julianusz/pia repository overview

⁠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 seamlessly 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 images provided here are for the command line execution of PIA.

⁠Performing PIA compilation

A PIA compilation can be run like the following:

docker run --rm -v /path/to/searchengineoutput:/data/in -v /path/for/output:/data/out pia --compile -o /data/out/pia-compilation.xml /data/in/search_result1.dat /data/in/search_result2.idXML [more search results]

⁠Performing PIA analysis

For a PIA analysis, you will need a compiled PIA intermediate file (see above) and an analysis file in JSON format. On how to generate the analysis file, please look at the wiki at the PIA GitHub page https://github.com/mpc-bioinformatics/pia/wiki⁠

To run the analysis, you just need to perform the following:

docker run --rm -v /path/to/analysis-and-pia-file:/data/in -v /path/for/output:/data/out pia /data/in/pia-analysis.json /data/in/pia-compilation.xml