The Hilbert-Huang transform is applied to analyze single-particle Lagrangian velocity data from numerical simulations of hydrodynamic turbulence. The velocity trajectory is described in terms of a set of intrinsic mode functions C(i)(t) and of their instantaneous frequency ω(i)(t). On the basis of this decomposition we define the ω-conditioned statistical moments of the C(i) modes, named q-order Hilbert spectra (HS). We show that such quantities have enhanced scaling properties as compared to traditional Fourier transform- or correlation-based (structure functions) statistical indicators, thus providing better insights into the turbulent energy transfer process. We present clear empirical evidence that the energylike quantity, i.e., the second-order HS, displays a linear scaling in time in the inertial range, as expected from a dimensional analysis. We also measure high-order moment scaling exponents in a direct way, without resorting to the extended self-similarity procedure. This leads to an estimate of the Lagrangian structure function exponents which are consistent with the multifractal prediction in the Lagrangian frame as proposed by Biferale et al. [Phys. Rev. Lett. 93, 064502 (2004)].