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Evaluation of experiment performances and biases

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

  • The Experiment performance evaluation module: Visualization and benchmarking of experimental performance parameters from spectral data (mzML) + proteomics data. This module processes and visualizes the performance evaluation dataset stored in the project.
  • The Community composition evaluation 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. Similarly to the Community composition module, this module visualizes the compositions and functions dataset stored in the project.

Evaluation_modules.PNG Experiment evaluation modules highlighted in the sidebar

In addition to dedicated experiment evaluation modules, meta-PepView 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.