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MassTRIX: Mass TRanslator into Pathways

This is MassTRIX reloaded, the 3rd version of MassTRIX.

The jobs on the old server remain still available at this link.
Should you encounter any unexpected behaviour, please let us know!


Here we present a walk-through example of how MassTRIX can be used in your research.
  • Click here to download the files used for the examples.

    These are the parameter used for the examples:
  • Scan mode: pos (human), neg (yeast)
  • Max error: 1 ppm
  • Database: KEGG with isotopes
  • Organism: homo sapiens, saccharomyces cerevisiae
  • log-fold change: SAGE 0.5
  • log-fold change: *.CEL Files 2.0
  • chip type: HuGene 1_0_st_v1

  • Click here to access the MassTRIX job result page for the examples.

    EXAMPLE_yeast: Exponential growth of Saccharomyces cerevisiae in rich medium

    • Click here to go to the MassTRIX results page for this example.
    • Saccharomyces cerevisiae cells were grown in rich (YPD) medium. Cell extract was collected following standard protocol and analyzed on a Bruker APEXQ 12 Tesla ICR-FT mass spectrometer.
    • Mass peaks with a signal-to-noise ratio larger than three were submitted to MassTRIX for identification.
    • Yeast genes that are highly expressed during exponential growth in YPD medium have been identified previously by Holstege et al., Cell, 1998. A list of genes has been retrieved from the YOUNG LAB. The corresponding raw data is available here. All genes with an expression level higher than five have been submitted to MassTRIX to be flagged on the pathway maps.
    • The main job result page gives an overview of all calculated metabolic pathway maps that are available in KEGG for the selected organism (here Homo sapiens). KEGG pathway maps are numbered and start with the identifier of the organism (here hsa). The overview table on the job result page indicates how many metabolites are on any specific map (Nmap), how many of these metabolites are associated to an enzyme that has been annotated in the selected organism (Norg), how many metabolites have been identified in the input data/mass spectrum (Nid), and how many of these identified metabolites are associated to the metabolism of the selected organism (Norgid).
    • Click on a pathway identifier to view the individual colored pathway maps (a legend to the color codes is given below each map). These maps are clickable.
    • The metabolites (circles) link to a MassTRIX page that shows all masses that correspond to the selected metabolite (i.e. isotope peaks). It also shows alternative interpretations (isomeres, compounds with identical chemical sum formular, compounds with masses within the selected error range). From that page, links to the KEGG descriptor of the compound are available.
    • The enzyme boxes directly link to the KEGG enzyme pages.
    • The pathway boxes link to the corresponding colored pathway maps in MassTRIX, so that you can easily access related pathways without having to go through the main result page.
    • Now let's look at the results. As you can see there are several genes of the Glycolysis/Gluconeogenesis pathway that are up or downregulated (indicated in green and red; yellow boxes indicate genes on the HuGene Chip that are normally expressed). Accordingly, metabolites have been identified on this pathway.
  • To verify the quality of your job, check out the error plot. This plot allows you to check whether there is any systematic error in the annotation of the peaks. In our example, all points scatter nicely around zero.
  • If something goes wrong with your job, you can take a look at the log file from your run. As MassTRIX makes use of the KEGG API SOAP/WSDL interface, one possible reason for a job to fail is when the connexion to KEGG breaks down due to problems on the internet.
  • In order to save your results from MassTRIX, you can download a file that contains all annotated mass peaks (including alternatives). All jobs are conserved for at least four weeks on the MassTRIX server.

KEGG Data is provided by the Kanehisa Laboratories for academic use. Any commercial use of KEGG data requires a license agreement from Pathway Solutions Inc. The Helmholtz Zentrum München imprint applies. If you find results from this site helpful for your research, please cite:

K. Suhre and P. Schmitt-Kopplin, MassTRIX: Mass TRanslator Into Pathways, Nucleic Acids Research, Volume 36, Web Server issue, W481-W484, 2008.

This page is maintained by Brigitte Waegele and Karsten Suhre, last modification: 07 December 2011

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