Produktbild: Microbiological Identification Using Maldi-Tof and Tandem Mass Spectrometry

Microbiological Identification Using Maldi-Tof and Tandem Mass Spectrometry Industrial and Environmental Applications

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Produktdetails

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Gebundene Ausgabe

Erscheinungsdatum

10.04.2023

Herausgeber

Shah Haroun N. + weitere

Verlag

John Wiley & Sons

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560

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24,9/17,4/3,5 cm

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1202 g

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1. Auflage

Sprache

Englisch

ISBN

978-1-119-81405-4

Beschreibung

Produktdetails

Einband

Gebundene Ausgabe

Erscheinungsdatum

10.04.2023

Herausgeber

Verlag

John Wiley & Sons

Seitenzahl

560

Maße (L/B/H)

24,9/17,4/3,5 cm

Gewicht

1202 g

Auflage

1. Auflage

Sprache

Englisch

ISBN

978-1-119-81405-4

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Libri GmbH
Europaallee 1
36244 Bad Hersfeld
DE

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  • Produktbild: Microbiological Identification Using Maldi-Tof and Tandem Mass Spectrometry
  • List of Contributors xix

    Preface xxiii

    1 Progress in the Microbiological Applications of Mass Spectrometry: from Electron Impact to Soft Ionization Techniques, MALDI- TOF MS and Beyond 1
    Emmanuel Raptakis, Ajit J. Shah, Saheer E. Gharbia, Laila M.N. Shah, Simona Francese, Erika Y. Tranfield, Louise Duncan, and Haroun N. Shah

    1.1 Introduction 1

    1.1.1 Algorithms Based upon Traditional Carbohydrate Fermentation Tests 1

    1.1.2 Dynamic Changes in the Chemotaxonomic Era (c. 1970-1985) through the Lens of the Genus Bacteroides 2

    1.1.3 Microbial Lipids as Diagnostic Biomarkers; Resurgence of Interest in MALDI- TOF MS with Advances in Lipidomics 3

    1.2 The Dawn of MALDI- TOF MS: Establishing Proof of Concept for Diagnostic Microbiology 7

    1.2.1 Development of a MALDI- TOF MS Database for Human Infectious Diseases 10

    1.2.2 The Dilemma with Clostridium difficile: from Intact Cells to Intracellular Proteins, MALDI- TOF MS Enters a New Phase 13

    1.3 Linear/Reflectron MALDI- TOF MS to Tandem Mass Spectrometry 15

    1.3.1 Tandem MALDI- TOF Mass Spectrometry 17

    1.3.2 Electrospray- based Mass Analysers 18

    1.3.3 Tandem Mass Spectrometry 18

    1.3.4 Mass Spectrometry- based Proteomics 19

    1.3.5 Case Study: LC- MS/MS of Biothreat Agents, Proteomes of Pathogens and Strain- level Tying Using Bottom- up and Top- down Proteomics 19

    1.3.6 Discovery Proteomics 21

    1.3.7 Targeted Proteomics 22

    1.3.8 Top- down Proteomics 23

    1.3.9 Targeted Protein Quantitation 24

    1.4 The Application of MALDI- MS Profiling and Imaging in Microbial Forensics: Perspectives 25

    1.4.1 MALDI- MSP of Microorganisms and their Products 26

    1.5 Hydrogen/Deuterium Exchange Mass Spectrometry in Microbiology 27

    1.6 The Omnitrap, a Novel MS Instrument that Combines Many Applications of Mass Spectrometry 29

    References 35

    2 Machine Learning in Analysis of Complex Flora Using Mass Spectrometry 45
    Luis Mancera, Manuel J. Arroyo, Gema Méndez, Omar Belgacem, Belén Rodríguez-Sánchez, and Marina Oviaño

    2.1 Introduction 45

    2.2 An Improved MALDI- TOF MS Data Analysis Pipeline for the Identification of Carbapenemase- producing Klebsiella pneumoniae 47

