PIA

PIA - Protein Inference Algorithms
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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.

For more information, please go to:
https://github.com/mpc-bioinformatics/pia