Fundamentals of Contemporary Mass Spectrometry by Chhabil Dass, Dominic Desiderio, and Nico Nibbering Hardcover - 585 pages Shipped in CLICK HERE Cat.# JW-SPE1 $129.05 BUY Published:  2007   ISBN:  9780471682295

Fundamentals of Contemporary Mass Spectrometry deftly explains mass spectrometry instrumentation and its application to analysis and identification of organic compounds, biological material, and inorganic compounds, as well as applications to quantitative analysis. The book is ideal for use as a textbook for graduate courses and is also a great reference for newcomers to mass spectrometry.

Table of Contents:

PART 1: INSTRUMENTATION

1. BASICS OF MASS SPECTROMETRY

1.1. A BRIEF HISTORY OF MASS SPECTROMETRY
1.2. UNIQUE FEATURES OF MASS SPECTROMETRY
1.3. BASIC PRINCIPLES OF MASS SPECTROMETRY
1.4. ANATOMY OF A MASS SPECTRUM
1.5. ATOMIC AND MOLECULAR MASSES

1.5.1. Mass-to-charge Ratio

1.6. GENERAL APPLICATIONS
1.7. OVERVIEW OF THE CHAPTER
1.8. EXERCISES
1.9. REFERENCES

2. MODES OF IONIZATION

2.1. WHY IONIZATION IS REQUIRED?
2.2. GENERAL CONSTRUCTION OF THE ION SOURCE

GAS-PHASE IONIZATION TECHNIQUES

2.3. ELECTRON IONIZATION
2.4. CHEMICAL IONIZATION

2.4.1. Charge-exchange Chemical Ionization
2.4.2. Negative-Ion Chemical Ionization

2.5. PHOTO IONIZATION
2.6. FIELD IONIZATION
2.7. METASTABLE ATOM BOMBARDMENT IONIZATION

CONDENSED-PHASE IONIZATION TECHNIQUES: IONIZATION OF SOLID-STATE SAMPLES

2.8. FIELD DESORPTION
2.9. PLASMA DESORPTION IONIZATION
2.10. SECONDARY-ION MASS SPECTROMETRY
2.11. FAST ATOM BOMBARDMENT
2.12. LASER DESORPTION/IONIZATION
2.13. MATRIX-ASSISTED LASER DESORPTION/IONIZATION

2.13.1. Analysis of Low Molecular Mass Compounds by MALDI
2.13.2. Atmospheric Pressure-MALDI
2.13.3. Surface-enhanced Laser Desorption/Ionization

CONDENSED-PHASE IONIZATION TECHNIQUES: IONIZATION OF LIQUID-STATE SAMPLES

2.14. THERMOSPRAY IONIZATION
2.15. ATMOSPHERIC PRESSURE CHEMICAL IONIZATION
2.16. ATMOSPHERIC PRESSURE PHOTO IONIZATION
2.17. ELECTROSPRAY IONIZATION

2.17.1. Mechanism of Electrospray Ionization
2.17.2. Sample Consideration
2.17.3. Nanoelectrospray Ionization

2.18. DESORPTION ELECTROSPRAY IONIZATION

2.18.1. DART Ion Source

2.19. OVERVIEW OF THE CHAPTER
2.19. EXERCISES
2.20. ADDITIONAL READING
2.21. REFERENCES

3. MASS ANALYSIS AND ION DETECTION

3.1. MASS RESOLUTION
3.2. KINETIC ENERGY OF IONS

MASS ANALYZERS

3.3. MAGNETIC SECTOR MASS SPECTROMETERS

3.3.1. Working Principle of a Magnetic Analyzer
3.3.2. Working Principle of an Electrostatic Analyzer
3.3.3. Working Principle of Double-Focusing Magnetic Sector Mass Spectrometers
3.3.4. Performance Characteristics

3.4. QUADRUPOLE MASS SPECTROMETERS

3.4.1. Working Principle
3.4.2. Performance Characteristics
3.4.3. RF-only quadrupole

3.5. TIME-OF-FLIGHT MASS SPECTROMETERS

3.5.1. Working Principle
3.5.2. Delayed Extraction of Ions
3.5.3. Reflectron TOF Instrument
3.5.4. Orthogonal Acceleration TOF Mass Spectrometer
3.5.5. Performance Characteristics

3.6. QUADRUPOLE ION TRAP MASS SPECTROMETERS

3.6.1. Working Principle
3.6.2. Operational Modes
3.6.3. Performance Characteristics

3.7. LINEAR ION TRAP MASS SPECTROMETERS

3.7.1. Rectilinear Ion Trap

3.8. FOURIER-TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETERS

3.8.1. Working Principle
3.8.2. Performance Characteristics

3.9. ORBITRAP MASS ANALYZER
3.10. ION MOBILITY MASS SPECTROMETERS
3.11. DETECTORS

3.11.1. Faraday Cup Detector
3.11.2. Electron Multipliers
3.11.3. Photomultiplier detectors
3.11.4. Post-acceleration Detectors
3.11.5. Low-temperature Calorimetric Detectors for High Mass Ions
3.11.6. Focal-plane Detectors

3.12. OVERVIEW OF THE CHAPTER
3. 13. EXERCISES
3. 14. ADDITIONAL READING
3.15. REFERENCES

4. TANDEM MASS SPECTROMETRY

4.1. BASIC PRINCIPLES OF TANDEM MASS SPECTROMETRY
4.2. TYPES OF SCAN FUNCTIONS
4.3. ION ACTIVATION AND DISSOCIATION

4.3.1. Collision-induced Dissociation
4.3.2. Surface-induced Dissociation
4.3.3. Absorption of Electromagnetic Radiations
4.3.4. Electron-capture Dissociation

