We investigate the long term evolution of trajectories in the Fermi-Pasta-Ulam (FPU) system, using as a probe the first non-trivial integral $J$ in the hierarchy of integrals of the corresponding Toda lattice model. To this end we perform simulations of FPU-trajectories for various classes of initial conditions produced by the excitation of isolated modes, packets, as well as 'generic' (random) initial data. For initial conditions corresponding to localized energy excitations, $J$ exhibits variations yielding 'sigmoid' curves similar to observables used in literature, e.g., the 'spectral entropy' or various types of 'correlation functions'. However, $J(t)$ is free of fluctuations inherent in such observables, hence it constitutes an ideal observable for probing the timescales involved in the stages of FPU dynamics. We observe two fundamental timescales: i) the 'time of stability' (in which, roughly, FPU trajectories behave like Toda), and ii) the 'time to equilibrium' (beyond which energy equipartition is reached). Below a specific energy crossover, both times are found to scale exponentially as an inverse power of the specific energy. However, this crossover goes to zero with increasing the degrees of freedom $N$ as $\varepsilon _c \sim N^{-b}$, with $b \in [1.5, 2.5]$. For 'generic data' initial conditions, instead, $J(t)$ allows to quantify the continuous in time slow diffusion of the FPU trajectories in a direction transverse to the Toda tori.