CONTENTS
CHAPTER 1 CULTURAL, SEROLOGICAL AND GENETIC METHODS FOR IDENTIFICATION OF BACTERIA
John B. Sutherland and Fatemeh Rafii
1.1 Introduction
1.2 Identification of bacteria by cultural methods
1.3 Identification of bacteria by serological methods
1.4 Identification of bacteria by genetic methods
1.5 Other methods used for bacterial characterization
1.6 Conclusions
1.7 Acknowledgments and Disclaimers
1.8 References
CHAPTER 2 MASS SPECTROMETRY: IDENTIFICATION AND BIODETECTION, LESSONS LEARNED AND FUTURE DEVELOPMENTS
Alvin Fox
2.1 Introduction
2.1.1 Analysis of Fatty Acid and Sugar Monomers using GC-FID, GC-MS and GC-MS-MS
2.1.2 2.2 Analysis of PCR products using PCR, PCR-MS and PCR-MS-MS
2.1.3 Analysis of proteins using MALDI-TOF MS
2.1.4 Chemical markers for protein-based identification or biodetection
2.1.5 Conclusions
2.1.6 References
CHAPTER 3 AN INTRODUCTION TO MALDI TOF MS ANALYSIS OF WHOLE BACTERIA
Rohana Liyanage and Jackson O. Lay, Jr.
3.1. Introduction
3.2. Mass Spectrometry and Time-of-Flight MS
3.3. Matrix Assisted Laser Desorption Ionization
3.4. MALDI/TOF Mass Spectrometry
3.5. MALDI TOF and Bacterial Identification
3.6. Conclusions
3.7. References
CHAPTER 4 THE DEVELOPMENT OF THE BLOCK II CHEMICAL BIOLOGICAL MASS SPECTROMETER
Wayne H. Griest and Stephen A. Lammert
4.1. Introduction
4.2. Development History and Design Philosophy
4.3. Requirements and Specifications
4.4. Performance Testing
4.5. Conclusions
4.6. Acknowledgements
4.7 References
CHAPTER 5 METHOD REPRODUCIBILITY AND SPECTRAL LIBRARY ASSEMBLY FOR RAPID BACTERIAL CHARACTERIZATION BY METASTABLE ATOM BOMBARDMENT PYROLYSIS MASS SPECTROMETRY
Jon G. Wilkes, Gary Miertschin, Todd Eschler, Les Hosey, Fatemeh Rafii, Larry Rushing, Dan A. Buzatu, and Michel J. Bertrand
5.1. Introduction
5.2. Sample Preparation for Rapid, Reproducible Cell Culture
5.3. Analytical instrumentation for sensitive detection and spectral reproducibility
5.4. Spectral library assembly
5.5. Pattern Recognition Methods for Objectively Classifying Bacteria
5.6. Conclusions
5.7. Acknowledgement and Disclaimer
5.8. References
CHAPTER 6 MALDI TOF MASS SPECTROMETRY OF INTACT BACTERIA
Jackson O. Lay, Jr., and Rohana Liyanage
6.1. Introduction
6.2. MALDI MS of Cellular Extracts
6.3. Taxonomy: From Isolates to Whole Cell MALDI
6.4 Whole Cell MALDI MS
6.5 Biology Based Changes in Whole Cell MALDI Spectra
6.6 Analysis of Mixtures
6.7 Experimental Approaches
6.8 Identification of Protein Markers
6.9 Analysis of Target Proteins
6.10 Analysis of Clinical Isolates
6.11 Conclusions
6.12 References
CHAPTER 7 DEVELOPMENT OF SPECTRAL PATTERN MATCHING APPROACHES TO MATRIX-ASSISTED LASER DESORPTION/IONIZATION TIME-OF-FLIGHT MASS SPECTROMETRY FOR BACTERIAL IDENTIFICATION
Kristin H. Jarman and Karen L. Wahl
7.1. Introduction
7.2. MALDI-MS Signature Library Construction and Identification
7.3.Future Directions
7.4. References
CHAPTER 8 STUDIES OF MALARIA BY MASS SPECTROMETRY
Plamen A. Demirev
8.1. Introduction
8.2. Plasmodium in Red Blood Cells