4.4. REACTIONS IN TANDEM MASS SPECTROMETRY
4.5. TANDEM MASS SPECTROMETRY INSTRUMENTATION

4.5.1. Magnetic Sector Tandem Mass Spectrometers
4.5.2. Tandem Mass Spectrometry with Multiple Quadrupole Devices
4.5.3. Tandem Mass Spectrometry with Time-of-Flight Instruments
4.5.4. Tandem Mass Spectrometry with a Quadrupole Ion Trap Mass Spectrometer
4.5.5. Tandem Mass Spectrometry with an FT-ICR Mass Spectrometer
4.5.6. Tandem Mass Spectrometry with Hybrid Instruments

4.6. OVERVIEW OF THE CHAPTER
4.7. EXERCISES
4.7. ADDITIONAL READING
4.8. REFERENCES

5. HYPHENATED SEPARATION TECHNIQUES

5.1. BENEFITS OF THE COUPLING OF SEPARATION DEVICES WITH MASS SPECTROMETRY
5.2. GENERAL CONSIDERATIONS

5.2.1. Characteristics of an Interface
5.2.2. Mass Spectral Data Acquisition
5.2.3. Characteristics of Mass Spectrometers

5.3. CHROMATOGRAPHIC PROPERTIES
5.4. GAS CHROMATOGRAPHY/MASS SPCTROMETRY

5.4.1 Basic Principles of Gas Chromatography
5.4.2 Interfaces for the Coupling of Gas Chromatography with Mass Spectrometry

5.5. LIQUID CHROMATOGRAPHY/MASS SPECTROMETRY

5.5.1. Basic Principle of HPLC Separation
5.5.2 Fast-Flow Liquid Chromatography

5.6. INTERFACES FOR THE COUPLING OF LIQUID CHROMATO-GRAPHY WITH MASS SPECTROMETRY

5.6.1. The Moving-belt Interface
5.6.2. The Direct-Liquid Introduction Probe
5.6.3. The Continuous-Flow Fast Atom Bombardment Interface
5.6.4. The Thermospray Interface
5.6.5. The Particle-beam Interface
5.6.6. The Electrospray Ionization Interface
5.6.7. The Atmospheric Pressure Chemical Ionization Interface
5.6.8. The Atmospheric Pressure Photo ionization (APPI) Interface
5.6.9. The Coupling of LC with TOF-MS

5.6.10. The Coupling of LC with MALDI-MS
5.7. MULTI-DIMENSIONAL LC/MS
5.8. CAPILLARY ELECTROPHORESIS/MASS SPECTROMETRY

5.8.1. The Basic Principles of Capillary Electrophoresis
5.8.2. Interfaces for the Coupling of Capillary Electrophoresis with Mass Spectrometry

5.9. AFFINITY CHROMATOGRAPHY/MASS SPECTROMETRY
5.10. SUPERCRITICAL-FLUID CHROMATOGRAPHY/MASS SPECTROMETRY
5.11. THE COUPLING OF PLANAR CHROMATOGRAPHY WITH MASS SPECTROMETRY
5.12. OVERVIEW OF THE CHAPTER
5.13. EXERCISES
5.14. ADDITIONAL READING
5.15. REFERENCES

PART 2: ORGANIC AND INORGANIC MASS SPECTROMETRY

6. ORGANIC MASS SPECTROMETRY

6.1. DETERMINATION OF MOLECULAR MASS

6.1.1. Molecular Mass Measurements at Low-mass Resolving Power
6.1.2. Molecular Mass Measurements at High-mass Resolving Power
6.1.3. Molecular Mass Measurements by ESI and MALDI
6.1.4. Mass Calibration Standards

6.2. MOLECULAR FORMULA FROM ACCURATE MASS VALUES
6.3. MOLECULAR FORMULA FROM ISOTOPIC PEAKS
6.4. GENERAL GUIDELINES FOR THE INTERPRETATION OF A MASS SPECTRUM

6.4.1. Odd- and Even-electron Ions
6.4.2. Recognize the Molecular Ion
6.4.3. The Nitrogen Rule
6.4.4. The Rings Plus Double Bonds (R + DB) Value
6.4.5. Systematic Steps to Interpret a Mass Spectrum
6.4.6. Mass Spectral Compilations

6.5. FRAGMENTATION PROCESSES

6.5.1. Simple Bond-cleavage Reactions
6.5.2. Rearrangement Reactions
6.5.3. Fragmentation of Cyclic Structures
6.5.4. Differentiation of Isomeric Structures
6.5.5. Structurally Diagnostic Fragment Ions

6.6. FRAGMENTATION REACTIONS OF SPECIFIC CLASSES OF COMPOUNDS

6.6.1. Hydrocarbons

6.6. FRAGMENTATION REACTIONS OF SPECIFIC CLASSES OF COMPOUNDS

6.6.1. Hydrocarbons

6.6. FRAGMENTATION REACTIONS OF SPECIFIC CLASSES OF COMPOUNDS

6.6.1. Hydrocarbons
6.6.2. Alcohols
6.6.3. Ethers
6.6.4. Aldehydes and Ketones
6.6.5. Carboxylic Acids
6.6.6. Esters
6.6.7. Nitrogen-containing Compounds6.6.8. Sulfur-containing Compounds
6.6.8. Sulfur-containing Compounds
6.6.9. Halogen-containing Compounds

6.7. THEORY OF ION DISSOCIATION
6.8. STRUCTURE DETERMINATION OF GAS-PHASE ORGANIC IONS
6.9. OVERVIEW OF THE CHAPTER
6. 10. EXERCISES
6.11. ADDITIONAL READING
6.12. REFERENCES

