83 3.7 Tyrosine Sulfation 84 3.8 Tyrosylprotein Sulfotransferases TPST1 and TPST2 87 3.9 O-Sulfated Human Proteins 89 3.10 Sulfated Peptide Product Ion Spectra 89 3.11 Use of Higher Energy Collisions 93 3.12 Electron Capture Dissociation (ECD) 94 3.13 Sulfation versus Phosphorylation 95 Reference 97 4 Eukaryote PTM as Phosphorylation: Normal State Studies 99 4.1 Mass Spectral Measurement with Examples of HeLa Cell Phosphoproteome 99 4.1.1 Introduction 99 4.1.2 Protein Phosphatase and Kinase 99 4.1.3 Hydroxy-Amino Acid Phosphorylation 100 4.1.4 Traditional Phosphoproteomic Approaches 102 4.1.5 Current Approaches 103 4.1.5.1 Phosphoproteomic Enrichment Techniques 103 4.1.5.2 IMAC 104 4.1.5.3 MOAC 105 4.1.5.4 Methylation of Peptides prior to IMAC or MOAC Enrichment 107 4.1.6 The Ideal Approach 107 4.1.7 One-Dimensional (1-D) Sodium Dodecyl Sulfate (SDS) PAGE 108 4.1.8 Tandem MS Approach 108 4.1.8.1 pS Loss of Phosphate Group 109 4.1.8.2 pT Loss of Phosphate Group 112 4.1.8.3 pY Loss of Phosphate Group 113 4.1.9 Alternative Methods: Infrared Multiphoton Dissociation (IRMPD) and Electron Capture Dissociation (ECD) 115 4.1.10 Electron Transfer Dissociation (ETD) 115 4.2 The HeLa Cell Phosphoproteome 118 4.2.1 Introduction 118 4.2.2 Background of Study 118 4.2.3 What is Covered 119 4.2.4 Optimized Methods to Use for Phosphoproteomic Studies 119 4.2.4.1 Cell Culture 119 4.2.4.2 Extraction of HeLa Cell Proteins 120 4.2.4.3 Trizol Extraction and Tryptic Digestion 120 4.2.4.4 Solid-Phase Extraction (SPE) Desalting 120 4.2.4.5 Converting Peptide Carboxyl Moieties to Methyl Esters 121 4.2.4.6 Roche Complete Lysis-M, EDTA-Free Extraction 122 4.2.4.7 1-D SDS-PAGE Cleanup 122 4.2.4.8 In-Gel Reduction, Alkylation, Digestion, and Extraction of Peptides 122 4.2.4.9 Phosphopeptide Enrichment Using IMAC 123 4.2.5 Description of Instrumental Analyses 123 4.2.5.1 RP/Nano-HPLC Separation 123 4.2.5.2 MS Analysis 125 4.2.6 Current Approaches for Peptide Identification and False Discovery Rate (FDR) Determination 125 4.2.7 Results of the Protein Extraction and Preparation 126 4.2.7.1 Detergent Lysis, Trizol, and Ultracentrifugation 126 4.2.7.2 Nucleic Acid Removal with SDS-PAGE 127 4.2.8 HeLa Cell Phosphoproteome Methodology Comparison 128 4.2.8.1 Roche In-Solution versus Trizol Extraction 129 4.2.8.2 In-Solution and In-Gel Digests Phosphoproteome Coverage 129 4.2.9 Overall Conclusion 134 4.3 Nonphosphoproteome HeLa Cell Analysis 135 4.3.1 IMAC Flow Through Peptide Analysis 135 4.3.2 IMAC NaCl Wash Peptide Analysis 136 4.3.3 IMAC Flow Through versus NaCl Wash Comparison 138 4.3.4 Gene Ontology Comparison 138 4.3.5 IMAC Bed Nonspecifi c Binding Study 140 4.4 Reviewing Spectra Using the SpectrumLook Software Package 143 Reference 144 5 Eukaryote PTM as Phosphorylation: Perturbed State Studies 147 5.1 Study of the Phosphoproteome of HeLa Cells under Perturbed Conditions by Nano-High-Performance Liquid Chromatography HPLC Electrospray Ionization (ESI) Linear Ion Trap (LTQ)-FT/Mass Spectrometry (MS) 147 5.1.1 Introduction 147 5.1.2 Ataxia Telangiectasia Mutated (ATM) and ATM and Rad3-Related (ATR) 149 5.1.3 Background of Study 149 5.1.3.1 PP5 149 5.1.3.2 Functions of PP5 151 5.1.3.3 DDR of PP5 151 5.1.4 Review of Optimized Approach to Study 151 5.1.4.1 Producing Cell Cultures 151 5.1.4.2 Protein Extraction 152 5.1.4.3 Phosphopeptide Enrichment by IMAC 154 5.1.4.4 Reversed-Phase (RP)/Nano-HPLC Separation 155 5.1.4.5 LTQ-FT/MS/MS 156 5.1.4.6 Protein Identifi cation and False Discovery Rate (FDR) Determination 156 5.1.4.7 Phosphopeptide Quantitative Differential Comparison 157 5.1.4.8 Data Set Peak Matching and Alignment 157 5.1.4.9 Phosphopeptide Response Normalization 160 5.1.5 Phosphoproteome Gene Ontology (GO) Comparison 160 5.1.5.1 GO Cellular Component 162 5.1.6 Potential Regulated Target Proteins of PP5 162 5.1.6.1 Analysis of Variance (ANOVA) 162 5.1.6.2 Four Potential Target Proteins 166 5.1.7 GO Differential Comparison 167 5.1.7.1 GO Cellular Component 168 5.1.7.2 Infl uence of Classes or Categories of Proteins 168 5.1.7.3 Molecular Function Interacting Modules 168 5.1.8 Conclusion 175 5.1.9 Reviewing Spectra Using the SpectrumLook Software Package 175 Reference 176 6 Prokaryotic Phosphorylation of Serine, Threonine, and Tyrosine 181 6.1 Introduction 181 6.1.1 Serine (Ser)/Threonine (Thr)/Tyrosine (Tyr) Phosphorylation 181 6.1.2 Histidine (His) Phosphorylation 181 6.1.3 Caulobacter crescentus 181 6.1.4 Ser/Thr/Tyr Phosphorylation of C. crescentus 183 6.1.5 Ser/Thr/Tyr Phosphorylation of Bacillus subtilis and Escherichia coli 184 6.1.6 C. crescentus as Cell Cycle Model 185 6.1.7 Bacteria Starvation Response 187 6.1.8 First Coverage of C. crescentus Phosphoproteome 188 6.2 Optimized Methodology for Phospho Ser/Thr/Tyr Studies 188 6.2.1 Bacterial Strain and Growth Conditions 188 6.2.2 C. crescentus Cell Protein Extraction: Phosphoproteomics 189 6.2.3 Solid-Phase Extraction (SPE) Desalting 190 6.2.4 In Vitro Methylation of Peptides 190 6.2.5 Phosphopeptide Enrichment by IMAC 191 6.2.6 Normal Proteomics 192 6.2.7 pY Enrichment by IP 192 6.2.8 RP/Nano-High-Performance Liquid Chromatography (HPLC) Separation 192 6.2.9 LC-Linear Ion Trap (LTQ)-Orbitrap MS/MS 193 6.2.10 LTQ-Fourier Transform (FT)/MS/MS 193 6.2.11 Peptide Identification and False Discovery Rate (FDR) Determination 193 6.2.12 Peptide Quantitative Comparison 194 6.3 Identifi cation of the Components of the Ser/Thr/Tyr Phosphoproteome in C. crescentus Grown in the Presence and Absence of Glucose 194 6.3.1 Total Phosphoprotein Identifications 194 6.3.2 MSA Spectra 196 6.3.3 Phosphorylation Sites Identifi ed 196 6.3.4 Ser/Thr/Tyr Phosphoproteome of C. crescentus 205 6.3.5 Phosphorylated His and Aspartate 213 6.3.6 Cell Cycle His Kinase CckA 215 6.3.7 Phosphoglutamate 216 6.3.8 Enriched Tyr Phosphoproteome of C. crescentus 216 6.3.8.1 Sensor His Kinase KdpD 216 6.3.8.2 TonB-Dependent Receptor Proteins 216 6.3.9 Carbon Environment-Shared Phosphoproteome 217 6.3.9.1 Two-Component His Kinases 217 6.3.9.2 Multiply Phosphorylated Kinases 217 6.3.9.3 pTPLAALpSAQSRRAR Peptide as Sensor His Kinase 217 6.3.9.4 Aspartate Phosphorylated Tyr Kinase DivL 217 6.3.10 Carbon-Rich versus Carbon-Starved Class/Category 225 6.3.10.1 Localization of Phosphoproteome of C. crescentus 225 6.3.10.2 Integral Membrane Proteins 225 6.3.10.3 Function of Phosphoproteome of C. crescentus 225 6.3.11 Carbon-Rich versus Carbon-Starved Unique Phosphorylated Proteins 227 6.3.11.1 Carbon-Rich Environment Phosphorylated Proteins 227 6.3.11.2 Carbon-Starved Environment Phosphorylated Proteins 227 6.3.11.3 Decreased Normal Activity 232 6.3.12 Confi rmation of Decreased Energy Pathways 232 6.3.12.1 Carbon-Rich Mitochondrial Localization 232 6.3.12.2 Normal Proteome Glycolytic Pathway 233 6.3.12.3 Starvation Survival Response 233 6.3.13 Phosphopeptide Quantitative Differential Comparison 233 6.3.13.1 Upregulation in Phosphorylation 234 6.3.13.2 Adaptive Response with Phosphorylation 234 6.3.13.3 Upregulation NAD-Dependent GDH 234 6.3.13.4 Downregulation of Flagellin Protein 235 6.3.14 Carbon-Rich versus Carbon-Starved Normal Proteome Time Course Study 235 6.3.14.1 Entire Proteome Localization and Function 235 6.3.14.2 Regulated Proteins 237 6.3.14.3 Localization of Regulated Proteins 237 6.3.14.4 Function of Regulated Proteins 238 6.3.14.5 Normal Proteome Energy Pathways 239 6.3.14.6 Overlap of Phosphorylated Proteins and Regulated Normal Proteome 239 6.3.14.7 Differences of Phosphorylated Proteins 240 6.3.14.8 Localization of Phosphorylated Proteins 240 6.3.14.9 Direct Relationships Observed 240 6.3.15 Conclusions 243 6.3.16 Supplementary Material 243 6.3.16.1 Reviewing Spectra Using the SpectrumLook Software Package 243 Reference 244 7 Prokaryotic Phosphorylation of Histidine 249 7.1 Phosphohistidine as Posttranslational Modification (PTM) 249 7.2 Bacterial Kinases and the Two-Component System 250 7.3 Measurement of Phosphorylated His (pH) 251 7.3.1 Stabilities of Phosphorylated Amino Acids 251 7.3.2 Immobilized Metal Affinity Chromatography (IMAC) and Mass Spectrometry (MS) 252 7.4 In Vitro and In Vivo Study of pH-Containing Peptides by Nano-ESI Tandem MS 255 7.4.1 Introduction 255 7.4.2 Background of Study 257 7.4.2.1 Bacteria Models of Ser/Thr/Tyr Phosphorylation 257 7.4.2.2 Prokaryotic Phosphorylation of His 258 7.4.2.3 C. crescentus 258 7.4.2.4 Mass Spectral Measurement of Phosphohistidine 258 7.4.3 Optimized Methodology for Phosphohistidine Studies 259 7.4.3.1 In Vitro Selective pHis Phosphorylation 259 7.4.3.2 In Vitro Phosphorylation of Angio II (Sar1Thr8) 261 7.4.3.3 In Vitro Methylation of Peptides 262 7.4.3.4 C. crescentus Cell Protein Extraction with V-8 Protease Digestion 262 7.4.3.5 1-D SDS-Polyacrylamide Gel Electrophoresis (PAGE) 263 7.4.3.6 Phosphohistidine Enrichment by Cu(II)-Based IMAC 264 7.4.3.7 Reversed-Phase (RP)/Nano-HPLC Separation 265 7.4.3.8 Nano-ESI Nano-HPLC MS 266 7.4.3.9 Peptide Identification and False Discovery Rate (FDR) Determination 268 7.4.4 C18 RP LC Behavior 268 7.4.5 Phosphohistidine Loses HPO3 and H3PO4 270 7.4.5.1 Rational for H3PO4 Loss 272 7.4.6 Q-TOF/MS/MS Product Ion Spectra 277 7.4.6.1 pH-Containing Peptide INpHDLR 277 7.4.6.2 Doubly Charged (2+) Peptide INpHDLR 279 7.4.6.3 pH-Containing Peptide pHLGLAR 279 7.4.6.4 Singly Charged (1+) Peptide pHLGLAR 280 7.4.7 Behavior of Monophosphohistidine and Diphosphohistidine Peptide 281 7.4.7.1 Peptide Angio I as DRVYIHPFHL 281 7.4.8 Behavior of Phosphotyrosine and Phosphohistidine Peptide 285 7.4.8.1 Peptide Angio II as DRVpYIHPF 285 7.4.8.2 Phosphorylated Angio II as DRVpYIpHPF 285 7.4.9 Behavior of Phosphotyrosine-, Phosphothreonine-, and Phosphohistidine-Containing Peptide 287 7.4.9.1 Peptide Angio II (Sar1Thr8) 287 7.4.10 Validation of Cu(II)-Based IMAC Phosphohistidine Enrichment 291 7.4.10.1 Fe(III)-Based IMAC versus Cu(II) Based 292 7.4.10.2 Cu(II)-Based IMAC of Angio I 292 7.4.10.3 Cu(II)-Based IMAC of Angio II 293 7.4.11 In Vivo Measurement of Phosphohistidine 293 7.4.11.1 Time-Based Digestion Study 293 7.4.11.2 Phosphohistidine-Containing Peptides 294 7.4.11.3 Phosphohistidine Product Ion Spectra 294 7.4.12 Gene Ontology of Phosphorylated Proteins 296 7.4.12.1 Localization of Phosphorylated Proteins 296 7.4.12.2 Function of Phosphorylated Proteins 304 7.4.13 Predicted Regulatory Protein Motif Study 307 7.4.14 Validation of Phosphohistidine-Containing Proteins 308 7.4.14.1 Phosphorylation Motif Study 308 7.4.14.2 Phosphohistidine Kinase Motif 309 7.4.15 The pDpH Motif 310 7.4.16 Conclusions 311 7.5 Supplementary Material 311 7.5.1 Reviewing Spectra Using the SpectrumLook Software Package 311 Reference 313 Appendix I Atomic Weights and Isotopic Compositions 317 Appendix II Periodic Table of the Elements 325 Appendix III Fundamental Physical Constants 327 Glossary 329 Index 345