8.3. Experimental Protocols for LDMS Detection of Malaria
8.4. Malaria Detection by Laser Desorption Mass Spectrometry
8.5. MS-Based Proteomics of the Plasmodium Parasite
8.6. Conclusions
8.7. Acknowledgements
8.8. References
CHAPTER 9 BACTERIAL STRAIN DIFFERENTIATION BY MASS SPECTROMETRY
Randy J. Arnold, Jonathan A. Karty and James P. Reilly
9.1. Introduction
9.2. Analysis of Cellular Proteins by Mass Spectrometry
9.3. Application of MALDI-TOF to Bacteria Identification
9.4. Conclusions
9.5. Acknowledgments
9.6. References
CHAPTER 10 BACTERIAL PROTEIN BIOMARKER DISCOVERY: A FOCUSED APPROACH TO DEVELOPING MOLECULAR BASED IDENTIFICATION SYSTEMS
Tracie L. Williams, Steven R. Monday, and Steven M. Musser
10.1. Introduction
10.2. Protein Extraction Methods
10.3. Mass Spectrometry
10.4. Automating the Process
10.5. Collecting and Sequencing Proteins
10.6. Conclusions
CHAPTER 11 HIGH THROUGHPUT MICROBIAL CHARACTERISATIONS USING ELECTROSPRAY IONISATION MASS SPECTROMETRY AND ITS ROLE IN FUNCTIONAL GENOMICS
Seetharaman Vaidyanathan and Royston Goodacre
11.1. Introduction
11.2. Microbial characterisations beyond the genomic level: Functional genomics
11.3. Electrospray (ionization) mass spectrometry (ESMS)
11.4. ESMS of Microbes
11.5. Direct infusion ESMS of crude cell extracts for high-throughput characterizations - metabolic fingerprinting and footprinting
11.6. Conclusions
11.7. Acknowledgements
11.8. References
CHAPTER 12 BIOINFORMATICS FOR FLEXIBILITY, RELIABILITY AND MIXTURE ANALYSIS OF INTACT MICROORGANISMS
Catherine Fenselau and Patrick Pribil
12.1. Introduction
12.2. Library Matching
12.3. Machine Learning
12.4. Bioinformatics
12.5. Protein Molecular Masses
12.6. Protein Maps
12.7 Microsequences from Peptides and Proteins
12.8 Remaining Challenges
12.9 Conclusions
12.10 References
CHAPTER 13 MALDI-FTMS OF WHOLE CELL BACTERIA
Jeffrey J. Jones, Michael J. Stump, and Charles L. Wilkins
13.1. Introduction
13.2. Fundamentals of MALDI-FTMS
13.3. Fundmentals of Complex Biological Analysis
13.4 Whole Cell Characterization Through MALDI-FTMS
13.5 Recombinant Over-Expressed Proteins Desorbed Directly from Whole Cells
13.6. Conclusions
13.7. References
CHAPTER 14 A REVIEW OF ANTIBODY CAPTURE AND BACTERIOPHAGE AMPLIFICATION IN CONNECTION WITH THE DIRECT ANALYSIS OF WHOLE CELL BACTERIA BY MALDI-TOF-MS
Kent J. Voorhees and Jon C. Rees
14.1. Introduction
14.2. Bacterial Identification
14.3. Immunocapture of Bacterial Mixtures
14.4. Bacteriophage Amplification of Bacteria
14.5. Conclusions
14.6. References
Chapter 15 DISCRIMINATION AND IDENTIFICATION OF MICROORGANISMS BY PPYROLYSIS MASS SPECTROMETRY: FROM BURNING AMBITIONS TO COOLING EMBERS - A HISTORICAL PERSPECTIVE
Éadaoin Timmins and Royston Goodacre
15.1 Introduction to microbial characterisation
15.2 Principles of PyMS
15.3 Early developments and investigations (1952 to 1985)
15.4 The mid 1980s and beyond
15.5 The move from cluster analyses to neural networks
15.6 Reproducibility of PyMS
15.7 Acknowledgements
15.8 References