Hi,
In my experiment I am interested to find interaction partner of the protein of my interest. For that I tagged my Protein with GFP and a pull down experiment was performed and then I analysed the pull down soup by mass spec. I have list of protein with me from mass spec. And now i want to group those proteins according to their biological process,molecular function and cellular localization.
It sounds like what you want to do is Gene Ontology analysis. There are many tools that can do that. These tools do not only assign gene ontology classes to genes (or in your case proteins derived from genes) and group the genes, they also calculate enrichment statistics for the different gene ontology classes. There are different ways to do that. The common (or maybe older) approaches just calculate the statistics for every class. That is a bit tricky since the Gene Ontology really is an ontology so terms at higher levels (near the trunk of the tree) contain groups of genes that also appear in branches that go from there. In that case you want to know about the change in the branch first and only get information about the more central class when that is still significant after you remove the subclass that already was found to be significant. A process often denoted as "pruning". The Bioconductor package "TopGO" can do that and so can our own tool GO-Elite. You can find it here: http://www.genmapp.org/go_elite/ and it is described here: http://bioinformatics.oxfordjournals.org/content/28/16/2209.abstract
I have had a lot of luck with Enrichr which combines a number of databases (Panther, Kegg, TRANSFAC etc.) into one tool. It's very easy to use - all you need is a list of IDs to paste in.
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