Fig. 2.

Network of molecular features putatively annotated as bile acids with average group intensities, fold change values, mass differences, and cosine scores displayed. Molecular family #75 is composed of eight bile acid structural analogues (see details in Online Resource 6). Coloring according to the fold change values makes it easier to spot the families with differential abundance in cases vs. controls. Displaying average intensities for the three groups (cases, controls, paper blanks) allows for a quick control of the matrix signals (paper blanks, here none of the features were detected in the matrix) and confirmation of fold change. On edges, while the thickness of the connection represents to what extent two metabolites are chemically similar, the mass difference is essential to support annotation as it translates into how molecules differ from one another (e.g., water loss, conjugation, adducts, etc.)