Identification Of Microorganisms By Mass

A multidisciplinary approach to understanding the fundamentals of mass spectrometry for bacterial analysisFrom chemotaxonomy to characterization of targeted proteins, Identification of Microorganisms by Mass Spectrometry provides an overview of both well-established and cutting-edge mass spectrometry techniques for identifying microorganisms. A vital tool for microbiologists, health professionals, and analytical chemists, the text is designed to help scientists select the most effective techniques for use in biomedical, biochemical, pharmaceutical, and bioterror defense applications.Since microbiological applications of mass spectrometry require a basic understanding of both microbiology and analytical chemistry, the editors have incorporated material from both disciplines so that readers from either field will come to understand the necessary principles of the other. Featuring contributions from some of the most recognized experts in both fields, this volume provides specific examples of fundamental methods as well as approaches developed in the last decade, including: Metastable atom bombardment pyrolysis mass spectrometry Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) MALDI time-of-flight mass spectrometry (MALDI-TOF MS) of intact bacteria High-resolution Fourier transform mass spectrometry (FTMS) Electrospray ionization (ESI) mass spectrometry Identification of Microorganisms by Mass Spectrometry represents the most comprehensive and up-to-date work on the topic currently available. It is liberally illustrated with figures and tables and covers every aspect of spectrometric identification of microorganisms, including experimental procedures, various means of sample preparation, data analysis, and interpretation of complex mass spectral data.

CHARLES L. WILKINS, PhD, is a Distinguished Professor in the Department of Chemistry and Biochemistry at the University of Arkansas. He is the author or coauthor of over 250 scientific publications and has received numerous awards for his research.

JACKSON O. LAY, Jr., PhD, is the Director of the Arkansas Statewide Mass Spectrometry Facility at the University of Arkansas, and the author or coauthor of more than 100 publications in the field. In addition to his work with bacteria, he has developed mass spectrometry methods for cancer research and toxicology.

Preface

xi

Contributors

xv

1 Cultural, Serological, and Genetic Methods for Identification of Bacteria

1

(22)

John B. Sutherland and Fatemeh Rafii

1.1 Introduction,

1

(2)

1.2 Identification of Bacteria by Cultural Methods,

3

(3)

1.3 Identification of Bacteria by Serological Methods,

6

(2)

1.4 Identification of Bacteria by Genetic Methods,

8

(4)

1.5 Other Methods Used for Bacterial Characterization,

12

(1)

1.6 Conclusions,

13

(1)

Acknowledgments,

13

(1)

References,

13

(10)

2 Mass Spectrometry: Identification and Biodetection, Lessons Learned and Future Developments

23

(16)

Alvin Fox

2.1 Introduction,

23

(1)

2.2 Analysis of Fatty Acid and Sugar Monomers by GC-FID, GC-MS, and GC-MS-MS,

24

(2)

2.3 Analysis of PCR Products by PCR, PCR-MS, and PCR-MS-MS,

26

(5)

2.4 Analysis of Proteins by MALDI-TOF MS,

31

(1)

2.5 Chemical Markers for Protein-Based Identification or Biodetection,

32

(1)

2.6 Conclusions,

33

(1)

References,

34

(5)

3 An Introduction to MALDI-TOF MS

39

(22)

Rohana Liyanage and Jackson O. Lay, Jr.

3.1 Introduction,

39

(1)

3.2 Mass Spectrometry and Time-of-Flight MS,

40

(7)

3.3 Matrix-Assisted Laser Desorption Ionization,

47

(4)

3.4 MALDI-TOF Mass Spectrometry,

51

(1)

3.5 MALDI-TOF and Bacterial Identification,

51

(4)

3.6 Conclusions,

55

(1)

References,

56

(5)

4 The Development of the Block II Chemical Biological Mass Spectrometer

61

(30)

Wayne H. Griest and Stephen A. Lammert

4.1 Introduction,

61

(2)

4.2 Development History and Design Philosophy,

63

(10)

4.3 Requirements and Specifications,

73

(6)

4.4 Performance Testing,

79

(7)

4.5 Conclusions,

86

(1)

Acknowledgments,

87

(1)

References,

87

(4)

5 Method Reproducibility and Spectral Library Assembly for Rapid Bacterial Characterization by Metastable Atom Bombardment Pyrolysis Mass Spectrometry

91

(34)

Jon G. Wilkes, Gary Miertschin, Todd Eschler, Les Hosey, Fatemeh Rafii, Larry Rushing, Dan A. Buzatu, and Michel J. Bertrand

5.1 Introduction,

91

(4)

5.2 Sample Preparation for Rapid, Reproducible Cell Culture,

95

(8)

5.3 Analytical Instrumentation for Sensitive Detection and Spectral Reproducibility,

103

(5)

5.4 Spectral Library Assembly,

108

(3)

5.5 Pattern Recognition Methods for Objectively Classifying Bacteria,

111

(9)

5.6 Conclusions,

120

(1)

Acknowledgment,

121

(1)

References,

121

(4)

6 MALDI-TOF Mass Spectrometry of Intact Bacteria

125

(28)

Jackson O. Lay, Jr., and Rohana Liyanage

6.1 Introduction,

125

(2)

6.2 MALDI MS of Cellular Extracts,

127

(2)

6.3 Taxonomy: From Isolates to Whole-Cell MALDI,

129

(2)

6.4 Whole-Cell MALDI MS,

131

(2)

6.5 Biology-Based Changes in Whole-Cell MALDI Spectra,

133

(1)

6.6 Analysis of Mixtures,

134

(2)

6.7 Experimental Approaches,

136

(5)

