I want to reproduce the results obtained in a paper where the authors generate a group of phosphoproteomics results under different conditions. They used the peak intensities based quantification and a software called MetaCore (not free) to make a pathway analysis.
I have heard about IPA (not free) and IPathwayGuide and I'm looking for a similar (and if its possible, free) tool. I would like to know which ones are the most popular softwares used in pathway analysis from proteomic/phosphoproteomic results and what databases do they use for it (KEGG, for example).
Thank you for your answers!!