Gas Chromatography Mass Spectrometry Applications in Microbiology

I. Introduction to Gas Chromatography/ Mass Spectrometry and Applications in Microbiology.- 1 Gas Chromatography.- 1. Introduction.- 2. Gas Chromatographie Separation Theory.- 3. Columns.- 3.1. Packed and Capillary Columns.- 3.2. Stationary Phases and Supports.- 4. Sample Injection.- 4.1. Injection onto Packed Columns.- 4.2. Injection onto Capillary Columns.- 4.3. Syringe Technique.- 5. Detectors.- 6. Applying Gas Chromatography.- References.- 2 Mass Spectrometry.- 1. Introduction.- 2. Methods of Ionization.- 2.1. Electron Impact.- 2.2. Chemical Ionization.- 2.3. Field Ionization.- 2.4. Atmospheric Pressure Ionization.- 2.5. 252Cf Plasma Desorption.- 2.6. Secondary Ion Mass Spectrometry.- 2.7. Fast Atom Bombardment.- 3. Further Aspects of Ion Formation.- 3.1. Metastable Ions.- 3.2. Negative Ions.- 4. Separation of Ions.- 4.1. Magnetic Instruments.- 4.2. Quadrupole Instruments.- 4.3. Time-of-Flight Instruments.- 4.4. Fourier Transform/Ion Cyclotron Resonance Instruments.- 5. Ion Detection.- 5.1. Electron Multipliers.- 5.2. Photographic Detection.- 6. Introdution of Sample.- 6.1. Direct Inlet.- 6.2. Gas Chromatography.- 6.3. Liquid Chromatography.- 6.4. Reservoir.- 7. Use of Computers.- 7.1. Computer Control of Low-Resolution Mass Spectrometers and Data Acquisition.- 7.2. High-Resolution Data Acquisition.- 7.3. Repetitive Scanning.- 7.4. Library Searching.- References.- II. Analysis of Microbial Constituents.- 3 Fatty Acids and Complex Lipids Cecile.- 1. Fatty Acids.- 1.1. Preparation of the Samples.- 1.2. Structural Information Given by GC Analysis.- 1.3. Structural Information Given by Mass Spectrometry.- 1.4. GC/MS Analysis of Microbial Fatty Acids.- 2. Aliphatic Hydrocarbons.- 3. Terpenic Derivatives and Sterols.- 3.1. Aliphatic Terpene Alcohols.- 3.2. Sterols and Polycyclic Terpene Alcohols.- 4. Sphingosine Derivatives.- 5. Complex Lipids.- 5.1. Phospholipids.- 5.2. Glycolipids.- 5.3. Lipoamino Acids and Peptidolipids.- 6. Conclusion.- References.- 4 Carbohydrates.- 1. Introduction.- 2. Derivatives from Monofunctional Reagents of the Cyclic Forms of Monosaccharides.- 2.1. Formation of Derivatives and GC Separations.- 2.2. Electron Impact Mass Spectra of Trimethylsilyl Ethers, Methyl Ethers, and Acetate Derivatives of Monosaccharides.- 2.3. Chemical Ionization Mass Spectra of Trimethylsilyl Ethers, Methyl Ethers, and Acetate Derivatives of Monosaccharides.- 2.4. Trimethylsilyl Derivatives of Partially Acylated Sugars.- 3. Derivatives of Acyclic Forms of Carbohydrates.- 3.1. Alditol Acetates.- 3.2. Other Derivatives of Polyols.- 3.3. Aldononitrile Peracetates.- 3.4. Oxime Derivatives.- 3.5. Derivatives of Thioacetals and Thioketals.- 4. Cyclic Derivatives of Monosaccharides and Polyols.- 4.1. Boronic Esters.- 4.2. Cyclic Acetals and Ketals.- 5. Oligosaccharide Derivatives.- 5.1. Permethylated Oligosaccharides.- 5.2. Pertrimethylsilylated Disaccharides.