Scripts developed for generating Figure_1d (python) and Figure_1e (R) are available in this folder along with the source data tables needed as input. This figure highlights the generation of Stage 1 MassQL query, caluculation of delta masses and the sunsequent visualization of their distribution based on the class of bile acids (non-, mono-, di-, tri-, tetra-, pentahydroxy).
Scripts for generating Figure 2a,2b,2c,2d (python) are available with the source data tables. The input tables are obtained after searching for similar spectra of MassQL MS/MS output using fastMASST. This figure demonstrates the distribution of unique delta masses across different body parts in rodents and humans. Using UpSet plots we also highlight delta masses that are present in multiple bile acid classes.
Input data for generating the taxomomic tree in Figure_3b using iToL is available in the Source_data subfolder, which includes 1)list of all NCBI IDs of microbes in microbeMASST repository 2) list of NCBI IDs of microbes with MS/MS matches to bile acids 3) newick file of taxonomy generated by phyloT. Scripts for generating Figure_3c,3d,3e (R) are available with the respective input data files. For Figure_3d, 3e the feature tables are generated by getting peak areas with manual integration in Skyline.
Script for generating the heatmap in Figure_4b is provided along with the input table obtained from fastMASST search of spectral matches based on health condiiton. Peak areas for Figure_4c are based on manual integration using Skyline of diet samples in carnivores, omnivores and herbivores. Script for generating the box plots in Figure_4c is provided and also the table with the peak area.
Extracted ion chromatograms (EICs) for the polyamine bile amidates used for the retention time matching plots is provided. An excel file with the USI links for each of the MS/MS spectrum of polyamine bile amidates is also provided.
This step_by_step quide provides screenshots of the workflow on GNPS to add the bile acid MS/MS library and start a molecular networking job.
Scripts and source data for generating supplementary figures are provided here.
Supporting tables for main figures are provided here.
Supplementary data to support results in the main text of the manuscript is provided here for inspection.
For more information and questions regarding scripts please reach out to [email protected] and [email protected]