Modules Overview

FERMO functionality is separated in modules: each module has a certain functionality and takes certain parameters that modify its behavior. All modules are optional and can be switched on/off as desired.

In the FERMO GUI, these parameters can be set using the input forms.

FERMO in command line mode (fermo_core) requires a specifically formatted parameters file in JSON format. The parameters are described in the individual modules.

Filtering

• Feature Filtering
• MS/MS Filtering

Networking

• Spectral Similarity (Molecular) Networking

Annotation

• Adduct Annotation
• Neutral Loss Annotation
• Fragment Annotation
• Spectral Library Annotation
• MS2Query Annotation
• antiSMASH KnownClusterBlast Annotation

Group Metadata

• Blank Assignment
• Group Assignment

Phenotype Assignment

• Phenotype Qualitative
• Phenotype Quantitative-Percentage
• Phenotype Quantitative-Concentration

Scores

• Feature Scores Calculation
• Sample Scores Calculation