A metabolomics tool from Glasgow University

PATHOS ( is a web facility that allows one to display metabolites identified by mass spectrometry in the context of the metabolic pathways in which they occur. Textual output provides a listing of areas of metabolism, with the option of generating a Kegg map on which identified metabolites are marked.

Input data may consist of either experimental M/z values from mass spectrometric peaks, or refined lists of metabolites generated from the mass spec. data by other means. Quantitative data for the abundance of metabolites in different experimental conditions may be included in the input file. In this case changes are indicated by colour-coding, and clicking on metabolites on the maps generates appropriate bar charts.

New users should consult the on-line Instructions (menu bar, above). There is also a downloadable Pathos Manual which can be used with the example files provided (links, below). Other details are provided in our original 2011 publication. The final link, below, is to a Utility that allows one to search for metabolites by name, formula or mass.

Manual Examples Utility

Select and Upload File

Select a suitable data file and then click ‘Upload’.

Map Problem: 26.09.2023 (updated 23.10.2023)

Maps are no longer being generated from the pathway links in the results tables due to undocumented changes in the Kegg API. Kegg have not responded to our attempts to contact them for clarification. We are considering trying to restore the feature using different technology, but, even if feasible, this will take time. If you wish to be kept informed of our progress, please provide your details on the Feedback form (available after upload).