    2.2.1 Motivation 47

    2.2.2 Materials and Methods 47

    2.2.3 Spectra Acquisition 50

    2.2.4 Results 51

    2.2.5 Discussion 54

    2.3 Detection of Vancomycin- Resistant Enterococcus faecium 55

    2.3.1 Motivation 55

    2.3.2 Materials and Methods 56

    2.3.3 Results and Discussion 59

    2.4 Detection of Azole Resistance in Aspergillus fumigatus Complex Isolates 59

    2.4.1 Introduction 59

    2.4.2 Material and Methods 60

    2.4.3 Results 60

    2.4.4 Discussion 64

    2.5 Peak Analysis for Discrimination of Cryptococcus neoformans Species Complex and their Interspecies Hybrids 64

    2.5.1 Motivation 64

    2.5.2 Material and Methods 65

    2.5.3 Results and Discussion 65

    2.6 Conclusions 66

    References 67

    3 Top- down Identification of Shiga Toxin (and Other Virulence Factors and Biomarkers) from Pathogenic E. coli using MALDI- TOF/TOF Tandem Mass Spectrometry 71
    Clifton K. Fagerquist

    3.1 Introduction 71

    3.2 Decay of Metastable Peptide and Protein Ions by the Aspartic Acid Effect 72

    3.3 Energy Deposition during Desorption/Ionization by MALDI 75

    3.4 Protein Denaturation and Fragmentation Efficiency of PSD 76

    3.5 Arginine and its Effect on Fragment Ion Detection and MS/MS Spectral Complexity 79

    3.6 Inducing Gene Expression in Wild- type Bacteria for Identification by Top- Down Proteomic Analysis 82

    3.7 Top- down Proteomic Identification of B- Subunit of Shiga Toxin from STEC Strains 83

    3.8 Furin- digested Shiga Toxin and Middle- down Proteomics 85

    3.9 Top- down Identification of an Immunity Cognate of a Bactericidal Protein Produced from a STEC Strain 87

    3.10 Lc- Maldi- Tof/tof 88

    3.11 Conclusions 89

    References 94

    4 Liquid Atmospheric Pressure (LAP) - MALDI MS(/MS) Biomolecular Profiling for Large- scale Detection of Animal Disease and Food Adulteration and Bacterial Identification 97
    Cristian Piras and Rainer Cramer

    4.1 Introduction 97

    4.2 Background to LAP- MALDI MS 98

    4.3 Bacterial Identification by LAP- MALDI MS 102

    4.4 Food Adulteration and Milk Quality Analysis by LAP- MALDI MS 105

    4.5 Animal Disease Detection by LAP- MALDI MS 108

    4.6 Antibiotic Resistance Detection of Microbial Consortia by Lap- Maldi Ms 110

    4.7 Future Directions for LAP- MALDI MS Applications 113

    References 114

    5 Development of a MALDI- TOF Mass Spectrometry Test for Viruses 117
    Ray K. Iles, Jason K. Iles, and Raminta Zmuidinaite

    5.1 Introduction 117

    5.2 Understanding the Systems Biology of the Virus and Viral Infections 120

    5.3 Understanding the Nature of Viral Proteins and Molecular Biology 121

    5.4 Virion Protein Solubilization and Extraction 123

    5.5 Sampling and Virion Enrichment 123

    5.6 Peak Identification: Quantification and Bioinformatics 125

    5.7 Promise and Pitfalls of Machine Learning Bioinformatics 126

    5.8 Accelerating MALDI- TOF Assay Protocol Development Using Pseudotypes/ pseudoviruses 128

    5.9 Understanding the Operational Parameters of your MALDI- TOF MS 130

    5.10 Understanding the Operational Requirements of the Clinical Testing Laboratory: Validation and International Accreditation 131