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Book SynopsisPresents the theory of NMR enhanced with Mathematica notebooks Provides short, focused chapters with brief explanations of well-defined topics with an emphasis on a mathematical description Presents essential results from quantum mechanics concisely and for easy use in predicting and simulating the results of NMR experiments Includes Mathematica notebooks that implement the theory in the form of text, graphics, sound, and calculations Based on class tested methods developed by the author over his 25 year teaching career. These notebooks show exactly how the theory works and provide useful calculation templates for NMR researchers Table of ContentsPreface viii Chapter 1 Introduction 1 Chapter 2 Using Mathematicac; Homework Philosophy 3 Chapter 3 The NMR Spectrometer 4 Chapter 4 The NMR Experiment 7 Chapter 5 Classical Magnets and Precession 11 Chapter 6 The Bloch Equation in the Laboratory Reference Frame 16 Chapter 7 The Bloch Equation in the Rotating Frame 19 Chapter 8 The Vector Model 23 Chapter 9 Fourier Transform of the NMR Signal 29 Chapter 10 Essentials of Quantum Mechanics 31 Chapter 11 The Time]Dependent Schrodinger Equation, Matrix Representation of Nuclear Spin Angular Momentum Operators 35 Chapter 12 The Density Operator 39 Chapter 13 The Liouville–von Neumann Equation 41 Chapter 14 The Density Operator at Thermal Equilibrium 42 Chapter 15 Hamiltonians of NMR: Isotropic Liquid]State Hamiltonians 45 Chapter 16 The Direct Product Matrix Representation of Coupling Hamiltonians HJ and HD 50 Chapter 17 Solving the Liouville–Von Neumann Equation for the Time Dependence of the Density Matrix 54 Chapter 18 The Observable NMR Signal 59 Chapter 19 Commutation Relations of Spin Angular Momentum Operators 61 Chapter 20 The Product Operator Formalism 65 Chapter 21 NMR Pulse Sequences and Phase Cycling 68 Chapter 22 Analysis of Liquid]State NMR Pulse Sequences with the Product Operator Formalism 72 Chapter 23 Analysis of the Inept Pulse Sequence with Program Shortspin and Program Poma 78 Chapter 24 The Radio Frequency Hamiltonian 82 Chapter 25 Comparison of 1D and 2D NMR 86 Chapter 26 Analysis of the HSQC, HMQC, and DQF]COSY 2D NMR Experiments 89 Chapter 27 Selection of Coherence Order Pathways with Phase Cycling 96 Chapter 28 Selection of Coherence Order Pathways with Pulsed Magnetic Field Gradients 104 Chapter 29 Hamiltonians of NMR: Anisotropic Solid]State Internal Hamiltonians in Rigid Solids 111 Chapter 30 Rotations of Real Space Axis Systems—Cartesian Method 120 Chapter 31 Wigner Rotations of Irreducible Spherical Tensors 123 Chapter 32 Solid]State NMR Real Space Spherical Tensors 129 Chapter 33 Time]Independent Perturbation Theory 134 Chapter 34 Average Hamiltonian Theory 141 Chapter 35 The Powder Average 144 Chapter 36 Overview of Molecular Motion and NMR 147 Chapter 37 Slow, Intermediate, And Fast Exchange In Liquid]State Nmr Spectra 150 Chapter 38 Exchange in Solid]State NMR Spectra 154 Chapter 39 N MR Relaxation: What is NMR Relaxation and what Causes it? 163 Chapter 40 Practical Considerations for the Calculation of NMR Relaxation Rates 168 Chapter 41 The Master Equation for NMR Relaxation—Single Spin Species I 170 Chapter 42 Heteronuclear Dipolar and J Relaxation 183 Chapter 43 Calculation of Autocorrelation Functions, Spectral Densities, and NMR Relaxation Times for Jump Motions in Solids 189 Chapter 44 Calculation of Autocorrelation Functions and Spectral Densities for Isotropic Rotational Diffusion 198 Chapter 45 Conclusion 202 Bibliography 203 INDEX 000

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Book SynopsisProvides a single-source reference for readers interested in the development of analytical methods for analyzing non-antimicrobial veterinary drug residues in food Provides a comprehensive set of information in the area of consumer food safety and international trade Covers general issues related to analytical quality control and quality assurance, measurement uncertainty, screening and confirmatory methods Details many techniques including nanotechnology and aptamer based assays covering current and potential applications for non-antimicrobial veterinary drugs Provides guidance for analysis of banned drugs including natural and synthetic steroids, Resorcylic acid lactones, and Beta-agonists Table of ContentsPreface xix List of Contributors xxi About the Editors xxv 1 Basic Considerations for the Analyst for Veterinary Drug Residue Analysis in Animal Tissues 1James D.MacNeil and Jack F. Kay 1.1 Introduction 1 1.2 Pharmacokinetics 1 1.3 Metabolism and Distribution 3 1.4 Choice of Analytical Method 5 1.5 Importance of Regulatory Limits 7 1.6 International Obligations for Regulatory Analytical Laboratories 13 1.7 Conclusions 21 2 Emerging Techniques in Sample Extraction and Rapid Analysis 27Wendy C. Andersen, Sherri B. Turnipseed, and Jack J. Lohne 2.1 Introduction 27 2.2 Sample Extraction 28 2.3 Extract Clean-up with Solid-Phase Sorbents 34 2.4 Micro-extraction Techniques for Solvent and Sorbent Extraction 47 2.5 Emerging Techniques in Liquid Chromatography 54 2.6 Direct Mass Spectrometry Analysis of Sample Extracts 57 2.7 Ion Mobility Spectrometry 66 2.8 Conclusions 67 3 Capabilities and Limitations of High-Resolution Mass Spectrometry (HRMS): time-of-flight and Orbitrap 93Anton Kaufmann and Phil Teale 3.1 Available Technology 93 3.2 Capabilities and Limitations of the Technology as Compared to LC-MS/MS (Tandem Quadrupole Mass Spectrometer) 104 3.3 Analytical Methods for Veterinary Drug Residues 112 3.4 Doping Control 121 3.5 Accurate Mass MS in Research and Metabolism Studies 124 3.6 Designer Drugs and Generic Detection Strategies 125 3.7 The Future of Accurate Mass Spectrometry in Residue Analysis 129 4 Hormones and β-Agonists 141Leendert A. van Ginkel, Toine Bovee, Marco H. Blokland, Saskia S. Sterk, Nathalie G.E. Smits, Jelka Pleadin and Ana Vulíc 4.1 Introduction 141 4.2 Advances in Classical Analysis of Exogenous Synthetic Hormones 143 4.3 Bio-Based Screening Methods for Steroid Hormones, β-Agonists, and Growth Hormones 161 4.4 Natural Hormones 180 4.5 Control for Synthetic β-Agonists: Screening and Confirmatory Methods 199 5 Analysis of Anthelmintic and Anticoccidial Drug Residues in Animal-Derived Foods 245Sarah Tuck, Ambrose Furey and Martin Danaher 5.1 Introduction 245 5.2 Chemistry and Mode of Action 246 5.3 Legislation 258 5.4 Sample Preparation Protocols for Anti-parasitic Agents in Food Matrices 264 5.5 LC-MS and GC-MS Detection of Anti-parasitic Agents in Food 275 5.6 Conclusions 292 6 Sedatives and Tranquilizers 311Vesna Cerkvenik Flajs and James D. MacNeil 6.1 Introduction 311 6.2 Classification and Representative Compounds 312 6.3 Use of Sedatives and Tranquilizers to Prevent Stress Syndrome during the Transport of Pigs to Slaughter 312 6.4 Sedatives and Tranquilizers with an Approved Veterinary Use in Food-Producing Animals 314 6.5 Sedatives and Tranquilizers without an Approved Veterinary Use in Food-Producing Animals 325 6.6 Cocktails 335 6.7 Issues of Environmental Contamination 335 6.8 Maximum Residue Limits (MRLs) 336 6.9 Systematic Veterinary Control over Residues and Surveillance Studies 336 6.10 Analyte Stability 339 6.11 Analytical Methods for Determination of Residues 340 6.12 Performance and Validation of the Analytical Methods 361 7 The Use of Pyrethroids, Carbamates, Organophosphates, and Other Pesticides in Veterinary Medicine 383Christine Akre 7.1 Introduction 383 7.2 Veterinary Drug Properties, Structures, and Regulation 386 7.3 Toxicology, Pharmacokinetics, and Metabolism 399 7.4 Analytical Methods 403 7.5 Conclusion 414 8 Non-steroidal Anti-inflammatory Drugs 427Joe O. Boison, Fernando J. Ramos and Alan Chicoine 8.1 Introduction: What Are Pain Killers (Analgesics) and NSAIDs? 427 8.2 Veterinary Drug Properties, Structures, and Regulation 441 8.3 Pharmacokinetics/Metabolism 442 8.4 Acceptable Daily Intake (ADI) 444 8.5 Maximum Residue Limits/Tolerances 445 8.6 Analysis of NSAID Residues in Food 448 8.7 Literature Reviews of Analytical Methods for NSAIDs in Biological Samples 474 8.8 New Developments in NSAIDs 475 8.9 Conclusion 476 9 Certain Dyes as Pharmacologically Active Substances in Fish Farming and Other Aquaculture Products 497Eric Verdon and Wendy C. Andersen 9.1 Introduction 497 9.2 Therapeutic Applications and Chemistry of Certain Dyes Used in Fish Farming 500 9.3 Toxicological Issues 506 9.4 Regulatory Issues 509 9.5 Analytical Methods for Residue Control 511 9.6 Recent Trading Issues with Dye Alerts 526 9.7 Conclusions 531 10 Method Validation and Quality Assurance/Quality Control Approaches for Multi-residue Methods 549Andrew Cannavan, Jack F. Kay and Zora Jandríc 10.1 Introduction 549 10.2 Sources of Guidance on Method Validation 550 10.3 Practical Considerations 557 10.4 Examples of Validation Protocols for MRMs 561 10.5 Quality Assurance/Quality Control 565 10.6 Conclusion 569 Index 575