- 5.3. Peracetates of Disaccharides (Aldohexosyl-Aldohexoses).- 5.4. Derivatives of Oligosaccharide Alditols.- 6. Conclusion.- References.- 5 Amino Acids and Peptides.- 1. Introduction.- 2. Amino Acids.- 2.1. Free Amino Acids.- 2.2. Derivatized Amino Acids.- 2.3. Applications.- 3. Peptides.- 3.1. Identification of Classical Sequencing Products.- 3.2. Sequencing Based on Peptide Bond Modification.- 3.3. Sequencing Using Dipeptidyl Aminopeptidases.- 3.4. Miscellaneous Peptide Derivatives.- 3.5. General Applications.- 4. Specialized Mass Spectrometric Techniques.- 5. Conclusions.- References.- III. Applications.- 6 Analysis of Volatile Metabolites in Indentification of Microbes and Diagnosis of Infectious Diseases.- 1. Introduction.- 2. Preparation of Specimens for Analysis of Microbial Volatiles.- 2.1. Direct Injection of Aqueous Solutions.- 2.2. Solvent Extraction.- 2.3. Head-Space Analysis.- 2.4. Adsorption Followed by Chemical or Thermal Desorption.- 2.5. Other Methods.- 3. GC Analytic Conditions.- 3.1. Packing Materials. Columns.- 3.2. Detectors.- 4. Analysis of Microbial Volatiles in Spent Culture Media.- 4.1. Direct Injection of Culture Media.- 4.2. Solvent Extraction.- 4.3. Direct Head-Space Analysis.- 4.4. Other Methods.- 5. Direct Analysis of Volatiles in Body Fluids.- 5.1. Direct Injection of Body Fluids.- 5.2. Solvent Extraction.- 5.3. Direct Head-Space Analysis.- 5.4. Other Methods.- References.- 7 Head-Space/Gas-Liquid Chromatography in Clinical Microbiology with Special Reference to the Laboratory Diagnosis of Urinary Tract Infections.- 1. Analysis by Head-Space/Gas-Liquid Chromatography.- 1.1. Indirect Analysis.- 1.2. Direct Analysis.- 2. Suitability of Direct Head-Space/Gas-Liquid Chromatography for Rapid Tests.- 3. Discovery of Specific Products to Act as Head-Space/Gas-Liquid Chromatography Markers for the Rapid Detection of Bacteria as Exemplified by Common Urinary Tract Pathogens.- 3.1. Ethanol as Marker for Escherichia coli and Related Species.- 3.2. Methyl Mercaptan and Dimethyl Disulfide as Markers for Proteus spp.- 3.3. Production of Markers in Mixed Cultures.- 3.4. Trimethylamine as Marker for Some Proteus spp.- 3.5. Necessity for Mass Spectrometry.- 4. Same-Day Head-Space/Gas-Liquid Chromatography Test on Urine Specimens.- 4.1. Introduction.- 4.2. Examples of Chromatograms Produced by Urine Specimens.- 5. Antibiotic Susceptibility Tests Using Head-Space/Gas-Liquid Chromatography.- 6. Comparison Between Same-Day Head-Space/Gas-Liquid Chromatography Test and Other Rapid Tests of Urinary Tract Infections.- 7. Conclusion.- References.- 8 Analysis of Cellular Components in Bacterial Classification and Diagnosis.- 1. Introduction.- 1.1. General.- 1.2. Cellular Substances of Diagnostic Potential.- 1.3. Current GC Approaches in Bacterial Taxonomy.- 2. Instrumentation.- 2.1. Gas Chromatograph.- 2.2. Detectors.- 2.3. Columns.- 2.4. Integrator-Recorder.- 2.5. Ancillary Equipment.- 2.6. Gas Chromatograph/Mass Spectrometer.