MS MetFrag XCMS Workflow
To try the workflow, please download and unzip first this data set to your own machine (click on the download button to the upper right of your browser window). Once you have that data unzipped, please follow the video tutorial MetFrag MS Workflow from a fresh VRE deployment, which will explain how to use the different pieces of data on the workflow.
Metabolite identification in clinical studies is a crucial step when trying to understand e.g. the courses of a disease on the metabolomic level. The MetFrag workflow goes a first step into this direction as it annotates molecules from compound (metabolite) databases to MS/MS spectra. This annotation is based on the mapping of in silico generated fragments to the experimental spectra and scoring of these mappings based on different criteria.
The workflow consists of different steps that include the pre-processing of the data using XCMS and CAMERA used to read the data from a given mzML file and to detect and annotate features. Given this annotation MetFrag parameter sets are generated that are passed to the MetFrag CLI Batch tool performing the actual processing that includes the annotation of molecular structures to the data. In the following the single steps will be described in detail.
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Funded by the EC Horizon 2020 programme, grant agreement number 654241 |  |
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