7. INORGANIC MASS SPECTROMETRY

7.1. IONIZATION OF INORGANIC COMPOUNDS
7.2. THERMAL IONIZATION MASS SPECTROMETRY
7.3. SPARK-SOURCE MASS SPECTROMETRY (SSMS)
7.4. GLOW DISCHARGE IONIZATION MASS SPECTROMETRY
7.5. INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY

7.5.1. Inductively Coupled Plasma Ion Source
7.5.2. Coupling of the ICP Source with Mass Spectrometry
7.5.3. Sample Introduction Systems for the ICP Source
7.5.4. Spectral Interferences
7.5.5. Laser Ablation-ICPMS

7.6. RESONANCE IONIZATION MASS SPECTROMETRY
7.7. ISOTOPE RATIO MASS SPECTROMETRY

7.7.1. Isotope Ratio MS Systems

7.8. ACCELERATOR MASS SPECTROMETRY
7.9. ISOTOPE DILUTION MASS SPECTROMETRY
7.10. OVERVIEW OF THE CHAPTER
7.11. EXERCISES
7.12. ADDITIONAL READING
7.13. REFERENCES

PART 3: BIOLOGICAL MASS SPECTROMETRY

8. PROTEINS AND PEPTIDES: STRUCTURE DETERMINATION

8.1. INTRODUCTION

8.1.1. Structure of Proteins

8.2. DETERMINATION OF THE SEQUENCE OF A PROTEIN
8.3. GENERAL PROTOCOL FOR THE AMINO ACID SEQUENCE DETERMINATION OF PROTEINS

8.3.1. Homogenization and Subcellular Fractionation
8.3.2. Enrichment and Purification of Proteins

8.4. MOLECULAR MASS MEASUREMENT OF PROTEINS
8.5. PEPTIDE MASS MAPPING

8.5.1. Reduction and Carboxymethylation
8.5.2. Cleavage of Proteins
8.5.3. Mass Spectrometry Analysis of Peptide Maps

8.6. PROTEOMICS

8.6.1. Strategies for Proteomics

8.7. QUANTITATIVE PROTEOMICS
8.8. BIOMARKER DISCOVERY
8.9. DE NOVO PROTEIN SEQUENCING
8.9. DETERMINATION OF THE AMINO ACID SEQUENCE OF PEPTIDES

8.9.1. Peptide Fragmentation Rules
8.9.2. Mass Spectrometry Techniques for Sequence Determination of Peptides
8.9.3. Guidelines to Obtain the Amino Acid Sequence from a Mass Spectrum

8.10. OVERVIEW OF THE CHAPTER
8.11. EXERCISES
8.12. ADDITIONAL READING
8.13. REFERENCES

9. Proteins and Peptides: Post-Translational Modifications Disulfide Bonds in Proteins

9.1. TRADITIONAL APPROACHES TO IDENTIFY DISULFIDE BONDS
9.2. MASS SPECTROMETRY-BASED METHODS TO IDENTIFY DISULFIDE BONDS

9.2.1. Determination of the Number of Disulfide Bonds
9.2.2. Generation of the Disulfide-containing Peptides
9.2.3. Identification of Disulfide-containing Peptides by FAB-MS
9.2.4. Identification of the Disulfide-containing Peptides by MALDI-MS
9.2.5. Identification of the Disulfide-containing Peptides by Electron-capture Dissociation (ECD)
9.2.6. Identification of Disulfide-containing Peptides by Tandem MS

ANALYSIS OF PHOPHOPROTEINS AND PHOSPHO-PROTEOMICS

9.3. 32[P]-Labeling for the Analysis of Phosphoproteins

9.4. MASS SPECTROMETRY PROTOCOL FOR THE ANALYSIS OF PHOSPHOPROTEINS.

9.4.1. Cleavage of Purified Phosphoproteins .

9.4.2. Fractionation of Peptide Fragments in the Digest .

9.4.3. Determination of the Average Number of Phosphate Groups .

9.4.4. Identification of Phosphopeptides
9.4.5. Identification of Phosphorylation Sites

ANALYSIS OF GLYCOPROTEINS

9.5. STRUCTURAL DIVERSITY OF GLYCOPROTEINS
9.6. ANALYSIS OF GLYCOPROTEINS

9.6.1. Molecular Mass Determination of Glycoproteins
9.6.2. Identification of Glycosylation
9.6.3. Site of Glycosylation

9.7. OVERVIEW OF THE CHAPTER

9.8. EXERCISES
9.9. REFERENCES

10. Proteins and Peptides: Higher-Order Structures

10.1. CHARGE-STATE DISTRIBUTION
10.2. HYDROGEN/DEUTERIUM EXCHANGE TO STUDY CONFORMATIONAL STATES OF PROTEINS

10.2.1. Folding/Unfolding Dynamics of Proteins
10.2.2. Experimental Measurements of the Amide Hydrogen Isotopic Exchange

10.3. CHEMICAL CROSS-LINKING AS A PROBE FOR THE 3-D STRUCTURE OF PROTEINS
10.4. ION MOBILITY MEASUREMENTS TO STUDY PROTEIN CONFORMATIONAL CHANGES
10.5. OVERVIEW OF THE CHAPTER
10.6. EXERCISES
10.7. ADDITIONAL READING
10.8. REFERENCES

11. Characterization of Oligosaccharides

11.1. STRUCTURAL DIVERSITY IN OLIGOSACCHARIDES
11.2. CLASSES OF GLYCANS
11.3. MASS SPECTROMETRIC METHODS FOR COMPLETE STRCUTURE ELUCIDATION OF OLIGOSACCHARIDES

