Preface
List of contributors Microbial Characterisation; the Transition from Conventional Methods to Proteomics.
1) CHANGING CONCEPTS IN THE CHARACTERISATION OF MICROBES AND THE INFLUENCE OF MASS SPECTROMETRY
Haroun Shah et al
2) MICROBIAL PHYLOGENY AND EVOLUTION BASED ON PROTEIN SEQUENCES (THE CHANGE FROM TARGETED GENES TO PROTEINS)
Radhey Gupta
2: PROTEOMICS TOOLS AND BIOMARKER DISCOVERY.
3) OVERVIEW OF THE PROTEOMIC TOOLS AND IT LINKS TO GENOMICS
Raju Misra.
4) HIGH THROUGHPUT BIOMARKER DISCOVERY IN MICROORGANISMS
Ming Fang
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
3: PROTEIN SAMPLES PREPARATION TECHNIQUES
CONVENTIONAL APPROACHES FOR SAMPLE PREPARATION FOR LIQUID
CHROMATOGRAPHY AND TWO-DIMENSIONAL GEL ELECTROPHORESIS
Vesela Encheva and Robert Parker
7) ISOLATION AND PREPARATION OF SPORE PROTEINS AND SUBSEQUENT CHARACTERISATION BY ELECTROPHORESIS AND MASS SPECTROMETRY Nicola Thorne, Saheer Gharbia and Haroun Shah
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
9) Wider Protein Detection from Biological Extracts by the Reduction of Dynamic Concentration Range.
Luc Guerrier, Egisto Boschetti and Piergiorgi Roghetti
10) 3D-gel electrophoresis - a new development in protein analysis.
Robert Ventzki and Josef Stegemann
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
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.
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
Bacillus spp.
Staphylococcus spp.
Streptococcus spp.
Mycobacterium spp.
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 spp.
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
14) The power of Gel-based proteomics to understand
physiology in Bacillus subtilis
Haike Antelmann and Michael Hecker
Introduction
Results
1 Proteomics of protein secretion mechanisms in Bacillus subtilis
2 Definition of proteomic signatures to study cell physiology
3 Proteomics as tool to visualize reversible and irreversible thiol- modifications
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.
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
* Machine Learning Techniques for the Analysis of Mass spectrometry Data.
Graham Ball and Ali Al-Shahib
18) Mass Spectrometry for microbial Proteomics: Issues in data analysis with
electrophoretic or mass spectrometric expression proteomic data.
Natasha A. Karp
Title page
Foreword
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
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
Biology
Pathogenesis
Clinical Disease
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
Flagellin sequences correspond directly to Salmonella serotype.
Specific SNPs
Subtyping by antigen sequence
Variation of the Rfb Genes
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
Closing Remarks
