Note: Intro -- Contents -- List of Contributors -- Chapter-1 -- Introduction -- Mass Spectrometry and Microbiology -- Chapters Included in This Book -- Emerging MS Methods and Technologies Not Covered Here -- Perspective -- Disclaimer -- References -- Part I -- Methodology and Techniques -- Chapter-2 -- Methods and Instrumentation inMass Spectrometry for the Differentiation of Closely Related Microorganisms -- Introduction -- Selectivity and Specificity in the Analysis of Microorganisms with MS -- MS Instrumentation -- MALDI and MALDI-MS Instrumentation -- TOF Mass Analyzer -- ESI and ESI-MS Instrumentation -- Quadrupole-Based Mass Analyzers -- Orbitrap Mass Analyzer -- MS-Based Methods and Instrumentation for the Differentiation of Closely Related Bacteria: Strain Level and Antibiotic Resistant -- Profile-Based Techniques for Strain-Level Differentiation -- Increasing the Reproducibility of the MALDI-MS Measurement -- Increasing the Selectivity in Protein Biomarkers Detection -- Top-Down Proteomic Approaches -- Differentiation and Detection of Antibiotic-Resistant Bacteria -- Conclusions -- References -- Chapter-3 -- Sample Preparation Methods for the Rapid MS Analysis of Microorganisms -- Enrichment Methods -- Enrichment of Microbial Cells/Biomarkers Involving Non-covalent Interactions -- Cells -- Biomarkers -- Enrichment of Cells/Biomarkers Involving Covalent Interactions -- Cells -- Biomarkers -- Immuno-Affinity Enrichment of Microbial Cells/Biomarkers -- Cells -- Biomarkers -- Cell Lysis -- Chemical Methods -- Physical Methods -- Separation of Cells and Biomarkers -- Intact Cells -- Biomarkers -- Sample Preparation for MALDI-MS -- References -- Chapter-4 -- Advantages Offered by Proteomic Strategies for Rapid Biodetection -- Identification of Components in Mixtures -- Rapid Detection of Genetic Engineering in Bacteria. , Characterizing Bacteria with Unsequenced Genomes -- Going Forward -- References -- Chapter-5 -- Bottom-Up Proteomics Methods for Strain-Level Typing and Identification of Bacteria -- Introduction -- Cell Harvesting and Protein Extraction -- Cell Lysis and the Preparation of Whole Cell Protein Extracts -- Preparation of Subcellular Fractions -- Outer Membrane Proteins -- Surface Layer Proteins -- Preparation of Flagella -- Extracellular Proteins -- Processing of Bacterial Proteins for Bottom-Up Proteomics Analysis -- Cell Shaving -- Protein Digestion Methods -- Solubilization and Denaturation of Proteins -- Reduction of Disulfide Bonds and Alkylation of Reduced Cysteines -- Protein Digestion Conditions -- Sample Digestion Strategies -- Liquid Phase Separation and Ionization of Peptides Followed by Acquisition of Tandem Mass Spectra -- Liquid Chromatography-ESI-MS -- Capillary Electrophoresis-ESI-MS -- Liquid Chromatography MALDI-MS/MS -- Database (DB) Construction and Searching -- Bacterial DBs -- DBs of Virulence Factors, Toxins, and Antibiotic Resistance Determinants -- Creation/Correction of Microbial Protein DBs Through Re-sequencing and Analysis of Genomes -- Custom DBs of E. coli and Salmonella Flagellins -- Search Engines -- Setting Search Parameters -- DB Searches -- Processing of DB Search Results -- Subspecies Differentiation and Strain-Level Typing of Bacteria Based on Searching Protein DBs with Peptide MS/MS Spectra -- Classification and Identification of Bacteria Based on the Number of Shared Peptides -- Peptide-to-Taxa Assignments: Determination of the Closest Neighbor -- Analysis of Subproteomes -- Confirmation of the Taxonomic Position of an Unknown Strain -- Relationship Between the Fraction of Shared Peptides (FSP) and Conservation of the Genome/Proteome. , Genomic Interrelationships Among Unknown Strains Revealed by Shotgun Proteomics -- Discrimination of Microbial Strains Based on Typing of Flagellin and Surface Layer Proteins -- Typing of E. coli and Salmonella Strains Based on Flagellin H Antigen Sequences -- Typing of Lactobacillus Strains Based on Surface Layer (S-Layer) Protein Sequences -- Discrimination of Strains Based on Antibiotic Resistance -- Concluding Remarks -- References -- Chapter-6 -- Maximizing the Taxonomic Resolution of MALDI-TOF-MS-Based Approaches to Bacterial Characterization: From Culture Conditions Through Data Analysis -- Introduction -- Overview of MALDI-TOF MS Profiling of Bacteria -- Library-Based Approaches -- Bioinformatics-Enabled Approaches -- Successes at the Genus and Species Levels -- Strain-Level