11.3.1. Release of Glycans
11.3.2. Derivatization of Carbohydrate chains
11.3.3. Composition Analysis by GC/MS
11.3.4. Linkage Analysis by GC/MS
11.3.5. Rapid Identification by a Precursor-ion Scan
11.3.6. Composition Analysis by Direct Mass Measurement
11.3.7. Structure Determination of Oligosaccharides by Sequential Digestion
11.3.8. Tandem Mass Spectrometry for Structural Analysis of Carbohydrates

11.4. OVERVIEW OF THE CHAPTER
11.5. EXERCISES
11.6. REFERENCES

12. Characterization of Lipids

12.1. CLASSIFICATION AND STRUCTURES OF LIPIDS
12.2. MASS SPECTROMETRY OF FATTY ACIDS AND ACYLGLYCEROLS

12.2.1. Analysis of Fatty Acids
12.2.2. Analysis of Acylglycerols

12.3. MASS SPECTROMETRY OF PHOSPHOLIPIDS
12.4. MASS SPECTROMETRY OF GLYCOLIPIDS
12.5. ANALYSIS OF BILE ACIDS AND STEROIDS
12.6. ANALYSIS OF EICOSANOIDS
12.7. LIPIDOMICS
12.8. OVERVIEW OF THE CHAPTER
12.9. EXERCISES
12.10. REFERENCES

13. Structure Determination of Oligonucleotides

13.1. STRUCTURES OF NUCLEOTIDES AND OLIGONUCLEOTIDES
13.2. MASS SPECTROMETRY ANALYSIS OF NUCLEOSIDES AND NUCLEOTIDES
13.3. CLEAVAGE OF OLIGONUCLEOTIDES
13.4. MOLECULAR MASS DETERMINATION OF OLIGONUCLEOTIDES

13.4.1. Electrospray Ionization for the Molecular Mass Determination
13.4.2. Matrix-assisted Laser Desorption/Ionization for Molecular Mass Determination
13.4.3. Base Composition from an Accurate Mass Measurement

13.5. MASS SPECTROMETRY SEQUENCING OF OLIGONUCLEAOTIDES

13.5.1. Gas-phase Fragmentation for Oligonucleotide Sequencing
13.5.2. Solution-phase Techniques for Oligonucleotide Sequencing

13.6. OVERVIEW OF THE CHAPTER
13.7. EXERCISES
13.8. REFERENCES

14. Quantitative Analysis

14.1. ADVANTAGES OF MASS SPECTROMETRY
14.2. DATA ACQUISITION

14.2.1. Selected-ion Monitoring
14.2.2. Selected-reaction Monitoring

14.3. CALIBRATION

14.3.1. External Standard Method
14.3.2. Standard Addition Method
14.3.3. Internal Standard Method

14.4 VALIDATION OF A QUANTITATIVE METHOD
14.5. SELECTED EXAMPLES

14.5.1. Applications of Gas Chromatography/Mass Spectrometry
14.5.2. Applications of Liquid Chromatography/Mass Spectrometry
14.5.3. Applications of MALDI-MS

14.6. OVERVIW OF THE CHAPTER
14.7. EXERCISES
14.8. ADDITIONAL READING
14.9. REFERENCES

15. Miscellaneous Topics

15.1. ENZYME KINETICS

15.1.1. Theory
15.1.2. Reaction Monitoring

15.2. IMAGING MASS SPECTROMETRY

15.2.2. Imaging with SIMS
15.2.2. Imaging with MALDI-MS

15.3. ANALYSIS OF MICROORGANISMS

15.3.1. Bacterial Identification
15.3.2. Analysis of Viruses

15.4. CLINICAL MASS SPECTROMETRY

15.4.1. Low Molecular Mass Compounds as Biomarkers of Disease
15.4.2. Analysis of DNA to diagnose Genetic Disorders
15.4.3. Proteins as Biomarkers of Disease

15.5. METABOLOMICS

15.6. FORENSIC MASS SPECTROMETRY

15.6.1. Analysis of Banned Substances of Abuse
15.6.2 Analysis of Explosives
15.6.3. Analysis of Glass and Paints
15.6.4. Authenticity of Questioned Documents
15.6.5. Mass spectrometry in Bioterror Defense

15.7. SCREENING COMBINATORIAL LIBRARIES

15.7.1. Combinatorial Synthetic Procedures
15.7.2. Screening Methods

15.8. ADDITIONAL READING
15.9. REFERENCES

Appendix A: Abbreviations
Appendix B: Physical Constants, Units, and Conversion Factors
Appendix C: Isotopes of Naturally Occurring Elements and their Abundances
Appendix D: Reference Ions and Their Exact Masses
Appendix E: Internet Resources
Appendix F. Answers and Hints to Exercises

Index

Metabolome Analysis: An Introduction by Silas G. Villas-Boas, Jens Nielsen, Jorn Smedsgaard, Michael E. Hansen, and Ute Roessner-Tunali Hardcover - 311 pages Shipped in CLICK HERE Cat.# JW-SPE2 $ 88.15 BUY Published:  2007   ISBN:  9780471743446

This book provides a concise and practical text to introduce students and researchers to metabolome analysis. The book begins with an introduction to the concepts behind metabolomics, discusses metabolites from a chemical standpoint and the analytical challenges that they present, and then moves on to sampling, sample preparation, analytical tools, and data analysis and management. While mass spectrometry is the primary tool for metabolome analysis, it is not on its own a perfect one, and so the authors also discuss liquid and gas chromatography, highlighting the advantages and limitations of each technique. Perhaps the most unique feature of this book is the inclusion of four chapters discussing successful metabolome studies of different organisms.

