Compound annotation
First, for all compounds in the dataset we used Mass Profiler Professional (v.B.14.5; Agilent Technologies, Inc.) to putatively annotate common chemical names based on mass and isotope ratios with an error window of < 10 ppm. In this workflow, compounds are first searched against an in-house database of authentic standards followed by a search against an in-house database compiled from METLIN, human metabolome database (HMDB), Kyoto encyclopedia of genes and genomes (KEGG), and Lipid Maps. Second, we used MS/MS to generate additional annotation information for all compounds used in our biomarker models. The LC/MS chromatographic method was replicated for LC–MS/MS using 10, 20, and 40 eV collision energies on an Agilent 6545 Q-TOF, at a scan rate of 2 spectra/s, 1.3 m/z isolation width, and 30 s retention time window. Fragmentation data were matched to standards from the NIST 14 and 17 MS/MS spectral libraries.