PIA - Protein Inference Algorithms

PIA is a toolbox for MS based protein inference and identification analysis.

PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them semlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins.

The main contributors of PIA are currently the Medical Bioinformatics Group of the Medizinisches Proteom-Center, Ruhr-University Bochum.

More information on PIA can be found on the GitHub pages, especially the corresponding wiki pages.

Source Code

The source code of PIA is hosted at GitHub and can be accessed at https://github.com/mpc-bioinformatics/pia. Note that this is the source code for PIA, the source code of the KNIME nodes is automatically generated by GKN


The PIA nodes are relased under 3 clause BSD license.