Table 1.

Comparison of the features of MetaboDirect with other available software for the analysis of FT-ICR MS-based metabolomics data sets

	Feature	MetaboDirect	MetaboAnalyst	PyKrev	ftmsRanalysis	UME
Software appearance	User interface	Command line	Web GUI	Python module	R packagea	Web GUI
	Platform	Cross platform
	Language	Python, R	R, Java	Python	R	R
	Coding knowledge required	Minimalb	No	Yes	Yes	No
	Open source	✔
	Documentation	✔
Data pre-processing	Raw spectra processing	✖	✔c	✖	✖	✖
	Mol. formula assignment	✖	✔	✖	✖	✔
	Filtering and normalization	✔
	Thermodynamic indices calculation	✔ (DBE, GFE, AI, NOSC)	✖	✔ (DBE, AI, NOSC)	✔ (DBE, GFE, AI, NOSC)	✔ (DBE)
	Molecular class assignment	✔	✖	✔	✔	No
Data Exploration	Van Krevelen diagrams	✔	✖	✔	✔	✔
	Molecular composition plots	✔	✖	✔	✖	✖
	Thermodynamic indices plots	✔	✖	✔	✔	✔
	Chemodiversity indices	✔	✖	✔	✖	✖
	Pairwise comparisons	✔	✖	✖	✔	✖
	Database mapping	✔	✔	✖	✔	✖
Statistical analysis	PERMANOVA	✔	✖	✖	✖	✖
	NMDS	✔	✖	✖	✖	✔
	PCA	✔	✔	✔	✖	✖
Molecular transformation network analysis	Transformation calculation	✔	✖	✖	✖	✖
	Network construction	✔	✖d	✖	✖	✖
	Network Analysis	✔	✖d	✖	✖	✖
Extras	Customizable plots	✔	Limited	✔	✔	✖
	Multiple grouping variables	✔ (up to 2)	✖	✖	✔	✖

Abbreviations: DBE Double-bond equivalent, NOSC Nominal oxidation state of carbon, AI Aromaticity index, GFE Gibbs free energy

^aAlso available as the web-app FREDA[28]

^bNo coding experience is required to run MetaboDirect, but some experience in R is needed if fully customized plots are desired

^cFor LC-MS spectra

^dMetaboAnalyst can construct and analyze networks, but the list of nodes and edges must be provided by the user and are not generated directly by their pipeline