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Mass Spectrometry for Microbial Proteomics. Edition No. 1

  • Book

  • 534 Pages
  • July 2010
  • John Wiley and Sons Ltd
  • ID: 1326070
New advances in proteomics, driven largely by developments in mass spectrometry, continue to reveal the complexity and diversity of pathogenic mechanisms among microbes that underpin infectious diseases. Therefore a new era in medical microbiology is demanding a rapid transition from current procedures to high throughput analytical systems for the diagnosis of microbial pathogens.

This book covers the broad microbiological applications of proteomics and mass spectrometry. It is divided into six sections that follow the general progression in which most microbiology laboratories are approaching the subject –Transition, Tools, Preparation, Profiling by Patterns, Target Proteins, and Data Analysis.

Table of Contents

1) CHANGING CONCEPTS IN THE CHARACTERISATION OF MICROBES AND THE INFLUENCE OF MASS SPECTROMETRY

Haroun Shah et al

1.1 Background and early attempts to use mass spectrometry on microbes.

1.2 Characterisation of microorganisms by MALDI-TOF mass spectrometry; from initial ideas to the development of the first comprehensive database.

1.3 Characterisation of microorganisms from their intracellular/membrane bound protein profiles using affinity capture with particular reference to SELDI-TOF-MS.

1.4 Comparative analysis of proteomes of diverse strains within a species; use of 2-d fluorescence difference gel electrophoresis (dige).

1.5 Searching for low abundant and low molecular weight proteins and peptides using nanoparticles as a selective and concentration probes for MALDI-TOF-MS analysis.

2) MICROBIAL PHYLOGENY AND EVOLUTION BASED ON PROTEIN SEQUENCES (THE CHANGE FROM TARGETED GENES TO PROTEINS)

Radhey Gupta

2.1 Abstract

2.2 Microbial phylogeny: overview and key unresolved issues

2.3 New protein-based molecular markers for systematic and evolutionary studies

2.4 Molecular markers elucidating the evolutionary relationships among alpha (a)-proteobacteria

2.5 Molecular markers for the bacteroidetes-chlorobi phyla

2.6 Branching order and interrelationships among bacterial phyla

2.7 Importance of protein markers for discovering unique properties for different groups of bacteria

2.8 Concluding remarks

2.9 Acknowledgements

2.10 References

 

3) OVERVIEW OF THE PROTEOMIC TOOLS AND IT LINKS TO GENOMICS

Raju Misra.

 

3.1 Protein identification

3.2 Peptide Mass Fingerprint (PMF)

3.3 Peptide Fragment Fingerprint (PFF)

3.4 Peptide sequencing

3.5 False discovery rates (FDR)

3.6 Validating protein identifications

3.7 Reference Database

3.8 Data storage

3.9 Biomarker discovery

3.10 Integrating genomics with proteomics

3.11 Reference List

 

4) HIGH THROUGHPUT BIOMARKER DISCOVERY IN MICROORGANISMS

Ming Fang

 

4.1 MALDI vs ESI

4.2 Tandem Mass Spectrometry and Hybrid Mass Spectrometers

4.3 Fragmentation in Tandem Mass Spectrometry

Proteomic Strategies for Protein Identification

1. Bottom-up Proteomics

2. Top-down Proteomics

 

Multidimensional Protein Identification

 

Mass Spectrometry Based Targeted Protein Quantification and Biomarker Discovery

 

Selected Reaction Monitoring

 

Conclusions

 

5) MALDI MASS SPECTROMETRY IMAGING, A NEW FRONTIER IN BIOSTRUCTURAL TECHNIQUES: APPLICATIONS IN BIOMEDICINE Simona Francese and Malcolm R. Clench

 

5.1 Introduction

 

5.2 Practical Aspects of MALDI-MSI

 

5.2 Applications

 

5.3 Microbial molecular investigation by MALDI TOF MS

 

5.4 Conclusions

 

5.5 References

 

3: PROTEIN SAMPLES PREPARATION TECHNIQUES

 

CONVENTIONAL APPROACHES FOR SAMPLE PREPARATION FOR LIQUID

 

CHROMATOGRAPHY AND TWO-DIMENSIONAL GEL ELECTROPHORESIS

 

Vesela Encheva and Robert Parker

 

6.1 Introduction

 

6.2 Cell lysis methods

 

6.3 Sample preparation for 2D GE

 

6.4 Fractionation strategies

 

6.5 Sample preparation for Liquid Chromatography coupled to mass

 