Table of Contents:

PREFACE
LIST OF CONTRIBUTORS

PART I: CONCEPTS AND METHODOLOGY

1. Metabolomics in Functional Genomics and Systems Biology

1.1 From genomic sequencing to functional genomics
1.2 Systems biology and metabolic models
1.3 Metabolomics
1.4 Future perspectives

2. The Chemical Challenge of the Metabolome

2.1 Metabolites and metabolism
2.2 The structural diversity of metabolites
2.2.1 The chemical and physical properties
2.2.2 Metabolite abundance
2.2.3 Primary and secondary metabolism
2.3 The number of metabolites in a biological system
2.4 Controlling rates and levels
2.4.1 Control by substrate level
2.4.2 Feedback and feedforward control
2.4.3 Control by “pathway independent” regulatory molecules
2.4.4 Allosteric control
2.4.5 Control by compartmentalization
2.4.6 The dynamics of the metabolism—the mass flow
2.4.7 Control by hormones
2.5 Metabolic channeling or metabolons
2.6 Metabolites are arranged in networks that are part of a cellular interactome

3. Sampling and Sample Preparation

3.1 Introduction
3.2 Quenching—the first step
3.2.1 Overview on metabolite turnover
3.2.2 Different methods for quenching
3.2.3 Quenching microbial and cell cultures
3.2.4 Quenching plant and animal tissues
3.3 Obtaining metabolites from biological samples
3.3.1 Release of intracellular metabolites
3.3.2 Structure of the cell envelopes—the main barrier to be broken
3.3.3 Cell disruption methods
3.3.4 Non-mechanical disruption of cell envelopes
3.3.5 Mechanical disruption of cell envelopes
3.4 Metabolites in the extracellular medium
3.4.1 Metabolites in solution
3.4.2 Metabolites in the gas phase
3.5 Improving detection via sample concentration

4. Analytical Tools

4.1 Introduction
4.2 Choosing a methodology
4.3 Starting point—samples
4.4 Principles of chromatography
4.4.1 Basics of chromatography
4.4.2 The chromatogram and terms in chromatography
4.5 Chromatographic systems
4.5.1 Gas chromatography
4.5.2 HPLC systems
4.6 Mass spectrometry
4.6.1 The mass spectrometer—an overview
4.6.2 GC-MS—the EI ion source
4.6.3 LC-MS—the ESI ion source
4.6.4 Mass analyzer—the quadrupole
4.6.5 Mass analyzer—the ion-trap
4.6.6 Mass analyzer—the time-of-flight
4.6.7 Detection and computing in MS
4.7 The analytical work-flow
4.7.1 Separation by chromatography
4.7.2 Mass spectrometry
4.7.3 General analytical considerations
4.8 Data evaluation
4.8.1 Structure of data
4.8.2 The chromatographic separation
4.8.3 Mass spectral data
4.8.4 Exporting data for processing
4.9 Beyond the core methods
4.9.1 Developments in chromatography
4.9.2 Capillary electrophoresis
4.9.3 Tandem MS and advanced scanning techniques
4.9.4 NMR spectrometry
4.10 Further reading

5. Data Analysis

5.1 Organizing the data
5.2 Scales of measurement
5.2.1 Qualitative data
5.2.2 Quantitative data
5.3 Data structures
5.4 Preprocessing of data
5.4.1 Calibration of data
5.4.2 Combining profile scans
5.4.3 Filtering
5.4.4 Centroid calculation
5.4.5 Internal mass scale correction
5.4.6 Binning
5.4.7 Baseline correction
5.4.8 Chromatographic profile matching
5.5 Deconvolution of spectroscopic data
5.6 Data standardization (normalization)
5.7 Data transformations
5.7.1 Principal component analysis
5.7.2 Fisher discriminant analysis
5.8 Similarities and distances between data
5.8.1 Continuous functions
5.8.2 Binary functions
5.9 Clustering techniques
5.9.1 Hierarchical clustering
5.9.2 k-means clustering
5.10 Classification techniques
5.10.1 Decision theory
5.10.2 k-nearest neighbor
5.10.3 Tree-based classification
5.11 Integrated tools for automation, libraries, and data evaluation

PART II: CASE STUDIES AND REVIEWS

6. Yeast Metabolomics: The Discovery of New Metabolic Pathways in Saccharomyces cerevisiae

6.1 Introduction
6.2 Brief description of the methodology used
6.2.1 Sample preparation
6.2.2 The analysis
6.3 Early discoveries
6.4 Yeast stress response gives evidence of alternative pathway for glyoxylate biosynthesis in S. cerevisiae
6.5 Biosynthesis of glyoxylate from glycine in S. cerevisiae
6.5.1 Stable isotope labeling experiment to investigate glycine catabolism in S. cerevisiae
6.5.2 Data leveraged for speculation

7. Microbial Metabolomics: Rapid Sampling Techniques to Investigate Intracellular Metabolite Dynamics—An Overview

7.1 Introduction
7.2 Starting with a simple sampling device proposed by Theobald et al. (1993)
7.3 An improved device reported by Lange et al. (2001)
7.4 Sampling tube device by Weuster-Botz (1997)
7.5 Fully automated device by Schaefer et al. (1999)
7.6 The stopped-flow technique by Buziol et al. (2002)
7.7 The BioScope: a system for continuous-pulse experiments
7.8 Conclusions and perspectives