Characterization: Successes, Challenges, and Strategies -- Commercially Available Software -- Assessing Strain-Level Performance -- Objectives -- Reproducibility -- Group Separation/Performance Metrics -- Score -- Jackknife/Bootstrapping/Threshold Cutoffs -- Culture Conditions -- Medium Type -- Medium Form (Broth/Agar) -- Sample Preparation -- Intact Cells -- Protein Extracts -- Pretreatment to Enhance Taxonomic Resolution -- Data Acquisition -- Data Analysis -- Summary -- Acknowledgments -- References -- Part II -- Subspecies Discrimination -- Chapter-7 -- Modulation of the Discriminatory Power of MALDI-TOF MS Profiling for Distinguishing Between Closely Related Bacterial Strains -- Introduction -- Differentiation Between Strains of L. acidophilus Group Grown under Different Cultivation Conditions -- Background -- Protocol -- Results -- Summary -- The Influence of Cultivation Conditions on Distinguishing Between Strains of Selected Mycobacterium spp. -- Background -- Protocol -- Results -- Summary. , Modulation of the Discriminatory Power Using an Alternative Matrix Solution -- Background -- Protocol -- Results -- Summary -- Modulation of the Discriminatory Power Using Microwave-Assisted Proteolysis -- Background -- Protocol -- Results -- Summary -- Conclusions -- References -- Chapter-8 -- Discriminatory Power of MALDI-TOF Mass Spectrometry for Phylogenetically Closely Related Microbial Strains -- Introduction -- Materials and Methods -- Sample Preparation -- MALDI-TOF Mass Spectrometry -- Data Analysis -- Staphylococcus Aureus -- Population Structure and Typing of S. aureus (Clonal Complexes) -- MS Biomarkers for Strain or CC Allocation of S. aureus/MRSA -- MS Biomarkers for Predicting Virulence Genes and Methicillin Resistance of S. aureus/MRSA -- Enterococcus faecium -- Population Structure and Typing of E. faecium -- MS Biomarkers for Strain or CC Allocation of E. faecium and Prediction of Vancomycin Resistance -- Differentiation of Bacillus anthracis, Bacillus cereus sensu stricto and Bacillus thuringiensis -- Summary and Outlook -- References -- Chapter-9 -- MALDI-TOF MS As a Novel Tool for Dereplication and Characterization of Microbiota in Bacterial Diversity Studies -- An Introduction to Dereplication in Bacterial Diversity Studies -- The Use of MALDI-TOF MS for Dereplication in Environmental Microbiology -- The Use of MALDI-TOF MS for Dereplication in Food Microbiology -- MALDI-TOF MS Can Combine Dereplication and Identification -- Detection of Taxonomic Novelty -- MALDI-TOF MS As a Dereplication Tool in Culturomics -- The Influence of Experimental Factors on MALDI-TOF Mass Spectra Generated -- Dereplication at an Infraspecific Level? -- Future Perspectives -- References -- Chapter-10 -- Bacterial Identification at the Serovar Level by Top-Down Mass Spectrometry -- Introduction -- Methods -- Bacterial Strains. , Extraction of Cellular Proteins -- HPLC of Intact Proteins -- LC-MS and Data Analysis -- MS Data Analysis -- Top-Down LC-MS/MS -- Top-Down Data Analysis -- Results and Discussion -- Intact Protein Expression Profiles -- Top-Down Protein Identification -- Proteogenomics -- Multiplexed Serovar Identification of Semi-blinded Isolates -- Conclusion -- References -- Part III -- Drug Resistance Monitoring and Assays -- Chapter-11 -- Rapid Profiling of Human Pathogenic Bacteria and Antibiotic Resistance Employing Specific Tryptic Peptides as Biomarkers -- Introduction -- Library-Based Approaches -- Proteomics-Based Approaches -- Approaches Based on Tryptic Peptides Toward Identification and Typing of Pathogens Below the Species Level -- Exploiting MALDI-TOF/TOF MS for Discrimination of Subspecies: In Search of Microorganism-Specific Tryptic Peptides -- Experimental Procedure -- Identification of Antibiotic Resistance Mechanisms in Bacteria Using Tryptic Peptides -- Limitations and Future Perspectives -- References -- Chapter-12 -- Detection of β-Lactamases and Their Activity Using MALDI-TOF MS -- β-Lactamases -- Detection of β-Lactam Hydrolysis -- Identification of β-Lactamases Using Inhibitors -- Comparison with Carba NP and Spectrophotometric Assays -- Automated Detection -- Detection of β-Lactamase Types -- Conclusion -- References -- Chapter-13 -- Stable-Isotope-Based Strategies for Rapid Determination of Drug Resistance by Mass Spectrometry -- Introduction -- Functional Assays for Establishing Drug Resistance -- Conclusion -- References -- Index.