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Book SynopsisFollowing its well-received predecessor, this book offers an essential guide to chemists for understanding fluorine in spectroscopy. With over 1000 compounds and 100 spectra, the second edition adds new data featuring fluorine effects on nitrogen NMR, chemical shifts, and coupling constants.Table of ContentsPREFACE xv 1 GENERAL INTRODUCTION 1 1.1. Why Fluorinated Compounds are Interesting? / 1 1.1.1. Steric Size / 1 1.1.2. Polar Effects / 2 1.1.3. Effect of Fluorine Substituents on Acidity and Basicity of Compounds / 2 1.1.4. Effect of Fluorinated Substituents on Lipophilicity of Molecules / 3 1.1.5. Other Effects / 4 1.1.6. Analytical Applications in Biomedicinal Chemistry / 4 1.2. Introduction to Fluorine NMR / 5 1.2.1. Chemical Shifts / 5 1.2.2. Coupling Constants / 7 2 AN OVERVIEW OF FLUORINE NMR 9 2.1. Introduction / 9 2.2. Fluorine Chemical Shifts / 10 2.2.1. Some Aspects of Shielding/Deshielding Effects on Fluorine Chemical Shifts / 11 2.2.2. Solvent Effects on Fluorine Chemical Shifts / 15 2.2.3. Overall Summary of Fluorine Chemical Shift Ranges / 16 2.3. The Effect of Fluorine Substituents on Proton Chemical Shifts / 17 2.4. The Effect of Fluorine Substituents on Carbon Chemical Shifts / 18 2.5. The Effect of Fluorine Substituents on 31P Chemical Shifts / 19 2.6. The Effect of Fluorine Substituents on 15N Chemical Shifts / 20 2.7. Spin–Spin Coupling Constants to Fluorine / 23 2.7.1. Effect of Molecule Chirality on Coupling / 27 2.7.2. Through-Space Coupling / 29 2.7.3. Fluorine–Fluorine Coupling / 32 2.7.4. Coupling Between Fluorine and Hydrogen / 33 2.7.5. Coupling Between Fluorine and Carbon / 35 2.7.6. Coupling Between Fluorine and Phosphorous / 38 2.7.7. Coupling Between Fluorine and Nitrogen / 39 2.8. Second-Order Spectra / 40 2.9. Isotope Effects on Chemical Shifts / 45 2.10. Advanced Topics / 48 2.10.1. Multidimensional 19F NMR / 50 3 THE SINGLE FLUORINE SUBSTITUENT 55 3.1. Introduction / 55 3.1.1. Chemical Shifts – General Considerations / 56 3.1.2. Spin–Spin Coupling Constants – General Considerations / 56 3.2. Saturated Hydrocarbons / 57 3.2.1. Primary Alkyl Fluorides / 57 3.2.2. Secondary Alkyl Fluorides / 61 3.2.3. Tertiary Alkyl Fluorides / 63 3.2.4. Cyclic and Bicyclic Alkyl Fluorides / 66 3.3. Influence of Substituents/Functional Groups / 70 3.3.1. Halogen Substitution / 70 3.3.2. Alcohol, Ether, Epoxide, Ester, Sulfide, Sulfone, Sulfonate, and Sulfonic Acid Groups / 77 3.3.3. Amino, Ammonium, Azide, and Nitro Groups / 80 3.3.4. Phosphorous Compounds / 83 3.3.5. Silanes, Stannanes, and Germanes / 83 3.4. Carbonyl Functional Groups / 84 3.4.1. Aldehydes and Ketones / 85 3.4.2. Carboxylic Acid Derivatives / 86 3.4.3. 1H and 13C NMR Data for Aldehydes, Ketones, and Esters / 86 3.4.4. β-Ketoesters, Diesters, and Nitroesters / 89 3.5. Nitriles / 89 3.5.1. 1H and 13C NMR Data for Nitriles / 89 3.6. Alkenes with a Single Fluorine Substituent / 90 3.6.1. Hydrocarbon Alkenes / 90 3.6.2. Conjugated Alkenyl Systems / 93 3.6.3. Allylic Alcohols, Ethers, and Halides / 94 3.6.4. Halofluoroalkenes and Fluorovinyl Ethers / 97 3.6.5. Geminal Fluoro, Hetero Alkenes / 98 3.6.6. Multifluoroalkenes / 98 3.6.7. α,β-Unsaturated Carbonyl Compounds / 101 3.7. Acetylenic Fluorine / 104 3.8. Allylic and Propargylic Fluorides / 105 3.8.1. 1H and 13C NMR Data / 106 3.9. Fluoroaromatics / 106 3.9.1. Monofluoroaromatics / 106 3.9.2. Fluoropolycyclic Aromatics: Fluoronaphthalenes / 111 3.9.3. Polyfluoroaromatics / 112 3.10. Fluoromethyl Aromatics / 114 3.11. Fluoroheterocycles / 119 3.11.1. Fluoropyridines, Quinolines, and Isoquinolines / 119 3.11.2. Fluoropyrimidines and Other Fluorine-Substituted Six-Membered Ring Heterocycles / 122 3.11.3. Fluoromethyl Pyridines and Quinolines / 123 3.11.4. Fluoropyrroles and Indoles / 123 3.11.5. Fluoromethyl Pyrroles and Indoles / 125 3.11.6. Fluorofurans and Benzofurans / 125 3.11.7. Fluoromethyl Furans and Benzofurans / 126 3.11.8. Fluorothiophene and Benzothiophene / 127 3.11.9. Fluoromethyl Thiophenes and Benzothiophenes / 128 3.11.10. Fluoroimidazoles and Pyrazoles / 128 3.11.11. Fluoromethyl and Fluoroalkyl Imidazoles, 1H-pyrazoles, Benzimidazoles, 1H-triazoles, Benzotriazoles, and Sydnones / 128 3.12. Other Common Groups with a Single Fluorine Substituent / 129 3.12.1. Acyl Fluorides / 130 3.12.2. Fluoroformates / 131 3.12.3. Sulfinyl and Sulfonyl Fluorides / 131 4 THE CF2 GROUP 133 4.1. Introduction / 133 4.1.1. Chemical Shifts – General Considerations / 134 4.1.2. Spin–Spin coupling Constants – General Considerations / 135 4.2. Saturated Hydrocarbons Containing a CF2 Group / 135 4.2.1. Alkanes Bearing a Primary CF2H Group / 136 4.2.2. Secondary CF2 Groups / 139 4.2.3. Discussion of Coupling Constants Within CF2 Groups / 142 4.2.4. Pertinent 1H Chemical Shift Data / 143 4.2.5. Pertinent 13C NMR Data / 146 4.3. Influence of Substituents/Functional Groups / 148 4.3.1. Halogen Substitution / 148 4.3.2. Alcohol, Ether, Esters, Thioether, and Related Substituents / 152 4.3.3. Epoxides / 155 4.3.4. Sulfoxides, Sulfones, Sulfoximines, and Sulfonic Acids / 156 4.3.5. Multifunctional β,β-Difluoro Alcohols / 157 4.3.6. Compounds with Two Different Heteroatom Groups Attached to CF2 Including Chloro- and Bromodifluoromethyl Ethers / 157 4.3.7. Amines, Azides, and Nitro Compounds / 158 4.3.8. Phosphines, Phosphonates, and Phosphonium Compounds / 162 4.3.9. Silanes, Stannanes, and Germanes / 162 4.3.10. Organometallics / 162 4.4. Carbonyl Functional Groups / 164 4.4.1. Aldehydes and Ketones / 164 4.4.2. Carboxylic Acids and Derivatives / 166 4.5. Nitriles / 168 4.5.1. 1H and 13C NMR Spectra of Nitriles / 168 4.6. Amino-, Hydroxyl-, and Keto-Difluorocarboxylic Acid Derivatives / 169 4.7. Sulfonic Acid Derivatives / 170 4.8. Alkenes and Alkynes / 170 4.8.1. Simple Alkenes with Terminal Vinylic CF2 Groups / 170 4.8.2. Conjugated Alkenes with Terminal Vinylic CF2 Group / 172 4.8.3. Cumulated Alkenes with a Terminal CF2 Group / 174 4.8.4. Effect of Vicinal Halogen or Ether Function / 174 4.8.5. Effect of Allylic Substituents / 174 4.8.6. Polyfluoroethylenes / 175 4.8.7. Trifluorovinyl Group / 175 4.8.8. α,β-Unsaturated Carbonyl Systems with a Terminal Vinylic CF2 Group / 176 4.8.9. Allylic and Propargylic CF2 Groups / 177 4.9. Benzenoid Aromatics Bearing a CF2H or CF2R Group / 178 4.9.1. 1H and 13C NMR Data / 179 4.9.2. CF2 Groups with More Distant Aryl Substitutents / 180 4.10. Heteroaromatic CF2 Groups / 180 4.10.1. Pyridines, Quinolones, Phenanthridines, and Acridines / 181 4.10.2. Furans, Benzofurans, Thiophenes, Pyrroles, and Indoles / 181 4.10.3. Pyrimidines / 183 4.10.4. Five-Membered Ring Heterocycles with Two Hetero Atoms: Imidazoles, Benzimidazoles, 1H-pyrazoles, Oxazoles, Isoxazoles, Thiazoles, and Indazoles / 183 4.10.5. Five-Membered Ring Heterocycles with Three or More Heteroatoms: Sydnones, Triazoles, and Benzotriazoles / 183 4.10.6. Various Other Difluoromethyl-Substituted Heterocyclic Systems / 185 5 THE TRIFLUOROMETHYL GROUP 187 5.1. Introduction / 187 5.1.1. NMR Spectra of Compounds Containing the CF3 Group – General Considerations / 187 5.2. Saturated Hydrocarbons Bearing a CF3 Group / 189 5.2.1. Alkanes Bearing a CF3 Group / 189 5.2.2. Cycloalkanes Bearing a CF3 Group / 189 5.2.3. 1H and 13C NMR Data, General Information / 191 5.3. Influence of Substituents and Functional Groups / 193 5.3.1. Impact of Halogens / 193 5.3.2. Ethers, Alcohols, Esters, Sulfides, and Selenides / 195 5.3.3. Sulfones, Sulfoxides, and Sulfoximines / 200 5.3.4. Amines and Nitro Compounds / 200 5.3.5. Trifluoromethyl Imines, Oximes, Hydrazones, Imidoyl Chlorides, Nitrones, Diazo and Diazirine Compounds / 204 5.3.6. Phosphines and Phosphonium Compounds / 205 5.3.7. Organometallics / 205 5.4. Boronic Esters / 207 5.5. Carbonyl Compounds / 207 5.5.1. 1H and 13C NMR Data / 209 5.6. Nitriles / 213 5.6.1. 13C NMR Data for Nitriles / 213 5.7. Bifunctional Compounds / 214 5.8. Sulfonic Acid Derivatives / 214 5.9. Allylic and Propargylic Trifluoromethyl Groups / 214 5.9.1. Allylic Trifluoromethyl Groups / 215 5.9.2. α,β-Unsaturated Carbonyl Compounds / 219 5.9.3. More Heavily Fluorinated Allylics / 222 5.9.4. Propargylic Trifluoromethyl Groups / 222 5.10. Aryl-Bound Trifluoromethyl Groups / 223 5.10.1. Proton and Carbon NMR Data / 224 5.10.2. Multitrifluoromethylated Benzenes / 225 5.11. Heteroaryl-Bound Trifluoromethyl Groups / 228 5.11.1. Pyridines, Quinolines, and Isoquinolines / 228 5.11.2. Pyrimidines and Quinoxalines / 229 5.11.3. Pyrroles and Indoles / 229 5.11.4. Thiophenes and Benzothiophenes / 230 5.11.5. Furans / 230 5.11.6. Imidazoles and Benzimidazoles / 232 5.11.7. Oxazoles, Isoxazoles, Oxazolidines, Thiazoles, 1H-pyrazoles, 1H-indazoles, Benzoxazoles, and Benzothiazoles / 234 5.11.8. Triazoles and Tetrazoles / 235 6 MORE HIGHLY FLUORINATED GROUPS 237 6.1. Introduction / 237 6.2. The 1,1,2- and 1,2,2-Trifluoroethyl Groups / 238 6.3. The 1,1,2,2-Tetrafluoroethyl and 2,2,3,3-Tetrafluoropropyl Groups / 241 6.4. The 1,2,2,2-Tetrafluoroethyl Group / 242 6.5. The Pentafluoroethyl Group / 245 6.5.1. Pentafluoroethyl Carbinols / 248 6.5.2. Pentafluoroethyl Ethers, Sulfides, and Phosphines / 248 6.5.3. Pentafluoroethyl Organometallics / 249 6.6. The 2,2,3,3,3-Pentafluoropropyl Group / 249 6.7. The 1,1,2,3,3,3-Hexafluoropropyl Group / 251 6.8. 1,1,2,2,3,3-Hexafluoropropyl System / 252 6.9. The Hexafluoro-Isopropyl Group / 254 6.10. The Heptafluoro-n-Propyl Group / 255 6.11. The Heptafluoro-iso-Propyl Group / 255 6.12. The Nonafluoro-n-Butyl Group / 255 6.13. The Nonafluoro-iso-Butyl Group / 258 6.14. The Nonafluoro-t-Butyl Group / 258 6.15. Fluorous Groups / 258 6.16. 1-Hydro-Perfluoroalkanes / 259 6.17. Perfluoroalkanes / 260 6.18. Perfluoro-n-Alkyl Halides / 263 6.19. Perfluoroalkyl Amines, Ethers, and Carboxylic Acid Derivatives / 263 6.20. Polyfluoroalkenes / 264 6.20.1. Trifluorovinyl Groups / 264 6.20.2. Perfluoroalkenes / 267 6.21. Polyfluorinated Aromatics / 268 6.21.1. 2,3,5,6-Tetrafluorobenzene Compounds / 268 6.21.2. The Pentafluorophenyl Group / 268 6.22. Polyfluoroheterocyclics / 269 6.22.1. Polyfluoropyridines / 269 6.22.2. Polyfluorofurans / 269 6.22.3. Polyfluorothiophenes / 269 6.22.4. Polyfluoropyrimidines / 271 7 COMPOUNDS AND SUBSTITUENTS WITH FLUORINE DIRECTLY BOUND TO A HETEROATOM 273 7.1. Introduction / 273 7.2. Boron Fluorides / 275 7.3. Fluorosilanes / 275 7.4. Nitrogen Fluorides / 275 7.4.1. Electrophilic Fluorinating Agents / 276 7.5. Phosphorous Fluorides / 277 7.5.1. Phosphorous (III) Fluorides / 277 7.5.2. Phosphorous (V) Fluorides / 277 7.5.3. Phosphorous (V) Oxyfluorides / 280 7.5.4. Cyclophosphazenes / 280 7.6. Oxygen Fluorides (Hypofluorites) / 281 7.7. Sulfur Fluorides / 282 7.7.1. Inorganic Sulfur, Selenium, and Tellurium Fluorides / 282 7.7.2. Diarylsulfur, Selenium, and Tellurium Difluorides / 282 7.7.3. Aryl and Alkyl SF3 Compounds / 283 7.7.4. Dialkylaminosulfur Trifluorides / 283 7.7.5. Hypervalent Sulfur Fluorides / 284 7.7.6. Related Hypervalent Selenium and Tellurium Fluorides / 287 7.7.7. Organic Sulfinyl and Sulfonyl Fluorides / 288 7.8. The Pentafluorosulfanyl (SF5) Group in Organic Chemistry / 289 7.8.1. Saturated Aliphatic Systems / 292 7.8.2. Vinylic SF5 Substituents / 294 7.8.3. Acetylenic SF5 Substituents / 296 7.8.4. Aromatic SF5 Substituents / 297 7.8.5. Heterocyclic SF5 Compounds / 302 7.9. Bromine Trifluoride, Iodine Trifluoride, and Iodine Pentafluoride / 304 7.10. Aryl and Alkyl Halogen Difluorides and Tetrafluorides / 304 7.11. Xenon Fluorides / 305 INDEX 307