8. Plant Metabolomics

8.1 Introduction
8.2 History of plant metabolomics
8.3 Plants, their metabolism and metabolomics
8.3.1 Plant structures
8.3.2 Plant metabolism
8.4 Specific challenges in plant metabolomics
8.4.1 Light dependency of plant metabolism
8.4.2 Extraction of plant metabolites
8.4.3 Many cell types in one tissue
8.4.4 The dynamical range of plant metabolites
8.4.5 Complexity of the plant metabolome
8.4.6 Development of databases for metabolomics-derived data in plant science
8.5 Applications of metabolomics approaches in plant research
8.5.1 Phenotyping
8.5.2 Functional genomics
8.5.3 Fluxomics
8.5.4 Metabolic trait analysis
8.5.5 Systems biology
8.6 Future perspectives

9. Mass Profiling of Fungal Extract from Penicillium Species

9.1 Introduction
9.2 Methodology for screening of fungi by DiMS
9.2.1 Cultures
9.2.2 Extraction
9.2.3 Analysis by direct infusion mass spectrometry
9.3 Discussion
9.3.1 Initial data processing
9.3.2 Metabolite prediction
9.3.3 Chemical diversity and similarity
9.4 Conclusion

10. Metabolomics in Humans and Other Mammals

10.1 Introduction
10.2 A brief history of mammalian metabolomics
10.3 Sample preparation for mammalian metabolomics studies
10.3.1 Working with blood
10.3.2 Working with urine
10.3.3 Working with cerebrospinal fluid
10.3.4 Working with cells and tissues
10.4 Sample analysis
10.4.1 GC-MS analysis of urine, plasma, and CSF
10.4.2 LC-MS analysis of urine, blood, and CFS
10.4.3 NMR analysis of CSF, urine, and blood
10.5 Applications
10.5.1 Identification and classification of metabolic disorders
10.6 Future outlook

INDEX

Cancer Biomarkers: Analytical Techniques for Discovery by Mahmoud H. Hamdan, Dominic M. Desiderio, Nico M. Nibbering Hardcover - 377 pages Shipped in CLICK HERE Cat.# JW-SPE3 $111.75 BUY Published:  2007   ISBN:  9780471745167

Tools, techniques, and progress in cancer biomarkers discovery

The completion of a number of gene sequencing projects, recent advances in genomic and proteomic technologies, and the availability of powerful bioinformatics tools have led to promising new avenues and approaches in the search for cancer biomarkers. This book provides a comprehensive overview of current methodologies and technologies. It discusses biomarker discovery as a whole, rather than focusing on one specific marker or cancer. With information on both existing and potential biomarkers, Cancer Biomarkers: Analytical Techniques for Discovery:

• Provides insights into the current technological platforms for biomarker discovery, including mass spectrometry combined with multidimensional chromatography, DIGE, and various chip technologies
• Includes a detailed discussion of protein networks and protein phosphorylation in cancer
• Details the use of imaging mass spectrometry, laser capture microdissection, serial analysis of gene expression, enzyme-linked immunosorbent assays, protein microarrays, antibody-based microarrays, and bioinformatics
• Covers the emerging role of surface-enhanced laser desorption ionization (SELDI) and various tagging and labeling strategies
• Discusses related regulatory and ethical issues

With a wealth of information that can be applied to a broad spectrum of biomarker research projects, this is a core reference for biomarker researchers, scientists working in proteomics and bioinformatics, pharmaceutical scientists, oncologists, biochemists, biologists, and chemists.

Table of Contents:

Preface
Acknowledgments
Introduction

1. Overview

1.1. Introduction
1.2. Cancer Biomarkers
1.3. Phases of Biomarkers Development
1.4. New Approach to Biomarkers Discovery
1.4.1. New and Powerful Technologies
1.4.2. Promising Sources for Biomarkers
1.4.2.1. DNA Methylation
1.4.2.2. Mitochondrial DNA Mutations
1.4.2.3. Phosphatidylinositol-3 Kinases (PI3Ks)
1.4.2.4. Profiling Tyrosine Phosphorylation
1.4.2.5. Proteins Expression
1.5. Initiatives Relevant to Biomarkers Discovery
1.5.1. Initiatives of the Human Proteome Organization (HUPO)
1.5.2. Data Mining in Cancer Research
1.6. Concluding Remarks

References

2. Proteomic Platforms for Biomarkers Discovery

2.1. Surface Enhanced Laser Desorption Ionization
2.1.1. Some Basic Considerations
2.1.2. Protein Capture Surfaces
2.1.3. Enrichment/prefractionation Prior to SELDI Analysis
2.1.3.1. Combinatorial Affinity
2.1.3.2. Magnetic Beads
2.1.3.3. Stacked Sorbents
2.1.3.4. Organic Solvent Extraction
2.2. Bioinformatics in SELDI
2.3. Some Representative SELDI Applications
2.3.1. Addressing Reproducibility in SELDI Analysis
2.3.2. Limitations and Other Open Questions Regarding Current SELDI
2.3.3. Other Open Questions
2.3.4. Outlook
2.4. Two-dimensional Polyacrylamide Gel Electrophoresis
2.4.1. Sample Preparation
2.4.2. Reducing Sample Complexity
2.4.3. Various Nomenclatures In-gel Analysis
2.4.3.1. Multiple-gels Two-dimensional Analyses
2.4.3.2. Two-dimensional DIGE Analysis
2.4.3.3. Multiphoton Detection Imaging
2.4.3.4. Stable-isotope Labeling with Amino Acids in Cell Culture (SILAC)
2.5. Laser Capture Microdissection
2.6. MS Analysis of Gel-separated Proteins
2.7. Representative Applications of 2-DE for Biomarkers Discovery
2.8. Protein Microarrays
2.8.1. Analytical Protein Microarrays
2.8.2. Substrates and Protein Attachment Methods
2.8.3. Detection Strategies
2.8.3.1. Surface Plasmon Resonance (SPR)
2.8.3.2. Atomic Force Microscopy (AFM)
2.8.3.3. Enzyme-linked Immunosorbent Assay (ELISA)
2.8.3.4. Radio Isotope Labeling
2.8.3.5. Fluorescence Detection
2.8.4. Functional Protein Microarrays
2.8.5. Reverse-phase Protein Microarrays
2.8.6. Future Prospects
2.9. Multidimensional Liquid Chromatography Coupled to MS
2.9.1. Protein Labeling
2.9.2. Labeling a Specific Amino Acid
2.9.3. Stable Isotope Incorporation
2.9.4. Limitations of Labeling
2.10. Chromatographic Separation
2.10.1. Three Dimensional Separation
2.10.2. Two-dimensional Chromatography
2.10.3. Basic Considerations Regarding MudPIT
2.10.4. Mass Spectrometry and Data Analysis
2.10.5. Data Analysis and Interpretation
2.10.6. Application of Multidimensional Chromatography/MS
2.10.7. Outlook for Multidimensional LC/MS
2.11. Imaging Mass Spectrometry
2.11.1. Tissue Preparation and Matrix Application
2.11.2. MS Acquisition
2.11.3. Some Representative Applications of Imaging MS
2.11.4. Current Limitations and Potential Developments

