This repository contains supplementary materials relating to the manuscript "Assessing Specialized Metabolite Diversity of Alnus species by a Digitized LC–MS/MS Data Analysis Workflow".
Kang, K.B., Woo, S., Ernst, M., van der Hooft, J.J.J., Nothias, L.F., da Silva, R.R., Dorrestein, P.C., Sung, S.H., Lee, M. (2020) Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow. Phytochemistry 173, 112292. doi:10.1016/j.phytochem.2020.112292
This folder contains Jupyter notebook and data files for calculating CSCS (Cemical structural and compositional similarity) metric and visualizing it via PCoA plot and chemodendrogram (Figs. 3A and 3B). The method and script was originally described in Brejnrod et al., 2019
This folder contains Jupyter notebook and a data file used to perform Hierarchycal Clustering Analysis (HCA) with Euclidean distance (Fig. 3D).
This folder contains Jupyter notebook and data files for principal component analysis (Fig. 3C).
This folder contains Jupyter notebook and a data file used to draw stacked chromatogram (Fig. 1).
This folder contains Jupyter notebook and data files for bioactive molecular networking, which was originally described in Nothias et al., 2018
This folder contains Jupyter notebook and data files for retreving class annotation for molecular familes using GNPS molecular networking, network annotation propagation (NAP) and Classyfire. More detailed description can be found at Ernst et al., 2019 -> Class annotation can be retreived using GNPS-embed MolNetEnhancer workflow which is described in the manuscript.
This folder contains Jupyter notebook and data files for integration of molecular networking and MS2LDA. More detailed description can be found at Ernst et al., 2019