For each metabolite (or feature – unique m/z & RT pair) identified, ion intensity (peak height or peak area) is reported for each sample and delivered in a spreadsheet format. Semi-quantitative analysis can be performed comparing the relative intensity of a specific metabolite between samples. However, due to differing ionization efficiencies of each metabolite, intensity cannot be compared between different metabolites. Quantitative analysis is possible when a standard is available (preferably an isotopically labeled standard) and a calibration curve has been generated for the experiment. Mass spectrometry data can be challenging to interpret due to a number of factors inherent to the technique, including competitive ionization of metabolites co-eluting in a sample, limits of detection, different metabolites that are isomers or isobars, in-source fragmentation, ionization efficiency and chromatographic resolution. The JGI Metabolomics group is available to discuss and aid with analysis and interpretation.
A metabolite “atlas” is also provided in spreadsheet format. This lists each identified metabolite identified as well as relevant compound information (e.g. structure; compound ids; description; links to pubchem, chebi, metacyc, etc).
As supplementary / supporting information, pdf images are also provided of (1) chromatograms of each compound in each sample and (2) MS/MS identification figures in which the MS/MS fragmentation spectra of a metabolite in a sample is given on the positive axis and MS/MS of the identified standard (if available) on the negative axis. An example is shown below: