Reporting metabolomics data

Metabolomcis data should be published in a format that is reliable and useful. There are guidelines/SOPs to achieve this. Also, MetaMapp mapping and visualization essentially need data in standardized format. 

Below papers would give you an idea what must be included in the final data matrix before sending it out for publications. Check the supplement sections. 

http://www.nature.com/nbt/journal/v25/n8/full/nbt0807-846b.html MSI metabolomics standard initiative, 2007 

http://www.ncbi.nlm.nih.gov/pubmed/18269577 by O Fiehn, Quality controls in plant metabolomics. 2008

http://www.plantcell.org/content/23/7/2477.full  Recommendations for reporting metabolite profiling data. 2011. Plant Cell. 

These efforts are highly appreciated, but unless the Journal editors adopt it as an mandatory guideline, only a small number of labs will be reporting metabolomics data according to MSI guidelines. One of obstacles is having a really good mass spectrometer but not the right informatics that generate the MSI compliance data. But, MetaboAnalyst.ca and MetabolomeExpress  can significantly assist you to convert raw MS data into useful data matrices.