6.6 Conclusion

 

6.7 Reference list

 

7) ISOLATION AND PREPARATION OF SPORE PROTEINS AND SUBSEQUENT CHARACTERISATION BY ELECTROPHORESIS AND MASS SPECTROMETRY Nicola Thorne, Saheer Gharbia and Haroun Shah

 

7.1 Introduction

 

7.2 Experimental

 

2.1 Sporulation media

 

7.3 Conclusion

 

8) CHARACTERIZATION OF BACTERIAL MEMBRANE PROTEINS USING A NOVEL COMBINATION OF A LIPID BASED PROTEIN IMMOBILIZATION TECHNIQUE WITH MASS SPECTROMETRY

 

Roger Karlsson, Darren Chooneea, Elisabet Carlsohn, Vesela Encheva and Haroun Shah

 

8.1 Introduction

 

8.2 The surface proteome

 

8.3 Proteomics of pathogenic bacteria

 

8.4 Lipid-based protein immobilization technology

 

8.5 Salmonella Typhimurium - disease mechanism and outer membrane proteins

 

8.6 Outer membrane proteins of S. Typhimurium

 

8.7 Helicobacter pylori - disease mechanism and outer membrane proteins

 

8.8 Surface proteins of intact Helicobacter pylori

 

9) Wider Protein Detection from Biological Extracts by the Reduction of Dynamic Concentration Range.

 

Luc Guerrier, Egisto Boschetti and Piergiorgi Roghetti

 

9.1 Introduction

 

9.2 Dealing with low-abundance protein discovery

 

9.3 Conclusions and future prospects

 

9.4 References

 

10) 3D-gel electrophoresis - a new development in protein analysis.

 

Robert Ventzki and Josef Stegemann

 

10.1. Introduction

 

10.2. Methods

 

10.3 Results and discussion

 

10.4 References

 

SECTION 4: CHARACTERISATION OF MICROORGANISMS BY PATTERN MATCHING OF MASS SPECTRAL PROFILES AND BIOMARKER APPROACHES REQUIRING MINIMAL SAMPLE PREPARATION.

 

11) Microbial Disease Biomarkers using ProteinChip Arrays

 

Shea Hamilton, Michael Levin, J. Simon Kroll, Paul R. Langford

 

11.1 Introduction

 

11.2 Biomarker studies involving patients infected with viruses

 

11.3 Biomarker studies involving patients infected with parasites

 

11.4 Biomarker studies involving patients infected with bacteria

 

11.5 Other diseases of possible infectious origin

 

11.6 Conclusions

 

11.7 References

 

12) MALDI-TOF MS and microbial identification: years of experimental

 

development to an established protocol.

 

Wibke Kallow, Marcel Erhard,

 

Haroun N. Shah, Emmanuel Raptakis, Martin Welker.

 

12.1 Identification of Microorganisms in Clinical Routine

 

12.2 Mass Spectrometry and Microbiology

 

12.3 Mass Spectral ‘Fingerprints’ of Whole Cells

 

12.4 Reproducibility of Mass Spectral Fingerprints

 

12.5 Species and Strain Discrimination by Mass Spectrometry

 

12.6 Pattern Matching Approaches for automated Identification

 

12.7 Mass Spectral Identification of Microorganism - Requirements for Routine Diagnostics

 

12.8 Automated Mass Spectral Analysis of Microorganisms in Clinical Routine Diagnostics

 

12.9 Acknowledgements and references

 

5: Targeted Molecules and Analysis of Specific Microorganisms.

 

13) Whole Cell MALDI Mass Spectrometry for the Rapid Characterisation of

 

Bacteria; A Survey of Applications to Major Phyletic Lines in Microbial

 

Kingdom.

 

Ben van Baar

 

13.1 Introduction

 

13.3.1 Factors concerning the sample

 

13.5 Sample application and ionisation

 

13.6 Spectrum libraries

 

13. and Haemophilus spp.1. Protein export machineries of B. subtilis

 

1.1 The extracellular proteome of B. subtilis

 

1.2 The cell wall proteome of B. subtilis

 

1.3. The membrane attached lipoproteome of B. subtilis

 

1.3 The proteome analysis of protein secretion mechanisms in B. subtilis

 

2 Definition of proteomic signatures to study cell physiology

 

2.1. Proteomic signatures of B. subtilis in response to stress and starvation

 

2.2. Proteomic signatures of B. subtilis in response to thiol-reactive electrophiles uncovered novel regulatory mechanisms

 

2.3. The MarR/DUF24-family YodB repressor is directly sensing thiol- reactive electrophiles via the conserved Cys6 residue

 

3 Proteomics as tool to visualize reversible and irreversible thiol- modifications

 

3.1. The thiol-redox proteome of B. subtilis in response to diamide and quinones

 

3.2. Depletion of thiol-containing proteins by quinones due to thiol-(S)- alkylation

 

4 Proteomics as tool to define regulon structures and targets for non- coding RNAs

 

5 Acknowledgment

 

15) Mass Spectrometry in the study of Tularemia Pathogenesis.

