The Parallel ROOT facility (PROOF) [3] is a distributed analysis system that enables to parallelize analysis jobs on a cluster of computers. The PROOF system dynamically identifies free resources on the worker nodes of the farm and it simplifies the job preparation for the user.The experience with a PROOF farm on an ATLAS Tier 3, integrated with a Xrootd distributed storage system is presented in this document.The performance of the parallel facility is evaluated for several ATLAS analyses with different requirements on I/O and CPU processing and on different environments. In particular the correlation of the parallel processing performance with the storage system is discussed for different scenarios, like a dCache storage on a distributed set of disk servers or a Xrootd system distributed among the local disks of the PROOF workers nodes.