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Book SynopsisA guide for scientists, pediatricians and students involved in metabolic studies in pediatric research Addresses the availability of modern analytical techniques and how to apply these techniques in metabolic studiesCovers the whole range of available mass spectrometric techniques used for metabolic studies including Stable Isotope MethodologyPresents the relevance of mass spectrometry and stable isotope methodology in pediatric research covering applications in Nutrition, Obesity, Metabolic Disorders, and Kidney DisordersFocuses on the interactions between nutrients and the endogenous metabolism within the body and how these factors affect the health of a growing infantTable of ContentsList of Contributors xvii Introduction xxi List of Abbreviations xxiii 1 Mass Spectrometry Techniques for In Vivo Stable Isotope Approaches 1Jean-Philippe Godin and Henk Schierbeek 1.1 Introduction 1 1.2 Nomenclature for Light-Stable Isotope Changes 3 1.3 Mass Spectrometry Techniques 6 1.4 Choice of Mass Spectrometric Techniques and Applications to Measure Isotopic Enrichments in Metabolic Studies 26 1.5 Conclusion and Future Perspectives 30 References 32 2 Stable Isotope Technology 45Dewi van Harskamp, Johannes B. van Goudoever, and Henk Schierbeek 2.1 History 45 2.2 Definition 45 2.3 Safety 46 2.4 Stable Isotopes and Natural Abundances 47 2.5 Stable Isotope Selection 48 2.6 Single or Multiple Label Selection 49 2.7 Precursor Model 49 2.8 Simultaneous Infusion 49 2.9 Infusion Techniques 50 2.10 Steady State 52 2.11 Pool Selection 52 2.12 Pool Models 53 2.13 Flux: Synthesis and Breakdown 55 2.14 Nitrogen Balance 57 2.15 Doubly LabeledWater Method 57 2.16 Whole-body Protein Synthesis 58 2.17 Specific Protein Synthesis 58 2.18 Calculations 59 2.19 Considerations and Drawbacks of Isotopic Tracers 62 2.20 Conclusion 63 References 63 3 Stable Isotopes in Nutritional and Pediatric Research 67Willemijn E. Corpeleijn and Johannes B. van Goudoever 3.1 Introduction 67 3.2 Ethical Aspects 69 3.3 Applications of Stable Isotopes in Nutritional and Pediatric Research 70 3.4 Conclusion 78 References 78 4 Early-Life Nutrition and Stable Isotope Techniques 81Stefanie M.P. Kouwenhoven and Marita deWaard 4.1 Introduction 81 4.2 Breast Milk versus Infant Formula 81 4.3 Techniques to Monitor Milk Intake 82 4.4 Body Composition in Term and Preterm Infants 86 4.5 Amino Acid Requirement 86 4.6 Clinical Applications 87 4.7 Additional Applications 95 4.8 Discussion 98 4.9 Conclusion 99 4.10 Future Perspectives 99 References 100 5 Assessment of Amino Acid Requirement in Children Using Stable Isotopes 108Femke Maingay-de Groof and Henk Schierbeek 5.1 Introduction 108 5.2 Nutrient Needs and Definitions 109 5.3 Methods to Determine Requirements 111 5.4 Isotopic Tracer Methods 112 5.5 Existing Methods to Determine Amino Acid Requirement for Neonates 114 5.6 Use of the IAAO Method in the Pediatric Population 115 5.7 Necessity for Performing the Study 117 5.8 Biochemistry 117 5.9 Available AnalyticalMethods 120 5.10 Clinical Application 120 5.11 Analysis and Calculations 125 5.12 Results 125 5.13 Statistical Analysis 128 5.14 Discussion 129 5.15 Conclusion 131 5.16 Future Perspectives 132 References 132 6 Metabolism of Glutamine, Citrulline, and Arginine; Stable Isotopes Analyzing the Intestinal–Renal Axis 139Nikki Buijs, Saskia J.H. Brinkmann, Gerdien C. Ligthart-Melis, and Henk Schierbeek 6.1 Introduction 139 6.2 Biochemistry 142 6.3 Isotopic Model 146 6.4 Study Design 148 6.5 Mass Spectrometry Methods 151 6.6 Clinical Applications 155 6.7 Calculations 158 6.8 Discussion and Future Perspectives 161 References 167 7 Applications in Fat Absorption andMetabolism 175Dirk-Jan Reijngoud and Henkjan J. Verkade 7.1 Introduction 175 7.2 Biochemistry of Fat Absorption 176 7.3 Isotope Model 178 7.4 Study Design/Infusion Protocols 179 7.5 Analytical Equipment 181 7.6 Analytical Conditions 181 7.7 Accuracy and Precision 183 7.8 Calculations 184 7.9 Clinical Applications 187 7.10 Future Perspectives 191 References 193 8 Materno-Fetal Lipid Kinetics 197Elvira Larqué, Hans Demmelmair, and Berthold Koletzko 8.1 Introduction 197 8.2 Biochemistry of Placental Lipid Transport 198 8.3 Investigation of Fatty Acid Metabolism Using Stable Isotopes 200 8.4 Mass Spectrometry Methods 202 8.5 Clinical Studies with Fatty Acids Labeled with Stable Isotopes in Healthy and Complicated Pregnancies 203 8.6 Calculations 207 8.7 Future Perspectives 209 Acknowledgments 210 References 210 9 Stable Isotope Applications in Human In Vivo Placental and Fetal Research 213Chris H.P. van den Akker 9.1 Introduction 213 9.2 Investigation of FetalMetabolism Using Stable Isotopes 214 9.3 Study Designs and Models 215 9.4 Infusion Protocols and Clinical Applications 216 9.5 Necessary Additional Clinical Parameters to be Analyzed 218 9.6 Necessary Analytical Mass-Spectrometry Equipment and Analytical Conditions 218 9.7 Calculations 219 9.8 Future Perspectives 222 References 222 10 Obesity 225Margriet Veldhorst and Henk Schierbeek 10.1 Introduction 225 10.2 Singly and Doubly LabeledWater 226 10.3 Substrate Oxidation 237 10.4 Glucose Metabolism 238 10.5 Fat Metabolism 239 10.6 Protein Turnover 242 10.7 Calculations 246 10.8 Discussion and Future Perspectives 249 References 250 11 Inborn Errors of Metabolism 258Hidde H. Huidekoper, Frits A.Wijburg, and Ronald J.A.Wanders 11.1 Introduction 258 11.2 Stable Isotope Techniques 260 11.3 Analytical Equipment and Methods 267 11.4 Study Protocol: Quantifying Endogenous Galactose Production 269 11.5 Calculations 271 11.6 Discussion 276 11.7 Future Perspectives 277 References 278 12 Renal Disease and Dialysis 284Gregorio P.Milani, Sander F. Garrelfs, and Michiel J.S. Oosterveld 12.1 Introduction 284 12.2 Total BodyWater and Its Distribution 286 12.3 Protein Metabolism in Chronic Kidney Disease 291 12.4 Dialysis – Metabolic Consequences and Nutrient Losses 293 12.5 Primary Hyperoxalurias 295 12.6 Clinical Applications 298 12.7 Calculations 303 12.8 Discussion 308 12.9 Future Perspectives 310 References 310 13 Application in Oxidative Stress and Glutathione Metabolism in Preterm Infants 320Denise Rook and Henk Schierbeek 13.1 Introduction 320 13.2 Biochemistry/Model 321 13.3 Guidelines and Safety Procedures 323 13.4 Mass Spectrometry Methods 323 13.5 Materials and Methods 324 13.6 Clinical Application (A Practical Example of a Study Protocol) 327 13.7 Calculations 329 13.8 Discussion and Future Perspectives 330 References 331 14 Nutrient Digestion and Absorption During Intestinal Malfunction and Diseases 336Margot Fijlstra 14.1 Introduction 336 14.2 Clinical Application 340 References 357 Index 365

