First four columns in the input file should be PubChem ID, KEGG ID, SMILES code and Name of Compounds, then followed by pair of columns for pvalue and fold-changes for each statistical comparison. Please use the example file as a templete. It is recommended to use median to calcualte the fold-changes, as median are not sensitive to outliers. For getting KEGG or PubChem IDs or SMILES codes for metabolites names, use CTS tool. For statistical analysis, use MetaBox software. A pvalue of 0.05 will be used to identify the significantly altered metabolites. Output files are a Cytoscape network in .SIF format and a node attribute file. Cytoscape can be downloaded from here Cytoscape.Org

Files downloaded from here need to be imported into Cytoscape for visualization. For more details - Visit this page

Barupal, Dinesh K., Pradeep K. Haldiya, Gert Wohlgemuth, Tobias Kind, Shanker L. Kothari, Kent E. Pinkerton, and Oliver Fiehn. "MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity." BMC bioinformatics 13, no. 1 (2012): 99.

Hartman, A. L., Lough, D. M., Barupal, D. K., Fiehn, O., Fishbein, T., Zasloff, M., & Eisen, J. A. (2009). Human gut microbiome adopts an alternative state following small bowel transplantation. Proceedings of the National Academy of Sciences, 106(40), 17187-17192.