Table 1.

Software tools commonly used for the preprocessing of metabolomics data

Tool	Instrument data type	Software type	Website	References
XCMS	LC–MS, GC–MS	R Package	http://bioconductor.org/packages/release/bioc/html/xcms.html	Smith et al. (2006)
OpenMS—FeatureFinderMetabo	LC–MS	GUI	http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html	Bertsch et al. (2010)
MetAlign	LC–MS	Windows GUI	http://www.wageningenur.nl/en/show/MetAlign-1.htm	Lommen & Kools (2012)
MS-DIAL	LC–MS	Windows GUI	http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/index.html	Tsugawa et al. (2015)
mzMatch	LC–MS	R Package	http://mzmatch.sourceforge.net/index.php	Scheltema et al. (2011)
IDEOM	LC–MS	Excel Template	http://mzmatch.sourceforge.net/ideom.php	Creek et al. (2012)
AMDIS	GC–MS	Windows GUI	http://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:amdis	Meyer et al. (2010)
MetaboliteDetector	GC–MS	CLI, GUI	http://md.tu-bs.de	Hiller et al. (2009)
MET-IDEA	GC–MS	Windows CLI	http://bioinfo.noble.org/download	Broeckling et al. (2006)
MeltDB	LC–MS, GC–MS	Web App	https://meltdb.cebitec.uni-bielefeld.de/cgi-bin/login.cgi	Kessler et al. (2013)
metaMS	GC–MS	R Package	http://bioconductor.org/packages/release/bioc/html/metaMS.html	Wehrens et al. (2014)
MSeasy	GC–MS	R Package	https://cran.r-project.org/web/packages/MSeasy/index.html	Nicolè et al. (2012)
SpectConnect	GC–MS	Web App	http://spectconnect.mit.edu	Styczynski et al. (2007)
rNMR	NMR	R Package	http://rnmr.nmrfam.wisc.edu	Lewis et al. (2009)

CLI command line interface, GUI graphical user interface