6.8 Identification of Protein Markers,

141

(1)

6.9 Detection of Target Proteins,

142

(1)

6.10 Analysis of Clinical Isolates,

143

(4)

6.11 Conclusions,

147

(1)

References,

147

(6)

7 Development of Spectral Pattern-Matching Approaches to Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Bacterial Identification

153

(8)

Kristin H. Jarman and Karen L. Wahl

7.1 Introduction,

153

(1)

7.2 MALDI MS Signature Library Construction and Identification,

154

(1)

7.3 Full Spectrum Pattern Methods,

155

(1)

7.4 Peak Table Based Methods,

156

(2)

7.5 Future Directions,

158

(1)

References,

159

(2)

8 Studies of Malaria by Mass Spectrometry

161

(20)

Plamen A. Demirev

8.1 Introduction,

161

(2)

8.2 Plasmodium in Red Blood Cells,

163

(1)

8.3 Experimental Protocols for LDMS Detection of Malaria,

164

(3)

8.4 Malaria Detection by Laser Desorption Mass Spectrometry,

167

(7)

8.5 MS-Based Proteomics of the Plasmodium Parasite,

174

(1)

8.6 Conclusions,

175

(1)

Acknowledgments,

176

(1)

References,

176

(5)

9 Bacterial Strain Differentiation by Mass Spectrometry

181

(22)

Randy J. Arnold, Jonathan A. Karty, and James P. Reilly

9.1 Introduction,

181

(1)

9.2 Analysis of Cellular Proteins by Mass Spectrometry,

182

(1)

9.3 Application of MALDI-TOF to Bacteria Identification,

183

(14)

9.4 Conclusions,

197

(1)

Acknowledgment,

197

(1)

References,

197

(6)

10 Bacterial Protein Biomarker Discovery: A Focused Approach to Developing Molecular-Based Identification Systems

203

(26)

Tracie L. Williams, Steven R. Monday, and Steven M. Musser

10.1 Introduction,

203

(3)

10.2 Protein Extraction Methods,

206

(1)

10.3 Protein Chromatography,

206

(4)

10.4 Mass Spectrometry,

210

(2)

10.5 Automating the Process,

212

(4)

10.6 Collecting and Sequencing Proteins,

216

(6)

10.7 Conclusions,

222

(1)

References,

222

(7)

11 High-Throughput Microbial Characterizations Using Electrospray Ionization Mass Spectrometry and Its Role in Functional Genomics

229

(28)

Seetharaman Vaidyanathan and Royston Goodacre

11.1 Introduction,

229

(1)

11.2 Microbial Characterizations beyond the Genomic Level: Functional Genomics,

230

(3)

11.3 Electrospray (Ionization) Mass Spectrometry (ESMS),

233

(4)

11.4 ESMS of Microbes,

237

(10)

11.5 Direct Infusion ESMS of Crude Cell extracts for High-Throughput Characterizations—Metabolic Fingerprinting and Footprinting,

247

(2)

11.6 Conclusions,

249

(1)

Acknowledgment,

250

(1)

References,

250

(7)

12 Bioinformatics for Flexibility, Reliability, and Mixture Analysis of Intact Microorganisms

257

(22)

Catherine Fenselau and Patrick Pribil

12.1 Introduction,

257

(2)

12.2 Library Matching,

259

(1)

12.3 Machine Learning,

259

(1)

12.4 Bioinformatics,

259

(3)

12.5 Protein Molecular Masses,

262

(3)

12.6 Peptide Maps,

265

(1)

12.7 Microsequences from Peptides and Proteins,

265

(4)

12.8 Remaining Challenges,

269

(1)

12.9 Conclusions,

270

(1)

Acknowledgments,

270

(1)

References,

270

(9)

13 MALDI-FTMS of Whole-Cell Bacteria

279

(22)

Jeffrey J. Jones, Michael J. Stump, and Charles L. Wilkins

13.1 Introduction,

279

(1)

13.2 Fundamentals of MALDI-FTMS,

280

(2)

13.3 Fundmentals of Complex Biological Analysis,

282

(1)

13.4 Whole-Cell Characterization through MALDI-FTMS,

283

(10)

13.5 Recombinant Overexpressed Proteins Desorbed Directly from Whole Cells,

293

(2)

13.6 Conclusions,

295

(1)

References,

296

(5)

14 A Review of Antibody Capture and Bacteriophage Amplification in Connection with the Direct Analysis of Whole-Cell Bacteria by MALDI-TOF-MS

301

(18)

Kent J. Voorhees and Jon C. Rees

14.1 Introduction,

301

(2)

14.2 Bacterial Identification,

303

(5)

14.3 Immunocapture of Bacterial Mixtures,

308

(3)

14.4 Bacteriophage Amplification of Bacteria,

311

(4)

14.5 Conclusions,

315

(1)

References,

316

(3)

15 Discrimination and Identification of Microorganisms by Pyrolysis Mass Spectrometry: From Burning Ambitions to Cooling Embers—A Historical Perspective

319

(26)

Éadaoin Timmins and Royston Goodacre

15.1 Introduction to Microbial Characterization,

319

(4)

15.2 Principles of PyMS,

323

(2)

15.3 Early Developments and Investigations, 1952 to 1985,

325

(2)

15.4 The mid-1980's and Beyond,

327

(3)

15.5 The Move from Cluster Analyses to Neural Networks,

330

(2)

15.6 Reproducibility of PyMS,

332

(2)

Acknowledgment,

334

(1)

References,

334

(11)

Index

345

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Identification Of Microorganisms By Mass Spectrometry

Summary

Author Biography

Table of Contents

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