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Manchester Centre for Integrative Systems Biology


PUTMEDID-LCMS is a tool operating in the Taverna environment for putative identification of metabolites from accurate mass data acquired in mass spectrometry-based metabolic profiling studies.

Three workflows, together defined as PUTMEDID-LCMS, have been developed using the open source Taverna environment to perform putative metabolite identification based on accurate mass data acquired from liquid chromatography-electrospray mass spectrometry instruments. Three workflows perform the following steps. (Step 1) Generation of a list of pairwise peak correlations required for input to workflow 2 (workflow 1) (Step 2) Annotation of features to group different ion types of the same metabolite based on mass differences, similar retention times and correlation coefficient between peak responses (workflow 2). (Step 3) Matching of accurate m/z to the accurate mass of neutral molecules and associated molecular formula in a reference file within a specified mass tolerance (workflow 2). (Step 4) Matching of the molecular formulae to a reference file of metabolites (workflow 3). The parameters employed in all workflows are user defined and can be optimized for particular datasets or instruments. The workflows have been validated with multiple sample types including intracellular extracts of yeast and human biofluids (urine and serum).

The following files are available (download zip):

  1. Standard Operating Procedure (PUTMEDID_LCMS_SOP_v1.0.doc)
  2. Three Workflows for operation in the Taverna environment (*.xml)
    • Workflow 1 (List_CorrData.xml)
    • Workflow 2 (annotate_Massmatch.xml)
    • Workflow 3 (matchMF_MF.xml)
  3. Pre-defined Files
    • Tav_isotopes.txtfile (for use in workflow 2)
    • Tav_adducts.txt file (for use in workflow 2)
    • trimMMD_sortAmass.txt file (for use in workflow 2)
    • trimMMD_sortMF.txt file (for use in workflow 3)
  4. Example Study Files
    • Study_pospeaks.txt (input for use in workflows 1 and 2)
    • Study_posdata.txt (input for use in workflow 1)
  5. Example output files
    • Study_pos_CorrListP.txt (output from workflow 1)
    • Study_pos_hits_3ppmMMD.txt (output from workflow 2 sorted by MatchedMF)
    • Study_pos_allpeaks_3ppmMMD.txt (output from workflow 3)
    • Study_pos_listpeaks_3ppmMMD.txt (output from workflow 3)
    • Study_pos_matchedpeaks_3ppmMMD.txt (output from workflow 3)