    5.10.1 Limitation and Advantages of CLIA LDTs 131

    5.11 MALDI- TOF MS Screening Test for SARS- CoV- 2s 132

    5.11.1 Prepare Positive Control 132

    5.11.2 Prepare Gargle- saliva Samples 132

    5.11.3 Viral Particle Enrichment 132

    5.11.4 Dissolution of Virions and Solubilization of Viral Proteins 133

    5.11.5 Maldi- Tof Ms 133

    5.12 CLIA LDT Validation of a MALDI- TOF MS Test for SARS- CoV- 2 133

    5.12.1 Limit of Detection 134

    5.12.2 Interfering Substances and Specificity 134

    5.12.3 Clinical Performance Evaluation 136

    5.12.3.1 Establishing Operational Cut- off Values 137

    5.12.3.2 Direct comparison with an RT- PCR SARS- CoV- 2 test 138

    5.12.3.3 Internal Sampling Quality Control 138

    5.12.3.4 Daily System Quality Control 138

    5.12.4 Reproducibility 139

    5.12.5 Stability 139

    5.12.6 Validation Disposition 141

    5.12.6.1 Global Biosecurity 141

    References 142

    6 A MALDI- TOF MS Proteotyping Approach for Environmental, Agricultural and Food Microbiology 147
    Hiroto Tamura

    6.1 Introduction 147

    6.2 Serotyping of Salmonella enterica Subspecies enterica 151

    6.3 Discrimination of the Lineages of Listeria monocytogenes and Species of

    Listeria 161

    6.4 Discrimination of the Bacillus cereus Group and Identification of Cereulide 167

    6.5 Identification of Alkylphenol Polyethoxylate- degrading Bacteria in the Environment 171

    6.6 Conclusions and Future Perspectives 173

    References 175

    7 Diversity, Transmission and Selective Pressure on the Proteome of Pseudomonas aeruginosa 183
    Louise Duncan, Ajit J. Shah, Malcolm Ward, Radhey S. Gupta, Bashudev Rudra, Alvin Han, Ken Bruce, and Haroun N. Shah

    7.1 Introduction: Diversity 183

    7.1.1 P. aeruginosa: from 'Atypical' to Diverse 183

    7.1.2 Phenotypical Diversity in Isolates from Different Environments 183

    7.1.2.1 Clinical Isolates 183

    7.1.2.2 Environmental Isolates 184

    7.1.2.3 Veterinary Isolates 184

    7.1.2.4 Comparing P. aeruginosa Phenotypical Profiles from Different Environments 184

    7.1.2.5 Antibiotic Resistance in P. aeruginosa from Different Environments 186

    7.1.3 The Relationship Between Phenotypical and Proteomic Diversity 186

    7.1.4 Techniques and Practical Considerations for Studying Proteomic Diversity 186

    7.1.5 Proteomic Diversity and MS Applications 189

    7.2 Transmission 189

    7.2.1 The History of P. aeruginosa Transmission 189

    7.2.2 Proteomics and P. aeruginosa Transmission 191

    7.2.3 The Impact of Proteomic Diversity on Transmission 191

    7.3 Selective Pressures on the Proteome 192

    7.3.1 Tandem MS Systems for Studying Selected Proteomes 192

    7.3.2 Microenvironment Selection 192

    7.3.2.1 The Human Body and CF Lung 192

    7.3.2.2 The Natural Environment 192

    7.3.3 Antimicrobial Selection 193

    7.4 Conclusions on Studies of the Proteome 193

    7.5 Genomic Studies on Pseudomonas aeruginosa Strains Revealing the Presence of Two Distinct Clades 195

    7.5.1 Phylogenomic Analysis Reveals the Presence of Two Distinct Clades Within

    P. aeruginosa 196

    7.5.2 Identification of Molecular Markers Distinguishing the Two P. aeruginosa

    Clades 198

    7.6 Final Conclusions 201

    References 201

    8 Characterization of Biodegradable Polymers by MALDI- TOF MS 211
    Hiroaki Sato

    8.1 Introduction 211

    8.2 Structural Characterization of Poly(¿- caprolactone) Using Maldi- Tof Ms 212

    8.3 Biodegradation Profiles of a Terminal- modified PCL Observed by Maldi- Tof Ms 216

    8.4 Bacterial Biodegradation Mechanisms of Non- ionic Surfactants 218

    8.5 Advanced Molecular Characterization by High- resolution MALDI- TOF MS Combined with KMD Analysis 221

    8.6 Structural Characterization of High- molecular- weight Biocopolyesters by High- resolution MALDI- TOF MS Combined with KMD Analysis 225

