Chapter
1. Proteomics: Technology and Applications
1.2 Definition and Importance of the Proteomics
1.3 Technical Methods in Proteomics
1.3.1 Isolation and separation of proteins
1.3.2 Analysis of the structure of the separated proteins
1.3.3 Utilization of computer databases to identify the characterized proteins
1.4 Proteomics’ Role in the Clinical Laboratory
1.5 Clinical Applications of Proteomics
1.6 Bioinformatics’ Application to Proteomics
1.7 Challenges of Proteomics
2. Basis of Mass Spectrometry: Technical Variants
2.2 MS: Definition and Basic Principles
2.3 A Brief Excursion to the History of MS and Related Nobel Prizes
2.4 Basic Components of a Mass Spectrometer
2.5 Ionization Techniques in Biological MS
2.8 Separation Techniques Hyphenated With MS
2.9 MSI and Other Ways of Examining Biological Tissues
2.10 Mass Spectrum, Data Representation, and Management
3. MALDI-TOF Commercial Platforms for Bacterial Identification
3.2 Commercial MALDI-TOF MS Systems
3.3 MALDI Biotyper System
3.5 MALDI Biotyper vs VITEK MS Systems’ Comparison
4. Work Procedures in MALDI-TOF Technology
4.2 Reagents and Equipment
4.2.2 MALDI Biotyper system
4.3 Calibration and Quality Control
4.3.2 MALDI Biotyper CA system
4.4 Preanalytical Processing Methods for Protein Extraction
4.4.1 Specimen collection
4.4.2 MALDI Biotyper clinical application system extraction protocol
4.4.3 VITEK MS extraction protocol
4.4.4 Special sample preparation methods (research use only)
4.4.4.1 Aerobic actinomycetes
4.4.4.2 Filamentous fungi
4.5.1 MALDI Biotyper system
4.5.1.2 Spectrum acquisition
4.5.2.2 Spectrum acquisition
4.6 Cleaning MALDI-TOF MS Target Plates
5. Indications, Interpretation of Results, Advantages, Disadvantages, and Limitations of MALDI-TOF
5.2 Indications for the Use of MALDI-TOF in Clinical Microbiology
5.3 Interpretation of Results
5.4 Advantages and Disadvantages
5.5 Limitations of MALDI-TOF Technique
5.5.2 Resistance and virulence factors
6. Quality Control in MALDI-TOF MS Techniques
6.1 General Description of the Operation of Matrix-Assisted Laser Desorption/Ionization–Time-of-Flight
6.2 Possible Sources of System Error
6.3 Quality Control Systems Applicable by the Technicians of the Commercial Houses
6.4 Quality Control Systems Applicable by System Users
6.4.1 Quality of the database
6.4.2 Controls when designing a database
6.4.3 Utility of the scores in the identification
7. Application of MALDI-TOF for Bacterial Identification
7.2 Historical Background
7.3 MALDI-TOF MS–Based Identification Work
7.4 Performance in Routine Clinical Microbiology
7.5 Identification of Bacteria From Culture Media
7.6 Inappropriate Sample Preparation
7.7 MS-Based Identification of Bacteria Directly From Clinical Samples
7.7.3 Cerebrospinal fluid
7.8.1 Detection of antibiotic resistance
8. Detecting Bacterial Resistance, Biomarkers, and Virulence Factors by MALDI-TOF Mass Spectrometry
8.1 Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Detection of Antibiotic Resistance
8.1.1 Detection of resistance mechanisms based on enzymatic degradation
8.1.1.1 Detection of β-lactamases
8.1.1.2 Detection of β-lactamases directly from blood culture
8.1.2 Detection of resistance through bacterial protein profiling
8.1.2.1 Detection of methicillin-resistant Staphylococcus aureus
8.1.2.2 Detection of other mechanisms of resistance
8.1.3 Determination of minimal profile changing concentration
8.1.4 MALDI-TOF-based resistance detection by stable isotope labeling
8.2 Identification of Diagnostic Serum Biomarkers for Infectious Diseases by Mass Spectrometric Profiling
8.3 Detection of Toxins and Microbial Antigens
