Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

Table 3

A summary of input and output file formats and availability of sample data for preprocessing tools. The precise formats are described in the instruction manuals for each tool.

Tool name	Input	Output	Availability of sample data
PowerGet	(1) PowerGet format (text file): MSGet tool is available for generating the text files from Xcalibur raw files; (2) MassBase SMS format (text file); (3) mzXML file generated from the Xcalibur raw files using the ReAdW tool^*a	(1) PowerGet format (text file): users can select the items and formats of the output file; (2) TogoMD format (text file)	KOMICS website
FragmentAlign	Deconvoluted peak data; (1) FragmentAlign format (text file, one of the NIST formats); (2) MassBase SMT format (text file); (3) GMD^*b format (text file in NIST^*c MSP format); (4).ELU file of AMDIS^*d software; Chromatogram data for deconvolution; CSV file exported by Pegasus III (text file)	FragmentAlign format (text file)	KOMICS website; A sample file of a standard compound library is included in the tutorial data
SpiceHit	Electropherogram data; (1) CSV file (text file); (2) ChemStation  .MS file (binary); Standard compound library; Excel file (binary)	(1) Tab-delimited text file; (2) Excel file	(1) KOMICS website; (2) Included in the tool; A sample of a standard compound library is included

^*aReAdW tool: available at http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW.
^*bGMD: Golm Metabolome Database, http://gmd.mpimp-golm.mpg.de.
^*cNIST: National Institute of Standards and Technology, http://www.nist.gov/.
^*dAMDIS: available at http://chemdata.nist.gov/mass-spc/amdis/.