    References 228

    9 Phytoconstituents and Antimicrobiological Activity 231
    Philip L. Poole and Giulia T.M. Getti

    9.1 Introduction to Phytochemicals 231

    9.2 An Application to Bacteriology 233

    9.2.1 Allicin Leads to a Breakdown of the Cell Wall of Staphylococcus aureus 234

    9.3 Applications to Parasitology 239

    9.3.1 Drug Discovery 239

    9.3.2 Parasite Characterization 240

    9.4 A Proteomic Approach: Leishmania Invasion of Macrophages 240

    9.5 Intracellular Leishmania Amastigote Spreading between Macrophages 243

    9.6 Potential Virus Applications 244

    Acknowledgements 246

    References 246

    10 Application of MALDI- TOF MS in Bioremediation and Environmental Research 255
    Cristina Russo and Diane Purchase

    10.1 Introduction 255

    10.2 Microbial Identification: Molecular Methods and MALDI- TOF MS 257

    10.2.1 PCR- based Methods 258

    10.2.2 Maldi- Tof Ms 260

    10.3 Combination of MALDI- TOF MS with Other Methods for the Identification of Microorganisms 261

    10.4 Application of MALDI- TOF MS in Environmental and Bioremediation Studies 263

    10.4.1 The Atmospheric Environment 263

    10.4.2 The Aquatic Environment 263

    10.4.3 The Terrestrial Environment 265

    10.4.4 Bioremediation Research Applications 266

    10.5 Microbial Products and Metabolite Activity 268

    10.6 Challenges of Environmental Applications 270

    10.7 Opportunities and Future Outlook 271

    10.8 Conclusions 272

    References 273

    11 From Genomics to MALDI- TOF MS: Diagnostic Identification and Typing of Bacteria in Veterinary Clinical Laboratories 283
    John Dustin Loy and Michael L. Clawson

    11.1 Introduction 283

    11.2 Genomics 284

    11.3 Defining Bacterial Species Through Genomics 286

    11.4 Maldi- Tof Ms 287

    11.5 Combining Genomics with MALDI- TOF MS to Classify Bacteria at the Subspecies Level 290

    11.6 Data Exploration with MALDI- TOF MS 292

    11.7 Validation of Typing Strategies 294

    11.8 Future Directions 294

    References 295

    12 MALDI- TOF MS Analysis for Identification of Veterinary Pathogens from Companion Animals and Livestock Species 303
    Dorina Timofte, Gudrun Overesch, and Joachim Spergser

    12.1 Veterinary Diagnostic Laboratories and the MALDI- TOF Clinical Microbiology Revolution 303

    12.1.1 MALDI- TOF MS: Reshaping the Workflow in Clinical Microbiology 304

    12.1.2 Identification of Bacterial Pathogens Directly from Clinical Specimens 305

    12.1.3 Prediction of Antimicrobial Resistance 307

    12.1.4 Impact in Veterinary Hospital Biosecurity and Epidemiological Surveillance 308

    12.2 Identification of Campylobacter spp. and Salmonella spp. in Routine Clinical Microbiology Laboratories 309

    12.2.1 General Aspects on the Importance of Species/Subspecies and Serovar Identification of Campylobacter spp. and Salmonella spp. 309

    12.2.2 General Aspects on Influence of Media/Culture Environment on Bacterial Species Identification by MALDI- TOF MS 311

