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featureMSEA Tutorial: Feature-based Metabolite Set Enrichment Analysis

2 Annotation and Filtering

In Step 1, metabolic features are annotated against the MS1 database via accurate mass matching within a user-specified tolerance window. Co-eluting features sharing similar retention times are further grouped into Metabolic Feature Clusters (MFCs), a grouping strategy that improves annotation confidence and reduces redundancy in the resulting annotation table.

Step 1: annotation and filtering parameters

Figure 2.1: Step 1: annotation and filtering parameters

2.1 Parameters

Parameter Description Default
Column Chromatographic column type "rp"
DB Type Annotation database "KEGG"
MS1 PPM Mass accuracy threshold (ppm) 15
RT Tol (s) Retention time tolerance for MFC clustering 10
Isotope No. Maximum isotopes considered per feature 3

Tip: Use "rp" (reverse phase) for most lipidomics and general metabolomics experiments. Switch to "hilic" for polar metabolite profiling.

Click Run Step 1. Annotation may take a few minutes depending on feature count.

Step 1 running

Figure 2.2: Step 1 running

When complete, a summary of annotated features appears below the parameters panel.