Mass Spectrometry for Microbial Proteomics

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  • Format: Hardcover
  • Copyright: 2010-08-23
  • Publisher: Wiley

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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.

Table of Contents

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)
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
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
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
Maldi Mass Spectrometry Imaging, a New Frontier in Biostructural Techniques: Applications in Biomedicine
Practical Aspects of MALDI-MSI
Microbial molecular investigation by MALDI TOF MS
Protein Samples Preparation Techniques≪/B≫
Conventional Approaches For Sample Preparation For Liquid
Chromatography and Two-Dimensional Gel Electrophoresis
Cell lysis methods
Sample preparation for 2D GE
Fractionation strategies
Sample preparation for Liquid Chromatography coupled to mass
Reference list
Isolation and Preparation of Spore Proteins and Subsequent Characterisation by Electrophoresis and Mass Spectrometry
Characterization of Bacterial Membrane Proteins Using a Novel Combination of a Lipid Based Protein Immobilization Technique with Mass Spectrometry
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.
Dealing with low-abundance protein discovery
Conclusions and future prospects
3D-gel electrophoresis - a new development in protein analysis.
Results and discussion
Characterisation of Microorganisms by Pattern Matching of Mass Spectral Profiles and Biomarker Approaches Requiring Minimal Sample Preparation
Microbial Disease Biomarkers using ProteinChip Arrays
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
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
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
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
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
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
Bacterial Post-Genomics for Vaccine development
comparative genomics
proteomics and immmunoproteomics
other high-throughput technologies
meningococcal vaccines and reverse vaccinology
Statistical Analysis of 2D Gels and Analysis of Mass Spectral Data
Machine Learning Techniques for the Analysis of Mass spectrometry Data
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
Experimental design
Data analysis
Figure legends
DNA Resequencing by MALDI-TOF-Mass Spectrometry and its Application to Traditional Microbiological Problems
Comparative DNA sequence analysis and typing using Mass Spectrometry
Comparative Sequence Analysis by MALDI-TOF MS
Applications of nucleic acid analysis by MALDI-TOF MS in clinical microbiology
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
Salmonella, the pathogen
Clinical Disease
Complex genetic structure and the need to subtype this genus
Virulence and Gene Transfer
Necessity to subtype
Antigenic Analysis - The Traditional Kauffmann - White Schema and its future
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
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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