    12.2.3 Possibilities and Limits of Identification of Campylobacter spp. by Maldi- Tof Ms 312

    12.2.3.1 Thermophilic Campylobacter spp. 312

    12.2.3.2 Human- hosted Campylobacter Species 313

    12.2.3.3 Campylobacter spp. of Veterinary Importance 313

    12.2.4 Possibilities and Limits of Identification of Salmonella spp. by Maldi- Tof Ms 314

    12.3 Identification and Differentiation of Mycoplasmas Isolated from Animals 316

    12.3.1 Animal Mycoplasmas at a Glance 316

    12.3.2 Laboratory Diagnosis of Animal Mycoplasmas 317

    12.3.3 MALDI- TOF MS for the Identification of Animal Mycoplasmas 318

    References 322

    13 MALDI- TOF MS: from Microbiology to Drug Discovery 333
    Ruth Walker, Maria E. Dueñas, Alan Ward, and Kaveh Emami

    13.1 Introduction 333

    13.2 Microbial Fingerprinting 334

    13.2.1 Environmental 335

    13.2.1.1 Actinobacteria 335

    13.2.1.2 Aquatic Microorganisms 335

    13.2.2 Terrestrial Microbiology 337

    13.2.3 Food and Food Safety 338

    13.2.3.1 Food Storage Effect on Identification 338

    13.2.3.2 Insects 339

    13.3 Mammalian Cell Fingerprinting 339

    13.3.1 Differentiation of Cell Lines and Response to Stimuli 339

    13.3.2 Cancer Diagnostics 341

    13.3.3 Biomarkers 342

    13.4 Drug Discovery Using MALDI- TOF 342

    13.4.1 Enzymatic Assays 343

    13.4.1.1 Targeting Antibiotic Resistance Using MALDI- TOF MS Enzymatic Assays 343

    13.4.2 Cellular- based Assays for Drug Discovery 344

    13.4.3 Automation in Drug Discovery 345

    13.4.4 Assay Multiplexing 345

    13.4.5 MS Imaging in Drug Discovery 346

    13.4.6 Maldi- 2 346

    13.5 Limitations/Challenges, Future Outlook, and Conclusions 347

    13.5.1 Sample Preparation Limitations 347

    13.5.1.1 Matrix 347

    13.5.1.2 Interference from Low- molecular- mass Matrix Clusters 348

    13.5.1.3 Buffer Compatibility 348

    13.5.1.4 TOF Mass Resolution Limitations 348

    13.5.2 Data Analysis and Application of Machine Learning 348

    13.6 Future Outlook/Conclusions 349

    References 350

    14 Rapid Pathogen Identification in a Routine Food Laboratory Using High- throughput MALDI- TOF Mass Spectrometry 359
    Andrew Tomlin

    14.1 Introduction 359

    14.2 MALDI- TOF MS in Food Microbiology 359

    14.3 Review of Existing Confirmation Techniques and Comparison to Maldi- Tof Ms 362

    14.4 Strain Typing Using MALDI- TOF MS 364

    14.5 Verification Trial 365

    14.6 Limitations of MALDI- TOF MS Strain Typing and Future Studies 369

    14.7 Listeria Detection by MALDI- TOF MS 370

    14.8 Trial Sample Preparation Procedure 370

    14.9 Initial Trial 374

    14.10 Limit of Detection Trial 375

    14.11 Method Optimization, Further Prospects, and Conclusions 376

    References 379

    15 Detection of Lipids in the MALDI Negative Ion Mode for Diagnostics, Food Quality Control, and Antimicrobial Resistance 381
    Yi Liu, Jade Pizzato, and Gerald Larrouy-Maumus

