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Untargeted pipeline demo (WIP)

Open joewandy opened this issue 6 months ago • 0 comments

PR to add demo using vimms to generate synthetic data so we can test the performance of a typical untargeted data processing pipeline in LC/MS metabolomics.

So we generate chemicals in various experimental setup, write their mzml files + corresponding ground truth. The mzml files are then passed into a pipeline that tries to infer back chemical identities from spectral data. Since it's synthetic data, we can easily evaluate pipeline performance for all these steps:

  1. Peak picking
  2. Alignment
  3. Group related peaks like isotopes and adducts together.
  4. Identification, by matching to standards / spectral library.

Still work in progress, do not merge yet!!

joewandy avatar Jun 10 '25 17:06 joewandy