- 3. Methods.- 3.1. Growth and Harvesting of Bacteria.- 3.2. Methanolysis, Hydrolysis, and Saponification.- 3.3. Derivatization of Hydroxylated Fatty Acids.- 3.4. Combined Analysis of Fatty Acids and Monosaccharides.- 3.5. Analysis of Fatty Acids Released by Methanolic HCl.- 3.6. Rapid Analysis of Fatty Acid Released by Saponification.- 3.7. Analysis of Monosaccharides.- 3.8. GC Conditions.- 4. Applications in Classification.- 4.1. Lipid Constituents.- 4.2. Sugars and Amino Acids.- 4.3. Influence of Growth Conditions.- 4.4. Taxonomic Resolution.- 5. Diagnostic Implications.- 5.1. General Discussion.- 5.2. Glucose Nonfermenters.- 5.3. Species of Neisseriaceae.- 5.4. Slow-Growing Mycobacteria.- 5.5. Detection of Bacterial Constituents in Clinical Material.- 6. Conclusions.- References.- 9 Quantitative Mass Spectrometry and its Application in Microbiology.- 1. Introduction.- 2. Mass Spectrometry.- 2.1. Methods of Ionization.- 2.2. Mass Filters.- 2.3. Extracted Ion Current Profile (EICP).- 2.4. Selected Ion Monitoring (SIM).- 3. Sample Handling.- 3.1. Pretreatment of Sample.- 3.2. Introduction of Sample Using Gas Chromatography (GC).- 3.3. Introduction of Sample Using Liquid Chromatography (LC).- 3.4. Direct Sample Introduction.- 4. Quantification.- 4.1. Calibration.- 4.2. Method of Standardization.- 4.3. Accuracy and Precision.- 4.4. Sensitivity and Detection Limit.- 4.5. Specificity.- 5. Applications.- 5.1. Clinical Microbiology.- 5.2. Ecological Microbiology.- 6. Conclusions.- References.- 10 Analytical Pyrolysis in Clinical and Pharmaceutical Microbiology.- 1. Introduction.- 2. Methods.- 2.1. Pyrolysis Techniques.- 2.2. Analytical Systems.- 3. Reproducibility.- 3.1. Culturing and Sampling.- 3.2. Pyrolysis.- 3.3. Pyrolyzate Transfer.- 3.4. Analytical System.- 4. Data Processing.- 4.1. Introduction ...- 4.2. Data Handling Packages.- 4.3. Visual Interpretation.- 4.4. The FOMPYR Package.- 4.5. Factor/Discriminant Analysis.- 5. Applications.- 5.1. Introduction.- 5.2. Streptococcus.- 5.3. Neisseria.- 5.4. Escherichia.- 5.5. Klebsieila.- 5.6. Yersinia.- 5.7. Salmonella.- 5.8. Vibrio.- 5.9. Pseudomonas.- 5.10. Bacillus.- 5.11. Clostridium.- 5.12. Mycobacterium.- 6. Conclusion.- References.- 11 Volatile C1-C8 Compounds in Marine Sediments.- 1. Introduction.- 2. Methods.- 2.1. Sample Collection and Storage.- 2.2. GC Analysis.- 2.3. GC/MS Analysis.- 3. Typical Results and Interpretation.- 3.1. Potential Sources of Votatile Organic Compounds in Marine Sediments.- 3.2. Examples.- References.- 12 Mass Spectrometry of Nitrogen Compounds in Ecological Microbiology.- 1. Introduction.- 2. Structure Determination.- 2.1. Cell Wall Components.- 2.2. Uptake and Exudation of Amino Acids.- 2.3. Stimulatory and Inhibitory N-Compounds.- 3. Isotope Mass Spectrometry.- 3.1. Analytical Methods.- 3.2. Isotope Fractionation.- 3.3. Assimilation Studies.- 3.4. Mineralization Studies.- 3.5. Microbial Synthesis of 15N Amino Acids.- 4. Conclusion.- References.