    15.1 Introduction 381

    15.2 Applications of Lipids in Clinical Microbiology Diagnostics 382

    15.2.1 Use of Cell Envelope Lipids for Bacterial Identification 382

    15.2.2 Detection of Cell Envelope Lipids and their Modifications to Determine Bacterial Drug Susceptibility 384

    15.2.3 Detection of Lipids in MALDI Negative Ion Mode for Fungal Identification 387

    15.2.4 Detection of Lipids in MALDI Negative Ion Mode for Parasite Identification 387

    15.2.5 Detection of Lipids in MALDI Negative Ion Mode for Virus Identification 388

    15.3 Applications of the Detection of Lipids in Negative Ion Mode MALDI- MS in Cancer Studies 388

    15.3.1 Lipids and MALDI Negative Ion Mode for Diagnosis of Lung Cancer 389

    15.3.2 Lipids and MALDI Negative Ion Mode for the Diagnosis of Breast Cancer 390

    15.3.3 Lipids and MALDI Negative Ion Mode for Diagnosis of Other Cancers 391

    15.3.4 Lipids and MALDI Negative Ion Mode for Drug-Cell Interactions and Prognosis 392

    15.4 Applications of the Detection of Lipids and MALDI- MS in Alzheimer's Disease Studies 392

    15.5 Applications of MALDI in Negative Ion Mode and the Detection of Lipids in Toxicology 393

    15.6 Lipids and MALDI Negative Ion Mode for Food Fraud Detection 394

    15.7 Conclusions and Future Development of Lipids and their Detection in MALDI in Negative Ion Mode 395

    Acknowledgments 395

    References 397

    16 Use of MALDI- TOF MS in Water Testing Laboratories 405
    Matthew Jones, Nadia Darwich, Rachel Chalmers, K. Clive Thompson, and Bjorn Nielsen

    16.1 Introduction 405

    16.2 Application in a Drinking Water Laboratory 408

    16.2.1 Introduction 408

    16.2.2 Method Validation 409

    16.2.2.1 Reference Database Validation 410

    16.2.2.2 Method Comparison 411

    16.2.2.3 Agar Assessment 412

    16.2.3 Application Within Drinking Water Laboratory 412

    16.3 Application in Water Hygiene and Environmental Laboratory Testing 413

    16.3.1 Introduction 413

    16.3.2 Legionella Testing 414

    16.3.3 Wastewater and Sewage Sludge Microbiology 415

    16.3.4 Healthcare Water Testing 416

    16.3.5 Investigative Analysis 417

    16.3.6 Method Validation 417

    16.3.6.1 Characterization of Intended Use 417

    16.3.6.2 Library Assessment 418

    16.3.6.3 Assessment of Variables 418

    16.3.6.4 Comparison Assessment 419

    16.3.6.5 Ongoing Verification 420

    16.3.7 Conclusion on Suitability for Use in an Environmental Testing Laboratory 422

    16.4 Potential Application for Cryptosporidium Identification 423

    References 425

    17 A New MALDI- TOF Database Based on MS Profiles of Isolates in Icelandic Seawaters for Rapid Identification of Marine Strains 431
    Sibylle Lebert, Viggó Þór Marteinsson, and Pauline Vannier

    17.1 Introduction 431

    17.2 Selection and Cultivation of the Strains 432

    17.3 Genotypic Identification 433

    17.4 MALDI- TOF MS Data Acquisition and Database Creation 438

    17.5 Verification of the Accuracy of the Home- made Database 441

    17.6 Conclusions 448

    Funding 448

    References 449

    18 MALDI- TOF MS Implementation Strategy for a Pharma Company Based upon a Network Microbial Identification Perspective 453
    Lynn Johnson, Christoph Hansy, and Hilary Chan

