Mass Spectrometry for Microbial Proteomics

by Shah, Haroun N.; Gharbia, Saheer E.

• ISBN13: 9780470681992
• ISBN10: 0470681993
• Edition: 1st
• Format: Hardcover
• Copyright: 2010-08-23
• Publisher: Wiley

Summary

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 #x13;Transition, Tools, Preparation, Profiling by Patterns, Target Proteins, and Data Analysis.

Author Biography

Professor Haroun N. Shah is Head of Molecular Identification Services Unit at the Centre for Infections, Health Protection Agency, London. The Centre for Infections provides infectious disease surveillance and microbial identification services, co-ordinating the investigation and cause of national and uncommon outbreaks of diseases. Haroun holds several chairs at various universities and spent 25 years in academic life at the University of London.

Professor Saheer E. Gharbia is Head of the Applied and Functional Genomics Unit at the HPA Centre for Infections. She has a PhD in molecular Genetics and Biochemistry, and has held various academic positions at the University of London and McGill University, Canada.

Table of Contents

Preface

List of contributors

Microbial Characterisation; the Transition from Conventional Methods to Proteomics

Changing Concepts in the Characterisation of Microbes and the Influence of Mass Spectrometry

Background and early attempts to use mass spectrometry on microbes

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

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

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

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

Microbial Phylogeny and Evolution Based on Protein Sequences (The Change From Targeted Genes to Proteins)

Abstract

Microbial phylogeny: overview and key unresolved issues

New protein-based molecular markers for systematic and evolutionary studies

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

Molecular markers for the bacteroidetes-chlorobi phyla

Branching order and interrelationships among bacterial phyla

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

Concluding remarks

Acknowledgements

References

Proteomics Tools and Biomarker Discovery

Overview of the Proteomic Tools and it Links to Genomics

Protein identification

Peptide Mass Fingerprint (PMF)

Peptide Fragment Fingerprint (PFF)

Peptide sequencing

False discovery rates (FDR)

Validating protein identifications

Reference Database

Data storage

Biomarker discovery

Integrating genomics with proteomics

Reference List

High Throughput Biomarker Discovery in Microorganisms

MALDI vs ESI

Tandem Mass Spectrometry and Hybrid Mass Spectrometers

Fragmentation in Tandem Mass Spectrometry

Proteomic Strategies for Protein Identification

Bottom-up Proteomics

Top-down Proteomics

Multidimensional Protein Identification

Mass Spectrometry Based Targeted Protein Quantification and Biomarker Discovery

Selected Reaction Monitoring

Conclusions

Maldi Mass Spectrometry Imaging, a New Frontier in Biostructural Techniques: Applications in Biomedicine

Introduction

Practical Aspects of MALDI-MSI

Applications

Microbial molecular investigation by MALDI TOF MS

Conclusions

References

Protein Samples Preparation Techniques≪/B≫

Conventional Approaches For Sample Preparation For Liquid

Chromatography and Two-Dimensional Gel Electrophoresis

Introduction

Cell lysis methods

Sample preparation for 2D GE

Fractionation strategies

Sample preparation for Liquid Chromatography coupled to mass

Conclusion

Reference list

Isolation and Preparation of Spore Proteins and Subsequent Characterisation by Electrophoresis and Mass Spectrometry

Introduction

Experimental

Conclusion

Characterization of Bacterial Membrane Proteins Using a Novel Combination of a Lipid Based Protein Immobilization Technique with Mass Spectrometry

Introduction

The surface proteome

Proteomics of pathogenic bacteria

Lipid-based protein immobilization technology

Salmonella Typhimurium – disease mechanism and outer membrane proteins

Outer membrane proteins of S. Typhimurium

Helicobacter pylori – disease mechanism and outer membrane proteins

Surface proteins of intact Helicobacter pylori

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

Introduction

Dealing with low-abundance protein discovery

Conclusions and future prospects

References

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

Introduction

Methods

Results and discussion

References

Characterisation of Microorganisms by Pattern Matching of Mass Spectral Profiles and Biomarker Approaches Requiring Minimal Sample Preparation

Microbial Disease Biomarkers using ProteinChip Arrays

Introduction

Biomarker studies involving patients infected with viruses

Biomarker studies involving patients infected with parasites

Biomarker studies involving patients infected with bacteria

Other diseases of possible infectious origin

Conclusions

References

MALDI-TOF MS and microbial identification: years of experimental development to an established protocol