 

Jiri Stulik, Juraj Lenco, Jiri Dresler, Jana Klimentova, Lenka Hernychova, Lucie Balonova and Alena Fucikova.

 

15.1 Introduction to molecular pathogenesis of Francisella tularensis infection

 

15.2 Francisella tularensis LVS proteome alterations induced by different temperatures and stationary phase of growth

 

15.3Analysis of membrane protein complexes of Francisella tularensis

 

15.4 Analysis of Francisella tularensis glycoproteins and phosphoproteins

 

15.5Identification of Francisella tularensis transcription factors potentially involved in its virulence

 

15.6 Acknowledgements

 

References

 

16) Bacterial Post-Genomics for Vaccine development

 

Giulia Bernardini, Daniela Braconi and Annalisa Santucci

 

Summary

 

comparative genomics

 

transcriptomics

 

proteomics and immmunoproteomics

 

other high-throughput technologies

 

meningococcal vaccines and reverse vaccinology

 

helicobacter pylori vaccines

 

conclusions

 

references

 

6 Statistical Analysis of 2D Gels and Analysis of Mass Spectral Data

  1. Machine Learning Techniques for the Analysis of Mass spectrometry Data.

 

Graham Ball and Ali Al-Shahib

 

17.1 Introduction

 

17.2 Pre-processing MS data

 

17.3 Classification of MS data

 

17.4 Evaluation of Classification Models

 

18) Mass Spectrometry for microbial Proteomics: Issues in data analysis with

 

electrophoretic or mass spectrometric expression proteomic data.

 

Natasha A. Karp

 

Title page

 

Foreword

 

18.1 Introduction

 

18.2 Experimental design

 

18.3 Data analysis

 

18.4 Validation

 

18.5 Conclusions

 

18.6 Figure legends

 

18.7 References

 

Section 7: DNA Resequencing by MALDI-TOF-Mass Spectrometry and its

 

Application to Traditional Microbiological Problems.

 

(19) Comparative DNA sequence analysis and typing using Mass

 

Spectrometry

 

Christiane Honisch,Yong Chen and Franz Hillenkamp

 

19.1 Introduction

 

19.2 Comparative Sequence Analysis by MALDI-TOF MS

 

19.3 Applications of nucleic acid analysis by MALDI-TOF MS in clinical microbiology

 

19.4 Conclusion

 

References

 

(20) Transfer of a Traditional Serotyping System (Kauffmann-White)

 

onto a MALDI-TOF-MS platform for the rapid Typing of Salmonella

 

isolates.

 

Chloe Bishop, Cath Arnold and Saheer Gharbia

 

Typing of salmonella isolates

 

1.1 Introduction

 

1.2 Salmonella, the pathogen

 

Biology

 

Pathogenesis

 

Clinical Disease

 

1.3 Complex genetic structure and the need to subtype this genus

 

Phylogeny

 

Virulence and Gene Transfer

 

Necessity to subtype

 

>1.4 Antigenic Analysis - The Traditional Kauffmann - White Schema and its future

 

Serotyping

 

Flagellar Antigens

 

Flagellar Variation

 

Somatic Antigens

 

1.5 Sequence-based methods to determine serotypes

 

Flagellin sequences correspond directly to Salmonella serotype.

 

Specific SNPs

 

Subtyping by antigen sequence

 

Variation of the Rfb Genes

 

1.6 Transferring the Sequences to a MALDI platform for Rapid Analysis

 

Intro

 

Different methods available

 

MALDI-TOF data analysis

 

Salmonella molecular serotyping as a Case Study

 

Gene Selection

 

Results Overview

 

Clustering and Sequence Variation of Amplicons

 

1.7 Conclusions and Summary

 

Closing Remarks

Authors

Haroun N. Shah Centre for Infections. Saheer E. Gharbia