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Book SynopsisCovers the area of lipidomics from fundamentals and theory to applications Presents a balanced discussion of the fundamentals, theory, experimental methods and applications of lipidomics Covers different characterizations of lipids including Glycerophospholipids; Sphingolipids; Glycerolipids and Glycolipids; and Fatty Acids and Modified Fatty Acids Includes a section on quantification of Lipids in Lipidomics such as sample preparation; factors affecting accurate quantification; and data processing and interpretation Details applications of Lipidomics Tools including for Health and Disease; Plant Lipidomics; and Lipidomics on Cellular Membranes Table of ContentsForeword xix Preface xxi Abbreviations xxv Part I Introduction 1 1 Lipids and Lipidomics 3 1.1 Lipids, 3 1.1.1 Definition, 3€ 1.1.2 Classification, 4 1.1.2.1 Lipid MAPS Approach, 7 1.1.2.2 Building Block Approach, 10 1.2 Lipidomics, 13 1.2.1 Definition, 13 1.2.2 History of Lipidomics, 14 References, 16 2 Mass Spectrometry for Lipidomics 21 2.1 Ionization Techniques, 21 2.1.1 Electrospray Ionization, 22 2.1.1.1 Principle of Electrospray Ionization, 22 2.1.1.2 Features of Electrospray Ionization for Lipid Analysis, 28 2.1.1.3 Advent of ESI for Lipid Analysis: Nano-ESI and Off-Axis Ion Inlets, 30 2.1.2 Matrix-Assisted Laser Desorption/Ionization, 30 2.2 Mass Analyzers, 32 2.2.1 Quadrupole, 32 2.2.2 Time of Flight, 33 2.2.3 Ion Trap, 35 2.3 Detector, 36 2.4 Tandem Mass Spectrometry Techniques, 37 2.4.1 Product-Ion Analysis, 37 2.4.2 Neutral-Loss Scan, 39 2.4.3 Precursor-Ion Scan, 39 2.4.4 Selected Reaction Monitoring, 39 2.4.5 Interweaving Tandem Mass Spectrometry Techniques, 40 2.5 Other Recent Advances in Mass Spectrometry for Lipid Analysis, 42 2.5.1 Ion-Mobility Mass Spectrometry, 43 2.5.2 Desorption Electrospray Ionization, 43 References, 45 3 Mass Spectrometry-Based Lipidomics Approaches 53 3.1 Introduction, 53 3.2 Shotgun Lipidomics: Direct Infusion-Based Approaches, 54 3.2.1 Devices for Direct Infusion, 54 3.2.2 Features of Shotgun Lipidomics, 55 3.2.3 Shotgun Lipidomics Approaches, 56 3.2.3.1 Tandem Mass Spectrometry-Based Shotgun Lipidomics, 56 3.2.3.2 High Mass Accuracy-Based Shotgun Lipidomics, 56 3.2.3.3 Multidimensional MS-Based Shotgun Lipidomics, 57 3.2.4 Advantages and Drawbacks, 63 3.2.4.1 Tandem Mass Spectrometry-Based Shotgun Lipidomics, 63 3.2.4.2 High Mass Accuracy-Based Shotgun Lipidomics, 63 3.2.4.3 Multidimensional Mass Spectrometry-Based Shotgun Lipidomics, 64 3.3 LC-MS-Based Approaches, 65 3.3.1 General, 65 3.3.1.1 Selected Ion Monitoring for LC-MS, 66 3.3.1.2 Selected/Multiple Reaction Monitoring for LC-MS, 67 3.3.1.3 Data-Dependent Analysis after LC-MS, 67 3.3.2 LC-MS-Based Approaches for Lipidomics, 68 3.3.2.1 Normal-Phase LC-MS-Based Approaches, 68 3.3.2.2 Reversed-Phase LC-MS-Based Approaches, 69 3.3.2.3 Hydrophilic Interaction LC-MS-Based Approaches, 71 3.3.2.4 Other LC-MS-Based Approaches, 72 3.3.3 Advantages and Drawbacks, 72 3.3.4 Identification of Lipid Species after LC-MS, 73 3.4 MALDI-MS for Lipidomics, 74 3.4.1 General, 74 3.4.2 Analysis of Lipid Extracts, 74 3.4.3 Advantages and Drawbacks, 75 3.4.4 Recent Advances in MALDI-MS for Lipidomics, 76 3.4.4.1 Utilization of Novel Matrices, 76 3.4.4.2 (HP)TLC-MALDI-MS, 78 3.4.4.3 Matrix-Free Laser Desorption/Ionization Approaches, 78 References, 79 4 Variables in Mass Spectrometry for Lipidomics 89 4.1 Introduction, 89 4.2 Variables in Lipid Extraction (i.e., Multiplex Extraction Conditions), 89 4.2.1 The pH Conditions of Lipid Extraction, 89 4.2.2 Solvent Polarity of Lipid Extraction, 90 4.2.3 Intrinsic Chemical Properties of Lipids, 90 4.3 Variables in the Infusion Solution, 91 4.3.1 Polarity, Composition, Ion Pairing, and Other Variations in the Infusion Solution, 91 4.3.2 Variations of the Levels or Composition of a Modifier in the Infusion Solution, 93 4.3.3 Lipid Concentration in the Infusion Solution, 97 4.4 Variables in Ionization, 98 4.4.1 Source Temperature, 98 4.4.2 Spray Voltage, 99 4.4.3 Injection/Eluent Flow Rate, 100 4.5 Variables in Building-Block monitoring with MS/MS Scanning, 102 4.5.1 Precursor-Ion Scanning of a Fragment Ion Whose m/z Serves as a Variable, 102 4.5.2 Neutral-Loss Scanning of a Neutral Fragment Whose Mass Serves as a Variable, 102 4.5.3 Fragments Associated with the Building Blocks are the Variables in Product-Ion MS Analysis, 103 4.6 Variables in Collision, 104 4.6.1 Collision Energy, 104 4.6.2 Collision-Gas Pressure, 104 4.6.3 Collision Gas Type, 108 4.7 Variables in Separation, 108 4.7.1 Charge Properties in Intrasource Separation, 108 4.7.2 Elution Time in LC Separation, 111 4.7.3 Matrix Properties in Selective Ionization by MALDI, 112 4.7.4 Drift Time (or Collision Cross Section) in Ion-Mobility Separation, 112 4.8 Conclusion, 114 References, 114 5 Bioinformatics in Lipidomics 121 5.1 Introduction, 121 5.2 Lipid Libraries and Databases, 122 5.2.1 Lipid MAPS Structure Database, 122 5.2.2 Building-Block Concept-Based Theoretical Databases, 123 5.2.3 LipidBlast – in silico Tandem Mass Spectral Library, 129 5.2.4 METLIN Database, 130 5.2.5 Human Metabolome Database, 131 5.2.6 LipidBank Database, 131 5.3 Bioinformatics Tools in Automated Lipid Data Processing, 132 5.3.1 LC-MS Spectral Processing, 132 5.3.2 Biostatistical Analyses and Visualization, 134 5.3.3 Annotation for Structure of Lipid Species, 135 5.3.4 Software Packages for Common Data Processing, 136 5.3.4.1 XCMS, 136 5.3.4.2 MZmine 2, 136 5.3.4.3 A Practical Approach for Determination of Mass Spectral Baselines, 137 5.3.4.4 LipidView, 137 5.3.4.5 LipidSearch, 137 5.3.4.6 SimLipid, 138 5.3.4.7 MultiQuant, 139 5.3.4.8 Software Packages for Shotgun Lipidomics, 139 5.4 Bioinformatics for Lipid Network/Pathway Analysis and Modeling, 139 5.4.1 Reconstruction of Lipid Network/Pathway, 139 5.4.2 Simulation of Lipidomics Data for Interpretation of Biosynthesis Pathways, 140 5.4.3 Modeling of Spatial Distributions and Biophysical 5.5 Integration of "Omics", 143 5.5.1 Integration of Lipidomics with Other Omics, 143 5.5.2 Lipidomics Guides Genomics Analysis, 144 References, 145 Part II Characterization of Lipids 151 6 Introduction 153 6.1 Structural Characterization for Lipid Identification, 153 6.2 Pattern Recognition for Lipid Identification, 157 6.2.1 Principles of Pattern Recognition, 157 6.2.2 Examples, 159 6.2.2.1 Choline Lysoglycerophospholipid, 159 6.2.2.2 Sphingomyelin, 161 6.2.2.3 Triacylglycerol, 164 6.2.3 Summary, 169 References, 170 7 Fragmentation Patterns of Glycerophospholipids 173 7.1 Introduction, 173 7.2 Choline Glycerophospholipid, 175 7.2.1 Positive Ion Mode, 175 7.2.1.1 Protonated Species, 175 7.2.1.2 Alkaline Adducts, 175 7.2.2 Negative-Ion Mode, 178 7.3 Ethanolamine Glycerophospholipid, 180 7.3.1 Positive-Ion Mode, 180 7.3.1.1 Protonated Species, 180 7.3.1.2 Alkaline Adducts, 180 7.3.2 Negative-Ion Mode, 182 7.3.2.1 Deprotonated Species, 182 7.3.2.2 Derivatized Species, 183 7.4 Phosphatidylinositol and Phosphatidylinositides, 184 7.4.1 Positive-Ion Mode, 184 7.4.2 Negative-Ion Mode, 184 7.5 Phosphatidylserine, 185 7.5.1 Positive-Ion Mode, 185 7.5.2 Negative-Ion Mode, 186 7.6 Phosphatidylglycerol, 186 7.6.1 Positive-Ion Mode, 186 7.6.2 Negative-Ion Mode, 186 7.7 Phosphatidic Acid, 187 7.7.1 Positive-Ion Mode, 187 7.7.2 Negative-Ion Mode, 188 7.8 Cardiolipin, 188 7.9 Lysoglycerophospholipids, 190 7.9.1 Choline Lysoglycerophospholipids, 190 7.9.2 Ethanolamine Lysoglycerophospholipids, 191 7.9.3 Anionic Lysoglycerophospholipids, 193 7.10 Other Glycerophospholipids, 193 7.10.1 N-Acyl Phosphatidylethanolamine, 193 7.10.2 N-Acyl Phosphatidylserine, 194 7.10.3 Acyl Phosphatidylglycerol, 194 7.10.4 Bis(monoacylglycero)phosphate, 194 7.10.5 Cyclic Phosphatidic Acid, 196 References, 196 8 Fragmentation Patterns of Sphingolipids 201 8.1 Introduction, 201 8.2 Ceramide, 202 8.2.1 Positive-Ion Mode, 202 8.2.2 Negative-Ion Mode, 203 8.3 Sphingomyelin, 205 8.3.1 Positive-Ion Mode, 205 8.3.2 Negative-Ion Mode, 205 8.4 Cerebroside, 205 8.4.1 Positive-Ion Mode, 205 8.4.2 Negative-Ion Mode, 207 8.5 Sulfatide, 208 8.6 Oligoglycosylceramide and Gangliosides, 208 8.7 Inositol Phosphorylceramide, 210 8.8 Sphingolipid Metabolites, 210 8.8.1 Sphingoid Bases, 210 8.8.2 Sphingoid-1-Phosphate, 212 8.8.3 Lysosphingomyelin, 212 8.8.4 Psychosine, 213 References, 213 9 Fragmentation Patterns of Glycerolipids 217 9.1 Introduction, 217 9.2 Monoglyceride, 218 9.3 Diglyceride, 218 9.4 Triglyceride, 222 9.5 Hexosyl Diacylglycerol, 223 9.6 Other Glycolipids, 224 References, 226 10 Fragmentation Patterns of Fatty Acids and Modified Fatty Acids 229 10.1 Introduction, 229 10.2 Nonesterified Fatty Acid, 230 10.2.1 Underivatized Nonesterified Fatty Acid, 230 10.2.1.1 Positive-Ion Mode, 230 10.2.1.2 Negative-Ion Mode, 230 10.2.2 Derivatized Nonesterified Fatty Acid, 233 10.2.2.1 Off-Line Derivatization, 233 10.2.2.2 Online Derivatization (Ozonolysis), 234 10.3 Modified Fatty Acid, 234 10.4 Fatty Acidomics, 238 References, 241 11 Fragmentation Patterns of other Bioactive Lipid Metabolites 243 11.1 Introduction, 243 11.2 Acylcarnitine, 244 11.3 Acyl CoA, 245 11.4 Endocannabinoids, 246 11.4.1 N-Acyl Ethanolamine, 247 11.4.2 2-Acyl Glycerol, 247 11.4.3 N-Acyl Amino Acid, 247 11.5 4-Hydroxyalkenal, 248 11.6 Chlorinated Lipids, 251 11.7 Sterols and Oxysterols, 251 11.8 Fatty Acid–Hydroxy Fatty Acids, 252 References, 253 12 Imaging Mass Spectrometry of Lipids 259 12.1 Introduction, 259 12.1.1 Samples Suitable for MS Imaging of Lipids, 260 12.1.2 Sample Processing/Preparation, 260 12.1.3 Matrix Application, 261 12.1.3.1 Matrix Application, 261 12.1.3.2 Matrix Application Methods, 262 12.1.4 Data Processing, 263 12.1.4.1 Biomap, 263 12.1.4.2 FlexImaging, 264 12.1.4.3 MALDI Imaging Team Imaging Computing System (MITICS), 264 12.1.4.4 DataCube Explorer, 264 12.1.4.5 imzML, 264 12.2 MALDI-MS Imaging, 264 12.3 Secondary-Ion Mass Spectrometry Imaging, 267 12.4 DESI-MS Imaging, 268 12.5 Ion-Mobility Imaging, 270 12.6 Advantages and Drawbacks of Imaging Mass Spectrometry for Analysis of Lipids, 270 12.6.1 Advantages, 270 12.6.2 Limitations, 272 References, 272 Part III Quantification of Lipids in Lipidomics 281 13 Sample Preparation 283 13.1 Introduction, 283 13.2 Sampling, Storage, and Related Concerns, 284 13.2.1 Sampling, 284 13.2.2 Sample Storage Prior to Extraction, 286 13.2.3 Minimizing Autoxidation, 287 13.3 Principles and Methods of Lipid Extraction, 288 13.3.1 Principles of Lipid Extraction, 289 13.3.2 Internal Standards, 292 13.3.3 Lipid Extraction Methods, 295 13.3.3.1 Folch Extraction, 295 13.3.3.2 Bligh–Dyer Extraction, 296 13.3.3.3 MTBE Extraction, 297 13.3.3.4 BUME Extraction, 298 13.3.3.5 Extraction of Plant Samples, 298 13.3.3.6 Special Cases, 298 13.3.4 Contaminants and Artifacts in Extraction, 299 13.3.5 Storage of Lipid Extracts, 300 References, 300 14 Quantification of Individual Lipid Species in Lipidomics 305 14.1 Introduction, 305 14.2 Principles of Quantifying Lipid Species by Mass Spectrometry, 308 14.3 Methods for Quantification in Lipidomics, 312 14.3.1 Tandem Mass Spectrometry-Based Method, 312 14.3.2 Two-Step Quantification Approach Used in MDMS-SL, 317 14.3.3 Selected Ion Monitoring Method, 321 14.3.4 Selected Reaction Monitoring Method, 324 14.3.5 High Mass Accuracy Mass Spectrometry Approach, 327 References, 329 15 Factors Affecting Accurate Quantification of Lipids 335 15.1 Introduction, 335 15.2 Lipid Aggregation, 336 15.3 Linear Dynamic Range of Quantification, 337 15.4 Nuts and Bolts of Tandem Mass Spectrometry for Quantification of Lipids, 339 15.5 Ion Suppression, 341 15.6 Spectral Baseline, 343 15.7 The Effects of Isotopes, 344 15.8 Minimal Number of Internal Standards for Quantification, 347 15.9 In-Source Fragmentation, 349 15.10 Quality of Solvents, 350 15.11 Miscellaneous in Quantitative Analysis of Lipids, 350 References, 350 16 Data Quality Control and Interpretation 353 16.1 Introduction, 353 16.2 Data Quality Control, 354 16.3 Recognition of Lipid Metabolism Pathways for Data Interpretation, 355 16.3.1 Sphingolipid Metabolic Pathway Network, 356 16.3.2 Network of Glycerophospholipid Biosynthesis Pathways, 356 16.3.3 Glycerolipid Metabolism, 359 16.3.4 Interrelationship between Different Lipid Categories, 360 16.4 Recognition of Lipid Functions for Data Interpretation, 360 16.4.1 Lipids Serve as Cellular Membrane Components, 360 16.4.2 Lipids Serve as Cellular Energy Storage Depots, 363 16.4.3 Lipids Serve as Signaling Molecules, 365 16.4.4 Lipids Play Other Cellular Roles, 366 16.5 Recognizing the Complication of Sample Inhomogeneity and Cellular Compartments in Data Interpretation, 368 16.6 Integration of "Omics" for Data Supporting, 369 References, 370 Part IV Applications of Lipidomics in Biomedical and Biological Research 377 17 Lipidomics for Health and Disease 379 17.1 Introduction, 379 17.2 Diabetes and Obesity, 380 17.3 Cardiovascular Diseases, 382 17.4 Nonalcohol Fatty Liver Disease, 383 17.5 Alzheimer’s disease, 385 17.6 Psychosis, 387 17.7 Cancer, 388 17.8 Lipidomics in Nutrition, 390 17.8.1 Lipidomics in Determination of the Effects of Specific Diets or Challenge Tests, 391 17.8.2 Lipidomics to Control Food Quality, 392 References, 393 18 Plant Lipidomics 405 18.1 Introduction, 405 18.2 Characterization of Lipids Special to Plant Lipidome, 406 18.2.1 Galactolipids, 407 18.2.2 Sphingolipids, 408 18.2.3 Sterols and Derivatives, 410 18.2.4 Sulfolipids, 410 18.2.5 Lipid A and Intermediates, 411 18.3 Lipidomics for Plant Biology, 411 18.3.1 Stress-Induced Changes of Plant Lipidomes, 411 18.3.1.1 Lipid Alterations in Plants Induced by Temperature Changes, 411 18.3.1.2 Wounding-Induced Alterations in Plastidic Lipids, 415 18.3.1.3 Phosphorus Deficiency-Resulted Changes of Glycerophospholipids and Galactolipids, 416 18.3.2 Changes of Plant Lipidomes during Development, 416 18.3.2.1 Alterations in Lipids during Development of Cotton Fibers, 416 18.3.2.2 Changes of Lipids during Potato Tuber Aging and Sprouting, 417 18.3.3 Characterization of Gene Function by Lipidomics, 417 18.3.3.1 Role of Fatty Acid Desaturases and DHAP Reductase in Systemic Acquired Resistance, 417 18.3.3.2 Roles of Phospholipases in Response to Freezing, 419 18.3.3.3 Role of PLDζ in Phosphorus Deficiency-Induced Lipid Changes, 419 18.3.4 Lipidomics Facilitates Improvement of Genetically Modified Food Quality, 420 References, 421 19 Lipidomics on Yeast and Mycobacterium Tuberculosis 427 19.1 Introduction, 427 19.2 Yeast Lipidomics, 428 19.2.1 Protocol for Analysis of Yeast Lipidomes by Mass Spectrometry, 428 19.2.2 Quantitative Analysis of Yeast Lipidome, 430 19.2.3 Comparative Lipidomics Studies on Different Yeast Strains, 431 19.2.4 Lipidomics of Yeast for Lipid Biosynthesis and Function, 432 19.2.5 Determining the Effects of Growth Conditions on Yeast Lipidomes, 435 19.3 Mycobacterium Tuberculosis Lipidomics, 436 References, 438 20 Lipidomics on Cell Organelle and Subcellular Membranes 443 20.1 Introduction, 443 20.2 Golgi, 444 20.3 Lipid Droplets, 445 20.4 Lipid Rafts, 447 20.5 Mitochondrion, 449 20.6 Nucleus, 452 20.7 Conclusion, 453 References, 454 Index 459