References

3. Some Existing Cancer Biomarkers

3.1. Introduction
3.2. Historic Glimpse at PSA
3.3. Prostate-specific Antigen
3.4. PSA as a Screening Marker
3.5. Improving the Specificity of PSA
3.5.1. Free/Complexed PSA
3.5.2. PSA Isoforms
3.5.3. Impact of Age, Race, and PSA Velocity
3.6. Looking for Other Solutions
3.6.1. Genetic Alterations
3.6.2. Phosphorylated Akt
3.7. Concluding Remarks
3.8. Existing Biomarkers for Ovarian Cancer
3.8.1. Genetic Disorder and Increased Risk of Ovarian Cancer
3.8.2. Association of BRCA1 and BRCA2 with Cancer-susceptibility
3.8.3. p53 Mutations in BRCA1-linked and Sporadic Ovarian Cancer
3.8.4. Carcinoma-associated Glycoprotein Antigen (CA-125)
3.8.5. Potential Uses of CA-125 in Prognosis and Patient Management
3.9. Osteopontin
3.9.1. Human Kallikrein 10
3.9.2. Prostasin
3.10. Combination of CA-125 with Other Potential Biomarkers
3.11. Profiling Proteins and Gene Expression in Ovarian Cancer
3.12. General Observations

References

4. Potential Cancer Biomarkers

4.1. Introduction
4.2. Human Tissue Kallikreins
4.2.1. Background and Nomenclature
4.2.2. Gene Locus and Gene Organization of Human Kallikreins
4.2.3. Tissue Expression and Regulation
4.2.4. Physiologic Roles
4.2.5. Kallikreins as Potential Cancer Biomarkers
4.2.6. Concluding Remarks
4.3. Protein Family 14-3-3
4.3.1. Functions Attributed to the 14-3-3 Proteins
4.3.2. Binding of 14-3-3 Proteins to Different Partners
4.3.3. The Role of 14-3-3 Proteins in Apoptosis
4.3.4. The Role of 14-3-3 Proteins in Cell-cycle Regulation
4.3.5. The Potential of Some 14-3-3 Proteins as Cancer Biomarkers
4.3.5.1. Down-regulation of 14-3-3σ in Various Types of Cancer
4.3.5.2. Down-regulation of 14-3-3σ in Breast Cancer
4.3.5.3. Perspectives
4.4. Heat Shock Proteins (HSPs)
4.4.1. Structure and Functions of HSP90
4.4.2. Association of HSP90 with Cancer
4.4.3. HSP90 as a Therapeutic Target
4.5. Heat Shock Protein 27 (HSP27)
4.5.1. The Role of HSP27 in Apoptosis
4.5.2. Expression of HSP27 in Cancer
4.6. Heat Shock Protein 70 (HSP70)
4.6.1. Structure and Mechanism of Action
4.6.2. Anti-apoptotic Role of HSP70
4.6.3. Overexpression of HSP70 in Cancer
4.7. General Remarks
4.8. Calcium Binding Proteins
4.8.1. Structure and Chromosomal Location of S100
4.8.2. S100A4 Protein
4.8.3. Association of S100A4 with Cancer
4.8.4. Overexpression of S100A4 in Pancreatic Ductal Adenocarcinoma
4.8.5. S100A4 in Human Breast Cancer
4.8.6. General Considerations
4.9. DNA Methylation
4.9.1. Detection of DNA Methylation
4.9.1.1. Restriction Landmark Genomic Screening (RLGS)
4.9.1.2. Methylation-specific PCR (MSP)
4.9.1.3. Other Variations
4.10. DNA Methylation in Cancer
4.10.1. CpG Island Methylation and Gene Silencing
4.10.1.1. Proteins that Mediate DNA Methylation
4.10.1.2. Nucleosomes
4.10.1.3. Histone Acetylation
4.10.2. Methylated Biomarkers in Cancer
4.10.3. Hypermethylation as a Biomarker in Lung Cancer
4.11. Inhibition of DNA Methylation
4.12. Concluding Remarks

