I have a question regarding processing DDA data. Once I perform findChromPeaks the MSMS part of my data disappear (which do not happen when I do the same thing in R). Is there any way to keep this information throughout the all workflow?
You can keep your MSMS if you use msPurity workflow available on W4M.
1- do your usual xcms workflow (Including you DDA files)
2- launch MSMS analysis with mspurity tools
3- merge xcms output and mspurity ones with frag4features
Un exemple Galaxy | France | Published Workflow | Workflow XCMS_CAMERA_msPurity
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