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Book SynopsisSecond edition of the guide to the modern techniques that demonstrate the potential of Raman spectroscopy Completely revised and updated, the second edition of Modern Raman Spectroscopy presents the information needed for clear understanding and application of the technique of Raman Spectroscopy in a range of areas such as pharmaceuticals, forensics, and biology. The authorsnoted experts on the topicreveal how to make full use of the critical information presented and include a wealth of examples of the pitfalls that can be encountered. The text opens with a description of the basic theory to assist readers in making a practical interpretation of Raman Spectra. Chapters include the main equations that are used in order to highlight the theory's meaning and relevance while avoiding a full mathematical treatment. Modern Raman Spectroscopy provides a firm grounding, combined with a variety of references, from which to approach a more comprehensive stuTable of ContentsPreface ix Acknowledgements xi Chapter 1 Introduction, Basic Theory and Principles 1 1.1 Introduction 1 1.2 History 2 1.3 Basic Theory 2 1.4 Molecular Vibrations 8 1.5 Group Vibrations 11 1.6 Basic Interpretation of a Spectrum 13 1.7 Summary 19 Chapter 2 The Raman Experiment – Raman Instrumentation, Sample Presentation, Data Handling and Practical Aspects of Interpretation 21 2.1 Introduction 21 2.2 Choice of Instrument 22 2.3 Transmission Raman Scattering and Spatially Offset Raman Scattering 29 2.4 Raman Sample Preparation and Handling 30 2.4.1 Sample Mounting – Optical Considerations 31 2.4.2 Raman Sample Handling 34 2.5 Sample Mounting Accessories 40 2.5.1 Small Fibres, Films, Liquids and Powders 40 2.5.2 Variable Temperature and Pressure Cells 40 2.5.3 Special Applications – Thin Films, Surfaces and Catalysts 42 2.5.4 Reaction Cells, Flow Through Cells, Sample Changers and Automated Mounts 44 2.6 Fibre‐Optic Coupling and Wave Guides 45 2.7 Microscopy 49 2.7.1 Raman Microscopes 49 2.7.2 Depth Profiling 51 2.7.3 Imaging and Mapping 51 2.8 Calibration 56 2.9 Data Manipulation, Presentation and Quantitation 59 2.9.1 Manipulation of Spectra for Presentation 59 2.9.2 Presentation of Spectra 63 2.9.3 Quantitation 64 2.10 An Approach to Qualitative Interpretation 66 2.10.1 Factors to Consider in the Interpretation of a Raman Spectrum of an Unknown Sample 67 2.10.1.1 Knowledge of the Sample and Sample Preparation Effects 68 2.10.1.2 Instrument and Software Effects 69 2.10.1.3 The Spectrum 69 2.10.2 Computer‐Aided Spectrum Interpretation 70 2.10.3 Spectra Formats for Transfer and Exchange of Data 73 2.11 Summary 74 Chapter 3 The Theory of Raman Spectroscopy 77 3.1 Introduction 77 3.2 Absorption and Scattering 78 3.3 States of a System and Hooke’s Law 79 3.4 The Basic Selection Rule 82 3.5 Number and Symmetry of Vibrations 83 3.6 The Mutual Exclusion Rule 84 3.7 Understanding Polarizability 85 3.8 Polarizability and the Measurement of Polarization 89 3.9 Symmetry Elements and Point Groups 93 3.10 Lattice Modes 97 3.11 Summary 98 Chapter 4 Resonance Raman Scattering 101 4.1 Introduction 101 4.2 The Basic Process 102 4.3 Key Differences Between Resonance and Normal Raman Scattering 102 4.3.1 Intensity Increase 103 4.3.2 Franck Condon and Herzberg Teller Scattering 105 4.3.3 Overtones 108 4.3.4 Wavelength Dependence 109 4.3.5 Electronic Information 111 4.4 Practical Aspects 113 4.5 Summary 116 Chapter 5 Surface Enhanced Raman Scattering and Surface Enhanced Resonance Raman Scattering 119 5.1 Introduction 119 5.2 Electromagnetic and Charge Transfer Enhancement 123 5.2.1 Electromagnetic Enhancement 124 5.2.2 Charge Transfer or Chemical Enhancement 128 5.2.3 Stages in the SERS Process 133 5.3 Surface Enhanced Resonance Raman Scattering (SERRS) 134 5.4 Selection Rules 135 5.5 Surface Chemistry 137 5.6 Substrates 139 5.7 Quantitation and Multiplex Detection 145 5.8 Summary 147 Chapter 6 Applications 151 6.1 Introduction 151 6.2 Inorganics and Minerals and Environmental Analysis 151 6.3 Art and Archaeology 156 6.4 Polymers and Emulsions 158 6.4.1 Overview 158 6.4.2 Simple Qualitative Polymer Studies 158 6.4.3 Quantitative Polymer Studies 162 6.5 Dyes and Pigments 163 6.5.1 Raman Colour Probes 163 6.5.2 In Situ Analysis 164 6.5.3 Raman Studies of Tautomerism in Azo Dyes 167 6.5.4 Polymorphism in Dyes 168 6.6 Electronics Applications 169 6.7 Biological and Clinical Applications 174 6.7.1 Introduction 174 6.8 Pharmaceuticals 176 6.9 Forensic Applications 180 6.10 Process Analysis and Reaction Following 183 6.10.1 Introduction 183 6.10.2 Electronics and Semiconductors 183 6.10.3 PCl3 Production Monitoring 184 6.10.4 Anatase and Rutile Forms of Titanium Dioxide 184 6.10.5 Polymers and Emulsions 185 6.10.6 Pharmaceutical Industry 186 6.10.7 Solid‐Phase Organic Synthesis/Combinatorial Chemistry 186 6.10.8 Fermentations 188 6.10.9 Gases 188 6.10.10 Catalysts 188 6.10.11 Nuclear Industry 191 6.11 Summary 191 Chapter 7 More Advanced Raman Scattering Techniques 199 7.1 Introduction 199 7.2 Flexible Optics 200 7.3 Spatial Resolution 204 7.4 Pulsed and Tunable Lasers 207 7.5 Tip‐Enhanced Raman Scattering and SNOM 214 7.6 Single‐Molecule Detection 216 7.7 Time‐Resolved Scattering 218 7.8 Fluorescence Rejection 222 7.9 Raman Optical Activity 222 7.10 UV Excitation 223 7.11 Summary 227 Appendix A Table of Inorganic Band Positions 229 Index 233

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Book SynopsisAPPLICATION OF AMBIENT PRESSURE X-RAY PHOTOELECTRON SPECTROSCOPY TO CATALYSIS Authoritative and detailed reference on ambient-pressure x-ray photoelectron spectroscopy for practitioners and researchers starting in the field Application of Ambient Pressure X-ray Photoelectron Spectroscopy to Catalysis introduces a relatively new analytical method and its applications to chemistry, energy, environmental, and materials sciences, particularly the field of heterogeneous catalysis, covering its background and historical development, its principles, the instrumentation required to use it, analysis of data collected with it, and the challenges it faces. The features of this method are described early in the text; the starting chapters provide a base for understanding how AP-XPS tracks crucial information in terms of the surface of a catalyst during catalysis. The second half of this book delves into the specific applications of AP-XPS to fundamental studies of diTable of ContentsPreface ix 1 From Surface of Model Catalyst in UHV to Surface of Nanoparticle Catalyst During Catalysis 1 2 Application of XPS: from Surface in UHV to Surface in Gas or Liquid Phase 7 2.1 Origin of X-ray Photoelectron Spectroscopy 7 2.2 Applications of XPS to Study Surface in High Vacuum 8 2.3 Applications of XPS to Study Sample in Gas Phase 8 2.4 Applications of XPS to Study Sample in Liquid Phase 8 3 Fundamentals of X-ray Photoelectron Spectroscopy 19 3.1 Principle of XPS 19 3.2 Generation of X-ray 32 3.3 Excitation of Photoelectron and Chemical Shift 36 3.4 Measurements of Energy of Photoelectrons 48 3.5 Measurements of Intensity of Photoelectrons 49 4 Instrumentation of XPS 51 4.1 Regular X-ray Source 51 4.2 X-ray Source with a Monochromator 53 4.3 Energy Analyzer 58 4.4 Detector 63 5 Significance and Challenge of Studying Surface of a Catalyst in Gaseous Phase 67 5.1 Origin of Difference between Surface in UHV and Surface in Reactant Gas 67 5.2 Intrinsic Feature of Catalytic Sites on Surface: Environmental Sensitivity 68 5.3 Ex Situ, Semi-in Situ, and In Situ/Operando Studies of Catalyst Surface at Ambient Pressure of Reactants 69 5.4 Ex Situ, Semi-in Situ, and In Situ/Operando Studies of Catalyst Structure at High Pressure 76 5.5 Technical Challenges in Studying Surface of a Catalyst in Gas Phase 77 6 Instrumentation of Ambient Pressure X-ray Photoelectron Spectrometer 81 6.1 X-ray Source for AP-XPS Studies 81 6.2 Reaction Cell with Capability of Flowing Gas 87 6.3 Differential Pumping Energy Analyzer with High Transmission 96 6.4 Mass Spectrometer with Capability of Measurement of Catalytic Performance 97 7 Experimental Methods of AP-XPS Studies 103 7.1 Leak Test of Reaction Cell 103 7.2 Exclusion of Catalysis by Reaction Cell 103 7.3 Tunning and Control of Sample-Aperture Distance 104 7.4 Sample Heating and Temperature Control 108 7.5 Online Measurement of Reactants and Products 108 7.6 Spectroscopic Titration of Surface Species 110 8 Difference in Data Analysis Between AP-XPS and High Vacuum XPS 113 8.1 Potential Difference in Measuring Atomic Ratio of Two Elements on Catalyst Surface 113 8.2 Difference in Intensity of Photoelectrons Collected by Energy Analyzer 114 8.3 Difference in Resolution and Baseline of Spectrum 114 8.4 Difference in Spectrum between Free Molecules in Gas and Adsorbed Molecules on Surface 116 8.5 Calibration of Nominal Atomic Ratio A/Z of a Catalyst Surface in a Pure Gas 118 8.6 Calibration of Nominal Atomic Ratio A/Z of a Catalyst Surface in a Mixture of Reactants 122 8.7 Calibration of Nominal Atomic Ratio A/Z of a Catalyst Surface in a Pure Gas Obtained at Different Temperature for Fair Comparison 123 9 Significance of Using AP-XPS in Studies of Catalysis 127 9.1 Fundamental of Catalyst Surface 127 9.2 Significance of Characterization of Surface of a Catalyst in Gas Phase 128 9.3 Significance of Using AP-XPS in Fundamental Studies of Catalysis 129 10 CO Oxidation on Single Crystal Model Catalysts 131 10.1 Pt(557) and Pt(332) in CO 131 10.2 CO Oxidation on Pd(100), Pd(111), and Pd(110) 136 10.3 CO Oxidation on Pt(110) and Pt(111) 144 10.4 CO Oxidation on Rh(110) 149 10.5 CO Oxidation on Cu(111) 153 11 CO Oxidation on High Surface Area Catalysts 157 11.1 CO Oxidation on Rh Nanoparticles 157 11.2 CO Oxidation on Ru Nanoparticles 161 12 Hydrogenation of Carbon Dioxide 165 13 Water--Gas Shift 171 13.1 Co3O4 and Pt/Co3O4 171 13.2 Pt, Au, Pd, and Cu Supported on CeO2 Nanorods 175 13.3 CuO--Cr2O3--Fe2O3 179 14 Complete Oxidation of Methane 185 14.1 Complete Oxidation of Methane on NiCo2O4 185 14.2 Complete Oxidation of Methane on NiFe2O4 188 14.3 Complete Oxidation of Methane on NiO with Different Surface Structures 195 15 Partial Oxidation of Methanol 203 15.1 Partial Oxidation of Methanol on Pd1Zn3/ZnO 203 15.2 Partial Oxidation of Methanol on Ir1Zn3/ZnO 207 16 Partial Oxidation of Methane 211 16.1 Partial Oxidation of Methane on Pd/CeO2 211 16.2 Partial Oxidation of Methane on Pt/CeO2 215 16.3 Partial Oxidation of Methane on Rh/CeO2 218 17 Oxidative Coupling of Methane 223 17.1 OCM on Supported Na2WO4 and Hypothesized Active Phase Na2O2 223 17.2 First Observation of Na2O2 through AP-XPS Studies at 800 °C 224 17.3 Formation of a Thin Layer of Na2O2 Supported on Na2WO4 227 18 Dry and Steam Reforming of Methane 231 18.1 Dry Reforming of CH4 on CeO2 Anchored with Ni1 and Ru1 Sites 231 18.2 Steam Reforming of CH4 on CeO2 Anchored with Ni1 and Ru1 Single-atom Sites 237 19 Reduction of NO with CO 243 19.1 Reduction of NO with CO on Co3O4 243 19.2 Reduction of NO with CO on Rh1Co3 Clusters Supported on CoO 247 20 Tuning Catalyst Surfaces for Developing Catalysts 253 20.1 Capability of Compositional Restructuring Checkable with AP-XPS 253 20.2 Tracking Restructuring of Bimetallic Surface under Reaction and Catalytic Conditions for Tuning Catalytic Performance of a Bimetallic Catalyst 255 21 Photocatalysis 263 References 268 Index 271