9. Direct Identification of Pathogens From Blood Cultures by MALDI-TOF Technology
9.2 MS Basics Applied to BCs
9.4 Benefits of Using MALDI-TOF MS Technology and Cost-Effectiveness
10. Use of MALDI-TOF Techniques in the Diagnosis of Urinary Tract Pathogens
10.1 Introduction: Epidemiology and Importance of UTIs
10.2 Conventional Diagnosis of UTIs
10.3 Matrix-Assisted Laser Desorption Ionization–Time-of-Flight Mass Spectrometry as a UTI Screening Tool
10.4 Identifying UTI Pathogens by MALDI-TOF MS
10.4.1 Gram-negative bacteria
10.4.2 Gram-positive bacteria
10.5 Direct Diagnosis of UTIs by MALDI-TOF MS
10.6 Strategies for MALDI-TOF MS Antibiotics Susceptibility Testing in UTIs
11. Direct Application of MALDI-TOF Mass Spectrometry to Cerebrospinal Fluid for Pathogen Identification
11.1.1 Acute bacterial meningitis
11.1.2 Application of matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry in clinical samples
11.2 Performance in Routine Clinical Microbiology
11.2.2 MALDI-TOF MS analysis
12. Application of MALDI-TOF Mass Spectrometry in Clinical Virology
12.3 Current Clinical Virology Applications
12.3.1.1 Diagnosis of mutations and identification of viral genotypes
12.3.1.2 Identification of drug resistance
12.3.1.3 Use of MALDI-TOF techniques in epidemiology
12.4 Advantages of MALDI-TOF MS Technology and Cost-Effectiveness
12.5 Data Management and Quality Control
13. Identification of Mycobacteria by Matrix-Assisted Laser Desorption Ionization–Time-of-Flight Mass Spectrometry
13.2 Structure and Composition Cell Wall of Mycobacteria
13.3 Commercial MS Platforms for Mycobacterial Identification
13.4 Identification of Mycobacteria by MS
13.4.1 Inactivation of microorganisms
13.4.2 Methods of sample preparation
13.4.3 Growth from solid and liquid cultures of Mycobacterium spp.
13.4.4 Reading and interpretation of protein profiles
14. Use of MALDI-TOF Mass Spectrometry in Fungal Diagnosis
14.1 Origins and Introduction to Mass Spectrometry in Mycology
14.2 MS Yeast Identification
14.3 MS Filamentous Fungi Identification
14.4 MS Dermatophytes Identification
14.5 Rapid Identification in Clinical Samples by MS
14.5.1 Direct identification in blood cultures
14.5.2 Direct identification in other types of samples
14.6 MS Application to Epidemiological Research
14.7 MS Application to Antifungal Susceptibility Testing
15. Application of MALDI-TOF MS in Bacterial Strain Typing and Taxonomy
15.2 Typing by MALDI-TOF MS
15.2.1 Requirements for culture and sample preparation
15.2.2 Data acquisition and spectrum quality
15.3 Overview of Published Studies
15.3.1 Gram-negative bacteria
15.3.1.1 Enterobacteriaceae
15.3.1.2 Nonfermenting Gram-negative bacteria
15.3.2 Gram-positive bacteria
15.3.2.1 Staphylococcus aureus
15.3.2.2 Enterococcus spp.
15.3.3 Other microorganisms
16. Application of MALDI-TOF in Parasitology
16.1.1 Diagnostic tools in clinical parasitology
16.1.2 The use of MALDI-TOF in parasitology: where are we now
16.2 Identification of Parasites by MALDI-TOF MS
16.2.1.1 Intestinal protozoa
16.2.1.2 Blood and tissue protozoa
16.2.1.2.2 Trypanosoma brucei and Trypanosoma cruzi
16.2.1.2.3 Plasmodium spp. and Babesia spp.
16.3 Implementation of MALDI-TOF in the Parasitology Laboratory: Prospects and Limitations
17. Future Applications of MALDI-TOF Mass Spectrometry in Clinical Microbiology
17.2 Laboratory Automation
17.3 Imaging Mass Spectrometry
17.4 Identifying Biomarkers in Clinical Samples for Infectious Diseases Diagnosis
The Use of Mass Spectrometry Technology (MALDI-TOF) in Clinical Microbiology
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