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Evaluation of experiment performances and biases

MetaPepView provides a number of tools to perform evaluation and benchmarking of metaproteomics experiments. Two modules are dedicated to evaluation of metaproteomics experiments:

  • The Experimental performance module: Visualization and benchmarking of experimental performance parameters from spectral data (mzML) + proteomics data.
  • The Evaluate community composition module: Validate database quality used in DB search matching by comparing taxonomy composition from DB search matching + local db annotation against taxonomy composition from peptides (DB search and de novo) annotated by Unipept.

Evaluation_modules.PNG Experiment evaluation modules highlighted in the sidebar

In addition to dedicated experiment evaluation modules, MetaPepView provides a tool for investigation potential over- or underrepresentation of taxa in community compositions: the Taxonomic drop-off. This tool is part of the Community composition module.