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Book SynopsisThis book offers a practical guide to the technique and applications of x-ray absorption spectroscopy that helps investigators choose the right experiment, carry it out properly, and analyse the data to obtain the most reliable result. The text gives readers crucial insights into the world of large scale experimental facilities like synchrotrons.Table of ContentsAbout the Author ix Preface xi Acknowledgments xiii Glossary and Abbreviations xv 1 Introduction to X]Ray Absorption Fine Structure (XAFS) 1 1.1 Materials: Texture and Order 1 1.2 Absorption and Emission of X]Rays 2 1.3 XANES and EXAFS 2 1.4 Information Content 3 1.5 Using X]Ray Sources as They Were 4 1.6 Using Light Sources Now and To Be 5 1.7 Questions 7 References 8 2 Basis of XAFS 9 2.1 Interactions of X]Rays With Matter 9 2.1.1 Absorption Coefficients 9 2.1.2 Absorption Edges 10 2.1.3 XANES and EXAFS 12 2.1.3.1 XANES Features 13 2.1.3.2 Edge Position 16 2.1.3.3 The EXAFS Effect 19 2.1.3.4 EXAFS Quantification 21 2.2 Secondary Emissions 24 2.2.1 X]Ray Fluorescence 26 2.2.2 Electron Emission 28 2.2.3 Resonant Inelastic X]Ray Scattering or Spectroscopy (RIXS) 29 2.3 Effects of Polarization 30 2.3.1 Plane (Linear) Polarization 30 2.3.2 Circular Polarization 30 2.3.3 Magnetic Dichroism 30 2.4 Questions 31 References 32 3 X]Ray Sources and Beamlines 33 3.1 Storage Rings 33 3.1.1 Second] and Third]Generation Sources 33 3.1.2 Bending Magnet Radiation 34 3.1.3 Insertion Devices 38 3.1.3.1 Wavelength Shifters and Multipole Wigglers 38 3.1.3.2 Planar Undulators 38 3.1.3.3 Helical Undulators 41 3.1.4 Time Structure 41 3.2 Other Sources 43 3.2.1 Laboratory Sources 43 3.2.2 Plasma Sources 44 3.2.3 High Harmonic Generation 44 3.2.4 Free Electron Lasers (FELs) 44 3.3 Beamline Architecture 45 3.3.1 Mirrors 48 3.3.2 Monochromators 49 3.3.3 Near]Sample Focusing Elements 55 3.3.3.1 Kirkpatrick]Baez (KB) Mirrors 55 3.3.3.2 X]Ray Lenses 56 3.3.3.3 Zone Plates 56 3.4 Effect of Photon Energy on Experiment Design 57 3.5 Questions 58 References 59 4 Experimental Methods 61 4.1 Sample Characteristics 62 4.1.1 X]Ray Absorption of Samples 62 4.1.2 Classes of Experimental Layouts 63 4.2 Scanning Modes 64 4.2.1 Scanning XAFS 64 4.2.2 Energy Dispersive XAFS 66 4.3 Detection Methods 67 4.3.1 Transmission 67 4.3.2 Electron Yield 74 4.3.3 Fluorescence 76 4.3.3.1 Total Fluorescence Yield 79 4.3.3.2 High]Resolution Fluorescence Detection (HERFD) and X]Ray Emission Spectroscopy (XES) 86 4.3.3.3 Resonant Inelastic X]Ray Scattering or Spectroscopy (RIXS) 90 4.3.3.4 Inelastic X]Ray Raman Scattering (XRS) or Nonresonant Inelastic X]Ray Scattering (NIXS) 91 4.3.4 X]Ray Excited Optical Luminescence (XEOL) 94 4.4 Spatial Resolution 95 4.4.1 Methods of Studying Textured Materials 95 4.4.2 Full]Field Transmission X]Ray Microscopy (TXM) 96 4.4.3 X]Ray Photoelectron Emission Microscopy (X]PEEM) 99 4.4.4 Focused]Beam Microscopies 100 4.4.4.1 Scanning Micro] and Nano]Focus Microscopy 100 4.4.4.2 Scanning (Transmission) X]Ray Microscopy (STXM) 102 4.5 Combining Techniques 103 4.5.1 Two]Color XAFS 103 4.5.2 X]Ray Scattering 104 4.6 X]Ray Free Electron Lasers (XFELs) 106 4.6.1 Laser]Pump Measurements 107 4.6.2 Sampling Environments 108 4.6.3 X]Ray Beam Intensity 109 4.6.4 XAS and XES 109 4.7 Questions 110 References 111 5 Data Analysis and Simulation Methods 117 5.1 Background Subtraction 119 5.1.1 Experimental Considerations 119 5.1.2 Background Subtraction Procedures 121 5.2 Compositional Analysis 123 5.2.1 Single Energy Comparisons 123 5.2.2 Least Squares Analysis 124 5.2.3 Principal Component Analysis 126 5.2.4 Mapping Procedures 129 5.3 Structural Analysis 130 5.3.1 EXAFS Analysis 130 5.3.1.1 Distance Measurement 132 5.3.1.2 Angle Estimation 133 5.3.1.3 Coordination Number Estimation 138 5.3.1.4 Speciation of Back]Scattering Elements 140 5.3.1.5 Goodness of Fit 143 5.3.2 XANES Simulations 145 5.3.2.1 K Edge XANES 145 5.3.2.2 L Edge XANES 146 5.3.3 XES and RIXS Simulations 150 5.4 Present To Future Opportunities 153 5.5 Questions 154 References 155 6 Case Studies 163 6.1 Chemical Processing 164 6.1.1 Liquid Phase Reactions 164 6.1.1.1 Steady State or Slow Reactions (Minutes]Hours) 165 6.1.1.2 Fast Reactions (Ms to Minutes) 166 6.1.1.3 Very Fast Reactions (~100 ps – ms) 173 6.1.1.4 Ultrafast Reactions (fs – ps) 177 6.1.2 Reactions of Solid]State Materials 178 6.1.2.1 Steady]State or Slow Reactions (Minutes]Hours) 179 6.1.2.2 Fast Reactions (Ms to Minutes) 181 6.2 Functional Materials 184 6.3 Imaging on Natural, Environmental, and Heritage Materials 186 6.4 Questions 191 References 193 Index 197

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Book SynopsisProton Transfer Reaction Mass Spectrometry (PTR-MS) is a rapidly growing analytical technique for detecting and identifying very small quantities of chemical compounds in air. It has seen widespread use in atmospheric monitoring and food science and shows increasing promise in applications such as industrial process monitoring, medical science and in crime and security scenarios. Written by leading researchers, this is the first book devoted to PTR-MS and it provides a comprehensive account of the basic principles, the experimental technique and various applications, thus making this book essential reading for researchers, technicians, postgraduate students and professionals in industry. The book contains nine chapters and is divided into two parts. The first part describes the underlying principles of the PTR-MS technique, including the relevant ion-molecule chemistry thermodynamics and reaction kinetics a discussion of ion sources, drifTable of ContentsQuotation xiii Preface xv SECTION 1 FUNDAMENTALS 1 Background 3 1.1 Volatile Organic Compounds in the Earth’s Atmosphere 3 1.2 Volatile Organic Compounds in Other Environments 5 1.3 Techniques for VOC Measurements 6 1.4 Emergence of Proton Transfer Reaction Mass Spectrometry 15 References 23 2 Chemical Ionization: Chemistry, Thermodynamics and Kinetics 25 2.1 Introduction 25 2.2 Proton Transfer 27 2.3 Other Chemical Ionization Processes 44 References 45 3 Experimental: Components and Principles 49 3.1 Introduction 49 3.2 Ion Extraction and Ion Optics 50 3.3 Ion Sources 57 3.4 Drift Tubes 64 3.5 Mass Spectrometry 76 3.6 Ion Detectors 97 3.7 Analogue versus Digital Signal Processing 103 References 106 4 Quantitative Analysis 111 4.1 Introduction 111 4.2 Extracting the Concentration of a Trace Gas from PTR-MS 111 4.3 Normalized Counts per Second 112 4.4 Why Calibrate? 113 4.5 Calibration Techniques 116 4.6 Effect of Humidity 120 4.7 Accuracy, Precision and Limit of Detection 122 4.8 Validation of PTR-MS 125 References 126 SECTION 2 APPLICATIONS 5 PTR-MS in the Environmental Sciences 131 5.1 Background 131 5.2 Use of Reagent Ions Other Than H3O+ 138 5.3 Biogenic VOCs 141 5.4 Anthropogenic VOCs 156 5.5 Biomass Burning 166 5.6 Applications of PTR-MS to Laboratory Studies of Atmospheric Chemistry 169 5.7 Plant Studies 178 5.8 Outlook for Atmospheric and Environmental Applications of PTR-MS 201 References 201 6 PTR-MS in the Food Sciences 219 6.1 Background 219 6.2 Combined GC–MS and PTR-MS Studies for Food Analysis 221 6.3 Mass Spectral Fingerprinting 224 6.4 Flavour Release and Perception 225 6.5 Food Classification, Food Quality and Food Control 243 6.6 Outlook for Food Science and Technology Applications 254 References 255 7 PTR-MS in the Medical Sciences 265 7.1 Background 265 7.2 Breath Analysis 266 7.3 Online PTR-MS Measurements of Volatile Emissions from Microbial Cultures 288 7.4 Other Medical Applications 295 References 300 8 Applications of PTR-MS to Homeland Security: The Detection of Threat Agents 309 8.1 Background 309 8.2 Explosives 310 8.3 Chemical Warfare Agents and Toxic Industrial Chemicals 319 8.4 Narcotics 320 8.5 Date Rape Drugs 323 8.6 Ion Mobility Mass Spectrometry and PTR-MS: A Brief Comparison for Homeland Security Applications 324 8.7 Future Directions 325 References 326 9 Liquid Analysis Using PTR-MS 329 9.1 Determination of Henry’s Law Constants Using PTR-MS 329 9.2 Analysis of Liquids 331 References 334 Index

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Book SynopsisCavity Ring-Down Spectroscopy: Techniques and Applications provides a practical overview of this valuable analytical tool, explaining the fundamental concepts and experimental methods, and illustrating important applications. Designed as both an introductory text and a reference source, this book is relevant for scientists unfamiliar with CRDS who are interested in using the technique in their research, as well as experienced users.Trade Review"Explain[s] introductory concepts and basic experimental techniques; useful variants such as continuous wave, phase shift, and broadband CRDS; and developments and applications." (Book News, December 2009) It is undoubtedly a good reference to have in the lab where CRDS experiments are done. Given the wide range of areas where CRDS and its variants are being applied, it seems likely that this book will generate broad interest in the chemical (and other scientific) communities. (JACS, January 2010)Table of ContentsPreface List of contributors Glossary Chapter 1 - An introduction to cavity ring-down spectroscopy 1.1 Introduction 1.2 Direct absorption spectroscopy 1.3 Basic cavity ring down spectroscopy setup 1.4 A more refined picture 1.5 Fitting of cavity ring down transients 1.6 A few examples 1.7 Going beyond the standard pulsed CRDS experiment 1.8 Summary 1.9 References Chapter 2 - Cavity enhanced techniques using continuous wave lasers 2.1 Introduction 2.1 Properties of optical cavities and cw lasers relevant to cavity enhanced spectroscopy 2.3 Experimental methods for cw laser cavity enhanced spectroscopy 2.4 Spectroscopy with resonant cavities 2.5 Summary Chapter 3 - Broadband cavity ring-down spectroscopy 3.1 Introduction. 3.2 The time and wavelength evolution of a single ringdown event. 3.3 Two dimensional techniques: resolving broadband cavity output in time and wavelength. 3.4 One dimensional techniques: time or wavelength. 3.5 How to extract quantitative information from broadband spectra. 3.6 Optimising the sensitivity of a broadband measurement. 3.7 Applications of broadband cavity methods. 3.8 References. Chapter 4 - Cavity ring-down spectroscopy in analytical chemistry 4.1 Introduction 4.2 Condensed media CRDS 4.3 Evanescent-wave CRDS 4.4 Future trends and perspectives Chapter 5 - Cavity ring-down spectroscopy using waveguides 5.1. Introduction 5.2. The basic experiments 5.3. Optics and Instrumentation 5.4. Review of waveguide CRD literature 5.5. Conclusion and outlook 5.6. Acknowledgements Chapter 6 - Cavity ring down spectroscopy of molecular transients of astrophysical interest 6.1. Introduction 6.2. Experimental 6.3. Astronomical considerations 6.4. Results 6.5. Outlook Acknowledgements References Chapter 7 - Applications of cavity ring-down spectroscopy in atmospheric chemistry 7.1. Brief overview 7.2. Measurement of trace atmospheric species by CRDS 7.3. Laboratory based studies of atmospheric interest 7.4. Optical properties of atmospheric aerosol particles 7.5. Future developments Chapter 8 - Cavity ring-down spectroscopy for medical applications 8.1. Introduction 8.2. Trace gases in medicine and biology 8.3. Instrumentation for laser analytics of breath and other biological gas samples 8.4. Applications to life sciences 8.5. Conclusion and Perspectives 8.6. References Chapter 9: Studies into the growth mechanism of a-Si:H using in situ cavity ring-down techniques 9.1. Introduction 9.2. Gas phase CRDS on SiHx­ radicals 9.3. Thin film CRDS on dangling bonds in a-Si:H films (ex situ) 9.4. Evanescent wave CRDS on dangling bonds during a-Si:H film growth Chapter 10 – Cavity ring down spectroscopy for combustion studies 10.1. Introduction 10.2. General description of cavity ring down spectroscopy in flames 10.3. Experimental set-up 10.4. Quantitative concentration measurements in flames 10.5. Concentration profile determination 10.6. Specific difficulties in combustion studies 10.7. Case of particles: soot volume fraction determination 10.8. Conclusion and prospective References Appendix A Literature

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Book SynopsisWidely used in medical research, pharmaceutical and fine chemicals industries, biological and physical sciences, and security and environmental agencies, mass spectrometry techniques are continually under development. In Practical Aspects of Trapped Ion Mass Spectrometry: Volume V, Applications of Ion Trapping Devices, an international panel of authors presents a world-wide view of the practical aspects of recent progress using trapped ion devices.In contrast to previous texts, which have concentrated generally on a single or limited range of ion trapping techniques, a key feature of this compilation of contributions is its coverage of all the ion trapping techniques currently in use. Spanning sixteen chapters, the text examines: Ion/neutral and ion/ion reactions Structural characterization of proteins and peptides using quadrupole ion trap mass spectrometry, Fourier transform ion cyclotron resonance (FT-ICR) mass spectromTable of ContentsIon Reactions. Ion/Ion Reactions in Electrodynamic Ion Traps. Gas-Phase Hydrogen/Deuterium Exchange in Quadrupole Ion Traps. Methods for Multi-Stage Ion Processing Involving Ion/Ion Chemistry in a Quadrupole Linear Ion Trap. Ion Conformation and Structure. Chemical Derivatization and Multistage Tandem Mass Spectrometry for Protein Structural Characterization. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry in the Analysis of Peptides and Proteins. MS/MS Analysis of Peptide-Polyphenols Supramolecular Assemblies: Wine Astringency Approached by ESI-IT-MS. Structure and Dynamics of Trapped Ions. Applications of Traveling Wave Ion Mobility-Mass Spectrometry. Ion Spectroscopy. The Spectroscopy of Ions Stored in Trapping Mass Spectrometers. Sympathetically-Cooled Single Ion Mass Spectrometry. Ion Trap: A Versatile Tool for the Atomic Clocks of the Future! Practical Applications. Boundary-Activated Dissociations (BAD) in a Digital Ion Trap (DIT). The Study of Ion/Molecule Reactions at Ambient Pressure with Ion Mobility Spectrometry and Ion Mobility/Mass Spectrometry.The Role of Trapped Ion Mass Spectrometry for Imaging.Technology Progress and Application in GC/MS and GC/MS/MS. Remote Monitoring of Volatile Organic Compounds in Water by Membrane Inlet Mass Spectrometry. Index.

