PeptideShaker

PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines

http://compomics.github.io/projects/peptide-shaker.html

SearchGUI

SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines and de novo sequencing algorithms.

http://compomics.github.io/projects/searchgui.html

Contributing to PeptideShaker (http://compomics.github.io/projects/peptide-shaker.html), SearchGUI (http://compomics.github.io/projects/searchgui.html) and their integration into Galaxy (https://galaxyproject.org/).