    18.1 Introduction 453

    18.1.1 Microbial Identifications from a Pharmaceutical Industry Perspective 453

    18.1.2 Historical Evolution 453

    18.2 Regulatory Requirements/Guidance for Microbial Identification 455

    18.3 Strategic Approaches to MALDI- TOF Implementation Within the Modern Microbial Methods Framework 455

    18.3.1 Incorporation of MALDI- TOF into a Technical Evaluation Roadmap 455

    18.3.2 Initial Implementation Planning Stage 456

    18.3.2.1 Roles and Responsibilities (Global/Local, Partners/IT, Stakeholders) 456

    18.3.2.2 Considerations When Selecting a Vendor/Model 457

    18.3.2.3 Overall Identification Process Flow and MALDI- TOF as the Defined Application 458

    18.3.2.4 Benefits of an In- house System for Pharmaceutical Companies Compared with Outsourcing 458

    18.3.2.5 The Center of Excellence (CoE) Approach 460

    18.3.2.6 Building a Business Case for the MALDI- TOF as a Network Strategy 461

    18.3.3 Implementation Strategy - From Feasibility Studies to Global Deployment 463

    18.3.3.1 Pilot Trials/Feasibility 463

    18.3.3.2 Risk Assessment/Risk- based Validation Approach 463

    18.3.3.3 Network Validation Approach 464

    18.4 Conclusions 467

    18.a Appendix 468

    References 470

    19 MALDI- TOF MS - Microbial Identification as Part of a Contamination Control Strategy for Regulated Industries 473
    Christine E. Farrance and Prasanna D. Khot

    19.1 Industry Perspective 473

    19.1.1 Introduction to Regulated Industries 473

    19.1.2 Contamination Control Strategy 474

    19.1.3 Tracking and Trending EM Data 474

    19.1.4 Drivers for Microbial Identification 476

    19.1.5 Level of Resolution of an Identification 476

    19.1.6 Global Harmonization 477

    19.1.7 Validation Requirements for Regulated Industries 477

    19.1.8 Summary 478

    19.2 Technical Perspective 478

    19.2.1 Identification Technologies 478

    19.2.2 Phenotypic Systems 479

    19.2.3 Proteotypic Systems 479

    19.2.4 Genotypic Systems 479

    19.2.5 The Importance of the Reference Database 480

    19.2.6 MALDI- TOF in Regulated Industries 480

    19.2.7 Outsourcing 480

    19.2.8 Summary 481

    19.3 MALDI- TOF MS Microbial Identification Workflow at a High- throughput Laboratory 481

    19.3.1 MALDI- TOF MS Principles for Microbial Identification 481

    19.3.2 Organism Cultivation for Microbial Identification with MALDI- TOF MS 482

    19.3.3 Sample Preparation for Microbial Identification with MALDI- TOF MS 482

    19.3.4 Sample Processing Workflow for Microbial Identification 482

    19.3.5 Data Interpretation 483

    19.3.6 Importance of a Sequence- based Secondary (or Fall- through) Identification System 484

    19.4 MALDI- TOF MS Library Development and Coverage 485

    19.4.1 Importance of Library Development Under a Quality System 485

    19.4.2 Targeted Library Development for Gram- positive Bacteria and Water Organisms 488

    19.4.2.1 Case Study 1: Impact of MALDI- TOF MS Library Coverage for Organisms of the Family Bacillaceae 488

    19.4.2.2 Case Study 2: Impact of MALDI- TOF MS Library Coverage for Organisms Recovered from Water Systems 489

    19.4.3 Supplemental and Custom MALDI- TOF MS Libraries 489

    19.5 Comparison of MALDI- TOF MS with Other Microbial Identification Methods 490

    19.6 Future Perspectives 490

    References 491

    20 Identification of Mold Species and Species Complex from the Food Environment Using MALDI- TOF MS 497
    Victoria Girard, Valérie Monnin, Nolwenn Rolland, Jérôme Mounier, and Jean-Luc Jany

    20.1 Fungal Taxonomy 497

    20.1.1 Defining What Is a Fungal Species 497

    20.1.2 Fungal Speciation within a Food Context 498

    20.1.3 Delimiting Species 498

    20.1.4 Foodborne Fungi within the Fungal Tree of Life 499

    20.2 Impact of Molds in Food 500

    20.2.1 Filamentous Fungi in Fermented Foods 500

    20.2.2 Filamentous Fungi with Undesirable Impacts on Food Quality and Safety 500

    20.3 Identification of Fungi 505

    20.4 Identification of Foodborne Molds Using MALDI- TOF MS 506

    20.4.1 Sample Preparation 506

    20.4.2 Database Building and Performance of MALDI- TOF for Identification of Foodborne Molds 507

    20.4.2.1 Database Building 507

    20.4.2.2 Performance of Foodborne Mold Database 508

    References 509

    Index 515