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Book SynopsisSince the completion of the first edition of this book, major developments have occurred in the pharmaceutical industry that have shaped the field of near-infrared (NIR) spectroscopy. A new initiative from the U.S. Food and Drug Administration (FDA) to modernize regulations of pharmaceutical manufacturing and drug quality has helped position NIR spectroscopy as an effective tool for pharmaceutical testing. Pharmaceutical and Medical Applications of Near-Infrared Spectroscopy: Second Edition reflects these developments and brings readers an up-to-date summary of how this technique is being applied to pharmaceutical manufacturing.Topics include: The origins and principles of NIR spectroscopy, including early instrumentation, spectroscopic theory, and light-particle interaction The physics of each instrument type, the strengths and weaknesses of each, and the manufacturers that produce them <Table of ContentsBasic principles and theory. History. Early instrumentation. Spectroscopic theory. Light-particle interaction. Instrumentation. Filter-based instruments. Scanning grating monochromators. Interferometer-based instruments. Acousto-optic tunable filters. Photodiode arrays. Specialty and custom instruments. Optical parameter instrumentation. Strengths and shortcomings of traditional types of equipment. Blend uniformity analysis. Mixing. Discussion of reported work. Sampling and data handling. Segregation, Demixing, and Particle Size. Granulation, Drying, and Coating. Monitoring Granulation and Drying. Coating and Pelletization. Pharmaceutical assays. Qualitative analysis. Quantitative analysis. Determination of actives in tablets and capsules. Considerations for intact dosage form analysis. Validation issues. International conference on harmonization. Historical perspective. Medical applications. Blood glucose. Blood oxygenation. Tissue. Major organs. Blood chemistry. Fetuses and newborns. Cancer and precancer. Photon migration in tissues. Review articles. Index.

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Book SynopsisDrawing on the author's practical work from the last 20 years, Techniques in High Pressure Neutron Scattering is one of the first books to gather recent methods that allow neutron scattering well beyond 10 GPa. The author shows how neutron scattering has to be adapted to the pressure range and type of measurement.Suitable for both newcomers and experienced high pressure scientists and engineers, the book describes various solutions spanning two to three orders of magnitude in pressure that have emerged in the past three decades. Many engineering concepts are illustrated through examples of real high pressure devices that have demonstrated their capacity and have produced scientific results.After introducing basic engineering concepts related to the elastic and plastic behavior of cylindrical pressure devices, the text emphasizes mechanical and neutronic properties of construction materials. Subsequent chapters describe numerous high pressTrade ReviewI was delighted when I learnt that Stefan Klotz was writing this book. He has an exceptional depth of knowledge and experience of high-pressure techniques, particularly as applied to neutron scattering, and it is to be greatly welcomed that he has drawn this all together and made it available. … After his 20 years at the centre of this field, there can be no one better placed to provide an authoritative and comprehensive account of state-of-the-art techniques for high-pressure neutron scattering, including all the major contemporary experimental techniques. Those who have benefited from his direct advice and assistance will know the high-level practical and intuitive skills he brings to bear on solving technical problems and advancing innovation. Throughout the book, he has included a large amount of the wealth of practical experience, working recipes and ‘rules of thumb’ that he has accumulated, working on his own research and with collaborators, but which has never before been gathered together and published in this accessible way.—From the Foreword by Richard Nelmes, University of EdinburghI was delighted when I learnt that Stefan Klotz was writing this book. He has an exceptional depth of knowledge and experience of high-pressure techniques, particularly as applied to neutron scattering, and it is to be greatly welcomed that he has drawn this all together and made it available. … After his 20 years at the centre of this field, there can be no one better placed to provide an authoritative and comprehensive account of state-of-the-art techniques for high-pressure neutron scattering, including all the major contemporary experimental techniques. Those who have benefited from his direct advice and assistance will know the high-level practical and intuitive skills he brings to bear on solving technical problems and advancing innovation. Throughout the book, he has included a large amount of the wealth of practical experience, working recipes and ‘rules of thumb’ that he has accumulated, working on his own research and with collaborators, but which has never before been gathered together and published in this accessible way.—From the Foreword by Richard Nelmes, University of EdinburghTable of ContentsBasic Concepts. Construction Materials I: Nonferrous Alloys. Construction Materials II: Steels and Super-Alloys. Construction Materials III: Sinter Materials. Liquid/Gas and Clamp Pressure Cells. McWhan-Type Cells. Sapphire, Moissanite and Diamond Anvil Cells. Special Designs. Uniaxial Pressure Cells. Paris-Edinburgh Cells I. Paris-Edinburgh Cells II: Low and High Temperatures. Paris-Edinburgh Cells III: Ancillary Equipment. Pressure Determination and Pressure Transmitting Media. Applications. Appendices. Bibliography. Index.

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Book SynopsisThe Focused Ion Beam Instrument.- Ion - Solid Interactions.- Focused Ion Beam Gases for Deposition and Enhanced Etch.- Three-Dimensional Nanofabrication Using Focused Ion Beams.- Device Edits and Modifications.- The Uses of Dual Beam FIB in Microelectronic Failure Analysis.- High Resolution Live Imaging of FIB Milling Processes for Optimum Accuracy.- FIB for Materials Science Applications - a Review.- Practical Aspects of FIB Tem Specimen Preparation.- FIB Lift-Out Specimen Preparation Techniques.- A FIB Micro-Sampling Technique and a Site Specific TEM Specimen Preparation Method.- Dual-Beam (FIB-SEM) Systems.- Focused Ion Beam Secondary Ion Mass Spectrometry (FIB-SIMS).- Quantitative Three-Dimensional Analysis Using Focused Ion Beam Microscopy.- Application of FIB in Combination with Auger Electron Spectroscopy.Table of ContentsThe Focused Ion Beam Instrument.- Ion - Solid Interactions.- Focused Ion Beam Gases for Deposition and Enhanced Etch.- Three-Dimensional Nanofabrication Using Focused Ion Beams.- Device Edits and Modifications.- The Uses of Dual Beam FIB in Microelectronic Failure Analysis.- High Resolution Live Imaging of FIB Milling Processes for Optimum Accuracy.- FIB for Materials Science Applications - a Review.- Practical Aspects of FIB Tem Specimen Preparation.- FIB Lift-Out Specimen Preparation Techniques.- A FIB Micro-Sampling Technique and a Site Specific TEM Specimen Preparation Method.- Dual-Beam (FIB-SEM) Systems.- Focused Ion Beam Secondary Ion Mass Spectrometry (FIB-SIMS).- Quantitative Three-Dimensional Analysis Using Focused Ion Beam Microscopy.- Application of FIB in Combination with Auger Electron Spectroscopy.

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Book SynopsisThis concise and carefully developed text offers a reader friendly guide to the basics of time-resolved spectroscopy with an emphasis on experimental implementation. The authors carefully explain and relate for the reader how measurements are connected to the core physical principles. They use the time-dependent wave packet as a building block for understanding quantum dynamics, progressively advancing to more complex topics. The topics are discussed in paired sections, one discussing the theory and the next presenting the related experimental methods.A wide range of readers including students and newcomers to the field will gain a clear and practical understanding of how to measure aspects of molecular dynamics such as wave packet motion, intramolecular vibrational relaxation, and electron-electron coupling, and how to describe such measurements mathematically.Trade Review"Weinacht and Pearson have produced a simple and direct introduction to the modern methods and motivations of ultrafast science, intended as a first text for students and scholars interested in this field. The chapter sections interleave physical concepts such as wave packets, correlated motion, or quantum tunneling with clear descriptions of the techniques that ultrafast optical scientists have developed in the last two decades, including the sources and tools of the trade. The result is an excellent introduction and practical guide to time resolved measurements." --Philip H. Bucksbaum, Marguerite Blake Wilbur Chair and Professor of Photon Science, Applied Physics, and Physics, Stanford University"How do I measure a ‘molecular movie’? Which observables do I obtain and how can they be interpreted? To answer these questions, a deeper understanding of the physics and the underlying models and assumptions, as well as the experimental techniques is essential. This is exactly the aim of this clearly written textbook. So far, no textbook exists that focuses on a time-dependent perspective accessible for both theoreticians and experimentalists. It succeeds in improving the common level of basic understanding of (quantum) dynamical models and experimental techniques…an excellent textbook" --Prof. Dr. Stefanie Gräfe, Institute of Physical Chemistry, Abbe Center for Photonics, Jena University "An excellent, well-written and easy to read text. The approach is insightful, nicely blending intuitive physical pictures with sufficient mathematical formalism to enable calculations of real quantities of interest. The authors explain what information can be extracted from a variety of standard measurement techniques, including strengths and weaknesses of the various methods. I do not see a comparable book out there. I recommend it highly, not only for lecture courses on ultrafast spectroscopy and/or molecular dynamics, but as a primer for undergraduate and graduate students as they begin research projects in these areas. I intend to make it standard reading for students joining my group." --Robert R. Jones, Department Chair and Francis H. Smith Professor of Physics, University of Virginia"Weinacht and Pearson have produced a simple and direct introduction to the modern methods and motivations of ultrafast science, intended as a first text for students and scholars interested in this field. The chapter sections interleave physical concepts such as wave packets, correlated motion, or quantum tunneling with clear descriptions of the techniques that ultrafast optical scientists have developed in the last two decades, including the sources and tools of the trade. The result is an excellent introduction and practical guide to time resolved measurements." --Philip H. Bucksbaum, Marguerite Blake Wilbur Chair and Professor of Photon Science, Applied Physics, and Physics, Stanford University"How do I measure a ‘molecular movie’? Which observables do I obtain and how can they be interpreted? To answer these questions, a deeper understanding of the physics and the underlying models and assumptions, as well as the experimental techniques is essential. This is exactly the aim of this clearly written textbook. So far, no textbook exists that focuses on a time-dependent perspective accessible for both theoreticians and experimentalists. It succeeds in improving the common level of basic understanding of (quantum) dynamical models and experimental techniques…an excellent textbook" --Prof. Dr. Stefanie Gräfe, Institute of Physical Chemistry, Abbe Center for Photonics, Jena University"An excellent, well-written and easy to read text. The approach is insightful, nicely blending intuitive physical pictures with sufficient mathematical formalism to enable calculations of real quantities of interest. The authors explain what information can be extracted from a variety of standard measurement techniques, including strengths and weaknesses of the various methods. I do not see a comparable book out there. I recommend it highly, not only for lecture courses on ultrafast spectroscopy and/or molecular dynamics, but as a primer for undergraduate and graduate students as they begin research projects in these areas. I intend to make it standard reading for students joining my group." --Robert R. Jones, Department Chair and Francis H. Smith Professor of Physics, University of VirginiaTable of ContentsContentsPreface ixAuthors xiPart I Introduction and Background 1Chapter 1 Introduction 3Chapter 2 Molecular Structure 11Chapter 3 Light–Matter Interaction 41Chapter 4 Introduction to Experimental Techniques 63Part II Quantum Dynamics in One Dimension 73Chapter 5 Field-Free Dynamics 75Chapter 6 Field-Driven Dynamics 93Part III Measurements of One Dimensional Dynamics 113Chapter 7 Incoherent Measurements in 1D 115Chapter 8 Coherent Optical Measurements in 1D 141Chapter 9 Coherent Diffractive Measurements in 1D 165Part IV Quantum Dynamics in Multiple Dimensions 183Chapter 10 Explicit Approach to N-D Dynamics 185Chapter 11 Implicit Approaches to N-D Dynamics 205Part V Measurements of Multidimensional Dynamics 215Chapter 12 Incoherent Measurements in ND 217Chapter 13 Coherent Optical Measurements in ND 241Chapter 14 Coherent Diffractive Measurements in ND 275Chapter 15 One System, Multiple Approaches 283Appendix A Quantum Mechanics Essentials 297Appendix B Experimental Considerations 317Appendix C Additional Problems 325Bibliography 327Index 337

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Book SynopsisHigh resolution Fourier transform spectra of linear molecules have evoked a great deal of interest during the last several years, which could be seen from the several hundreds of papers published in the journal on the spectra of diatomic and small linear polyatomic molecules. This book describes the advantages of FT Spectroscopy, the techniques employed in absorption and emission spectroscopy, and presents the theoretical models and formulas used in the analyses and interpretation of the spectra. The Perturbations observed in the spectra due to Fermi, Darling-Dennison, Coriolis, and other anharmonic resonances; and vibrational and rotational l-type resonances etc. are discussed with suitable examples. The types of information obtained from FT spectroscopy of two to ten atomic linear molecules, their observed transitions and spectral perturbation etc. are presented along with figures and curves.

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