References

5. Protein Networks and Protein Phosphorylation in Cancer

5.1. Introduction
5.2. Protein Interaction Networks
5.2.1. Experimental Approaches
5.2.2. Yeast Two Hybrid (Y2H) System
5.2.3. Tandem Affinity Purification/Mass Spectrometry (TAP-MS)
5.2.4. Y2H and TAP-MS as Complementary Approaches
5.2.5. DNA Microarrays
5.2.6. Other Approaches
5.3. Computational Approaches
5.3.1. Phylogentic Profiles
5.3.2. Similarity of Phylogenetic Trees (Mirrortree)
5.3.3. In Silico Two-hybrid Method
5.4. Human Protein Intractome
5.4.1. Human Intractome Based on Orthologs
5.4.2. Human Interactome Based on Experimental Data
5.5. Relationship Between Gene Expression and Protein Interaction
5.6. Gene Signatures in Cancer Prediction/Classification
5.6.1. Breast Cancer
5.6.2. Follicular Lymphoma
5.6.3. Lymphocytic Leukemia
5.6.4. Lung Adenocarcinoma
5.7. Concluding Remarks
5.8. Protein Phosphorylation
5.8.1. Introduction
5.8.2. Experimental Approaches for the Detection and Quantifi cation of Protein Phosphorylation
5.8.3. Enrichment Strategies
5.8.4. MS Detection of Phosphorylation
5.8.4.1. Analyses Using Electrospray Ionization (ESI)
5.8.4.2. Liquid Chromatography/Mass Spectrometry
5.9. Other Approaches
5.10. The Phosphatidylinositol 3-Kinase-Akt Pathway (PI3K-Akt)
5.10.1. Phosphatidylinositol 3-Kinase (PI3K)
5.10.2. Akt (PKB) and Its Activation
5.10.3. Biological Consequences of Akt Activation
5.10.4. Altered PI3K-Akt Signaling in Human Cancer
5.11. PIK3/Akt Alterations and Prognostic Biomarkers
5.11.1. Melanoma
5.11.2. Non-small-cell Lung Cancer (NSCLC)
5.11.3. Prostate Cancer
5.12. General Observations

References

6. Ethical Issues and Initiatives Relevant to Cancer Biomarkers

6.1. Introduction
6.2. Background
6.3. Ethical Committees/Organizations
6.4. Human Biobanks
6.4.1. Ethical Issues in Biobanking
6.5. Large Population Screening
6.5.1. Screening for Colorectal Cancer
6.5.2. Screening for Early Prostate Cancer
6.5.3. Screening for Cervical Cancer
6.6. Genetic Testing for Cancer Susceptibility
6.7. Ethics in Phase I Oncology Trials
6.7.1. Risks and Benefi ts of Phase I Oncology Trials
6.8. Initiatives Relevant to Biomarkers Discovery
6.8.1. The Human Proteome Organization (HUPO)
6.8.2. HUPO Initiative Around Biological Fluids
6.8.3. Early Detection Research Network (EDRN)
6.8.4. Other Initiatives
6.9. Genomic Initiatives/Resources
6.9.1. The Cancer Genome Anatomy Project (CGAP)
6.9.2. The Human Cancer Genome Project (HCGP)
6.10. Achievements and Perspectives
6.10.1. Molecular Biomarkers
6.10.2. Integrative Analysis of Cancer

References
Abbreviations
Index

Discrimination of Chiral Compounds Using NMR Spectroscopy by T. J. Wenzel Hardcover - 576 pages Shipped in CLICK HERE Cat.# JW-SPE4 $129.05 BUY Published:  2007   ISBN:  9780471763529

This book provides a comprehensive discussion of the use of NMR spectroscopy for chiral discrimination. One goal is to show the full scope of the work that has been done in this area as a way of guiding future investigations into other potential chiral reagents for use in NMR spectroscopy. It describes the systems that have been developed and the utility of these. More importantly, the book provides a comprehensive guide for investigators who may be considering using NMR spectroscopy to determine enantiomeric excess (ee) or assign the absolute configuration of a compound under study. While the book mentions all of the available chiral systems that have been reported in the literature for use in NMR spectroscopy, it focuses primarily on the systems that are commercially available. The book catalogs the range of compounds for which different reagents have been shown to be effective, and the extent to which they successfully discriminate the compounds being studied. This allows comparisons of the reagents and enables investigators to make recommendations on which reagents are most likely to be effective for particular types of compounds. Throughout the book, where appropriate, the author provides experimental strategies for using the reagents that are likely to improve the quality of results.

Table of Contents:

Chapter 1. Introduction.
Chapter 2. Aryl-containing Carboxylic Acids.
Chapter 3. Other Carboxylic Acid-Based Reagents.
Chapter 4. Hydroxyl- and Thiol-Containing Reagents.
Chapter 5. Amine-based Reagents.
Chapter 6. Miscellaneous Organic-Based Chiral Derivatizing and Solvating Agents.
Chapter 7. Reagents Incorporating Phosphorus, Selenium, Boron, and Silicon Atoms.
Chapter 8. Host Compounds as Chiral NMR Discriminating Agents.
Chapter 9. Chiral Discrimination with Metal-Based Reagents.
Chapter 10. Chiral NMR Discrimination with Highly Ordered Systems.

Applications of Vibrational Spectroscopy in Pharmaceutical Industry by Don Pivonka, John Chalmers, and Peter Griffiths Softcover - 384 pages Shipped in CLICK HERE Cat.# JW-SPE5 $225.40 BUY Published:  2007   ISBN:  9780470870877

Applications of Vibrational Spectroscopy in the Pharmaceutical Industry is the first book to bring together the diverse aspects of vibrational spectroscopy at a level that provides value to the dedicated spectroscopist as well as to the synthetic, development, and medicinal based chemists. This volume presents key themes, established and emerging, within current research as well as presenting detailed contributions on the instrumentation, methodology, data treatment, and applications associated within this area of research.