Bile acid overlap in the structural and mass spectrometry databases for GNPS/MassIVE BILELIB1932, Human Metabolome Database (HMDB)50 (only considering detected bile acids), and LipidMAPS51 was derived from deposited SMILES codes (links to databases are provided in the code availability section). For the purpose of this figure to visualize the data in the three repositories all SMILES79 with the (SMARTS string-defined) substructure “C-,=C12-,=C-,=C-,=C-,=C-,=C-,=1-,=C-,=C-,=C3-,=C4-,=C-,=C-,=C-,=C-,=4(-,=C-,=C-,=C-,=3-,=2)-,=C” and a carboxylic acid ester (“C(=O)O”), (thio)ester (“C(=O)S”), or amide (“C(=O)N”) in their caboxy-tail were considered as bile acids. Substructure searches were conducted via RDKit (http://www.rdkit.org). Diastereomeric information was not considered for the comparisons across bile acids.
Mass shifts were calculated by subtracting the mass of the unconjugated bile acid (e.g., C24H40+xO2+x with x = ‘number of hydroxyl modifications’ on the respective bile acid for C24 bile acids; formula was adjusted for C22-C28 bile acids (as defined in LipidMAPS), respectively) from the mass of the (potentially) conjugated bile acid. Only mass differences > 40 mz are shown.
Average quantification values of individual bile acids reported by the Human Metabolome Database (HMDB)50 in blood and bile. Cholic acid is the most concentrated in both blood and bile at 48.5 μM and ~32 mM respectively. It should be noted that values reported in HMDB used for this figure originate from values reported in published studies and that HMDB has the citations to each study. The bars indicate the average of the reported values in HMDB, but oftentimes only a single value is available. The numbers in the parentheses represent the number of data points from HMDB in bile and blood, in that order. The vertical lines indicate the range from the lowest to the highest reported value, including the ranges of the value and uncertainties reported in HMDB. Important to note here is that the lines should not be considered a statistical interpretation as they only inform on the dynamic range of literature reported values in HMDB. For ursodeoxycholic acid 3-sulfate, additional concentrations from literature (Bathena et al. 2013, Murata et al. 1983) were included along with the one HMDB reported value that was reported.