Details of my dataset: Phospho-proteomics data generated from MS LTQ Thermo Finigan. Sample are from 2 groups: control v/s disease model of heart. The samples were collected from 3 different animals in each group. The method uses two phase column (enrichment column IMAC and RP C18(analysis column)). The details of the method used is published in this journal article http://www.sciencedirect.com/science/article/pii/S1570023211005617
I need your advise regarding few softwares / easy methods that can be used to identify deferentially phospho-sites (TSY residues phosphorylated) from Thermo Finigan RAW files or from mZxml files. What I mean is: for example say on the protein-A if there are several residues which can be phosphorylated only in treatment sample but not in control. I want to list out proteins that will hold such differential regulated phospho-sites having statistical significance.
Thank you