Identification of Microorganisms in Clinical Routine

Mass Spectrometry and Microbiology

Mass Spectral 'Fingerprints' of Whole Cells

Reproducibility of Mass Spectral Fingerprints

Species and Strain Discrimination by Mass Spectrometry

Pattern Matching Approaches for automated Identification

Mass Spectral Identification of Microorganism – Requirements for Routine Diagnostics

Automated Mass Spectral Analysis of Microorganisms in Clinical Routine Diagnostics

Acknowledgements and references

Targeted Molecules and Analysis of Specific Microorganisms

Whole Cell MALDI Mass Spectrometry for the Rapid Characterisation of Bacteria; A Survey of Applications to Major Phyletic Lines in Microbial Kingdom

Introduction

Scope

Reproducibility

Factors concerning the sample

Factors concerning the MALDI MS process

Sample application and ionisation

Data analysis

Spectrum libraries

Whole cell MALDI MS of particular bacteria genera and species

Staphylococcus

Streptococcus

Mycobacterium

Other Gram-positive bacteria

Escherichia coli

Gram-negative food- and waterborne pathogen proteobacteria, other than E. Coli

Typical sexually transmitted pathogens: Neisseria spp. and Haemophilus

Gram-negative biothreat agent bacteria

Other Gram-negative bacteria

Pathogenic Cyanobacteria

Strategies for the identification of biomarkers in whole cell MALDI MS spectra

Protein database consideration

On-target treatment and analysis

Off-target' Analysis and correlation with proteomics studies

General consideration of biomarker identification strategies

Conclusions and outlook

The power of Gel-based proteomics to understand physiology in Bacillus subtilis

Introduction

Results

Proteomics of protein secretion mechanisms in Bacillus subtilis

Protein export machineries of B. subtilis

The extracellular proteome of B. subtilis

The cell wall proteome of B. subtilis

The membrane attached lipoproteome of B. subtilis

The proteome analysis of protein secretion mechanisms in B. subtilis

Definition of proteomic signatures to study cell physiology

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

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

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

Proteomics as tool to visualize reversible and irreversible thiol- modifications

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

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

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

Acknowledgment

Mass Spectrometry in the study of Tularemia Pathogenesis

Introduction to molecular hogenesis of Francisella tularensis infection

Francisella tularensis LVS proteome alterions induced by different temperures and stionary phase of growth

Analysis of membrane protein complexes of Francisella tularensis

Analysis of Francisella tularensis glycoproteins and phosphoproteins

Identificion of Francisella tularensis transcription factors potentially involved in its virulence

Acknowledgements

References

Bacterial Post-Genomics for Vaccine development

Summary

comparative genomics

transcriptomics

proteomics and immmunoproteomics

other high-throughput technologies

meningococcal vaccines and reverse vaccinology

conclusions

references

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

Machine Learning Techniques for the Analysis of Mass spectrometry Data

Introduction

Pre-processing MS data

Classification of MS data

Evaluation of Classification Models

Mass Spectrometry for microbial Proteomics: Issues in data analysis with electrophoretic or mass spectrometric expression proteomic data

Title page

Foreword

Introduction

Experimental design

Data analysis

Validation

Conclusions

Figure legends

References

DNA Resequencing by MALDI-TOF-Mass Spectrometry and its Application to Traditional Microbiological Problems

Comparative DNA sequence analysis and typing using Mass Spectrometry

Introduction

Comparative Sequence Analysis by MALDI-TOF MS

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

Conclusion

References

Transfer of a Traditional Serotyping System (Kauffmann-White) onto a MALDI-TOF-MS platform for the rapid Typing of Salmonella isolates

Typing of salmonella isolates

Introduction

Salmonella, the pathogen

Biology

Pathogenesis

Clinical Disease

Complex genetic structure and the need to subtype this genus

Phylogeny

Virulence and Gene Transfer

Necessity to subtype

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

Serotyping

Flagellar Antigens

Flagellar Variation

Somatic Antigens

Sequence-based methods to determine serotypes

Flagellin sequences correspond directly to Salmonella serotype

Specific SNPs

Subtyping by antigen sequence

Variation of the Rfb Genes

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

Conclusions and Summary

Closing Remarks

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