Hi Naveen,

there several different approaches to target this and also several interaction databases that you can get additional information from.

A variety of analysis approaches can be done in cytoscape and there are a lot of tutorials out there (http://www.cytoscape.org/) .

A) Getting data from open source databses:

Enter your Gene Names or Uniprot IDs in

String:

http://string-db.org/cgi/input.pl?UserId=kXT5dSd6d0Co&sessionId=AKVEPnUzDcYy&input_page_show_search=on   -> Multiple Proteins.

BioGrid:

https://thebiogrid.org/

or

Interact:

https://www.ebi.ac.uk/intact/

In each case, you are able to download interactions in txt format. These include usually:

Bait - Interactor - and some Scores.

This is a format that you can easily import into Cytoscape for a custom visualization. For Example you could adjust line width by using the interaction score (as it is done by string by default). 

If you simply want to use your data and not rely on public databases, you can generate these tables by your mass spec output data:

Bait - Interactor - Fold change - p value .. something like this.

(Fold change - IP versus control (IgG, bead)).

Hope this helps.

P.S.  You can also add public data directly in Cytoscape but I think the web interface is the easiest solution in the beginning.

Cheers

H.

thank you so much hendrik.I have used the string-db but its doesn't help much. I have uniprot id. 

you may have to enter Gene names , if you don't have them you get can them from the uniprot page as a list: 

http://www.uniprot.org/uploadlists/