As the launch of LISA Pathfinder (LPF) draws near, more and more effort is being put in to the preparation of the data analysis activities that will be carried out during the mission operations. The operations phase of the mission will be composed of a series of experiments that will be carried out on the satellite. These experiments will be directed and analysed by the data analysis team, which is part of the operations team. The operations phase will last about 90 days, during which time the data analysis team aims to fully characterize the LPF, and in particular, its core instrument the LISA Technology Package. By analysing the various couplings present in the system, the different noise sources that will disturb the system, and through the identification of the key physical parameters of the system, a detailed noise budget of the instrument will be constructed that will allow the performance of the different subsystems to be assessed and projected towards LISA. This paper describes the various aspects of the full data analysis chain that are needed to successfully characterize the LPF and build up the noise budget during mission operations. © 2011 IOP Publishing Ltd.