This repository contains supplementary materials relating to the manuscript "Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae".
Kang KB#, Ernst M#, van der Hooft JJJ#, da Silva RR, Park J, Medema M, Sung SH, Dorrestein PC. Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolite reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae. The Plant Journal (in press) (2019) (#Denotes equal contribution) DOI:10.1111/tpj.14292
Jupyter notebook used to map metadata onto the mass spectral molecular network in Cytoscape version 3.4.0 (Shannon et al., 2003) for the MZmine 2 (Pluskal et al., 2010) preprocessed dataset.
The folder called ClassyFire contains R scripts and data files used for performing automated chemical classification of the in silico annotated structures using ClassyFire (Djoumbou Feunang et al., 2016).
The folder called Mass2Motifs_2_MolecularNetwork contains R scripts and data files used for mapping Mass2Motifs (Van der Hooft et al., 2016; Wandy et al., 2018) on the mass spectral molecular networks (Wang et al., 2016; Watrous et al., 2012).
The folder called Heatmap_subclasses contains Jupyter notebook and data files for chemical subclass distribution heatmap (Figure 3(c)).
The folder called Heatmap_Mass2Motifs contains Jupyter notebook and data files for Mass2Motifs distribution heatmap (Figure 4).
Jupyter notebook used for creating Mass2Motifs-related feature table with ion count cutoff 1000.
Jupyter notebook used for drawing the heatmap.