Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry

David P Leader,Michael P Barrett,Karl Burgess,Darren Creek

doi:10.1002/rcm.5245

Abstract

This work describes a freely available web-based facility which can be used to analyse raw or processed mass spectrometric data from metabolomics experiments and display the metabolites identified – and changes in their experimental abundance – in the context of the metabolic pathways in which they occur. The facility, Pathos (http://motif.gla.ac.uk/Pathos/), employs Java servlets and is underpinned by a relational database populated from the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Input files can contain either raw m/z values from experiments conducted in different modes, or KEGG or MetaCyc IDs assigned by the user on the basis of the m/z values and other criteria. The textual output lists the KEGG pathways on an XHTML page according to the number of metabolites or potential metabolites that they contain. Filtering by organism is also available. For metabolic pathways of interest, the user is able to retrieve a pathway map with identified metabolites highlighted. A particular feature of Pathos is its ability to process relative quantification data for metabolites identified under different experimental conditions, and to present this in an easily comprehensible manner. Results are colour-coded according to the degree of experimental change, and bar charts of the results can be generated interactively from either the text listings or the pathway maps. The visual presentation of the output from Pathos is designed to allow the rapid identification of metabolic areas of potential interest, after which particular results may be examined in detail. Copyright © 2011 John Wiley & Sons, Ltd.

Highlights

The application of high-resolution mass spectrometry to the analysis of the abundance of small molecules[1] has allowed large numbers of cellular metabolites to be identified simultaneously and changes in their concentrations to be studied under different experimental conditions
Raw data from mass spectrometry typically contain both noise and a large number of genuine metabolite peaks, and sophisticated methods have been developed for refining these data and determining the possible molecular formulae corresponding to each detected molecular mass
Bespoke facilities[16,17] for visualizing metabolites from mass spectrometry have been provided for the different representations offered by the two main databases of metabolic pathways, MetaCyc[18] and Kyoto Encyclopaedia of Genes and Genomes (KEGG).[19]

Summary

Introduction

The application of high-resolution mass spectrometry to the analysis of the abundance of small molecules[1] has allowed large numbers of cellular metabolites to be identified simultaneously and changes in their concentrations to be studied under different experimental conditions. KEGG has developed a Mapper tool[14] that enables interactive imposition and colour highlighting of metabolites in their pathway maps, and this interactive approach has been extended further in iPath.[15] these facilities are not designed for routine analysis of mass spectrometry data. Bespoke facilities[16,17] for visualizing metabolites from mass spectrometry have been provided for the different representations offered by the two main databases of metabolic pathways, MetaCyc[18] and KEGG.[19] The MassTRIX facility,[17] which employs the KEGG pathways environment to represent metabolomics data, has been a useful and simple tool with which to contextualize metabolomics data sets. If a metabolite in an experimental data set is identified on the basis of more than one m/z value (e.g. from different adducts) only the data containing the highest value are taken and the others discarded

Results

Discussion

Conclusion