MALDI-TOF MS has become the standard method for routine identification of most microbial organisms in clinical laboratories and has largely replaced biochemical assays. Classification relies on extensive well curated databases, ideally covering the full spectrum of microorganisms encountered in the specimens at hands. The protocols for harvesting cells and procuring material suitable for downstream MALDI-TOF MS analyses vary in specific details between the different groups of organisms, e.g., gram-positive or -negative bacteria, mycobacteria, or fungi. With respect to fungi, methods further vary between yeasts and moulds; and even among different mould genera if they do not lyse in a similar fashion. Purification of microbial materials from clinical specimen allows the direct identification of bacteria; however this is not yet fully adapted to fungi. In this chapter, I look into the differences between the underlying methods for yeast and moulds, and for production of samples suitable for MALDI-TOF MS species identification from cultures and different clinical materials.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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