Background: Generalized polarizabilities (GPs) are important observables to describe the nucleon structure, and measurements of these observables are still scarce. Purpose: This paper presents details of a virtual Compton scattering (VCS) experiment, performed at the A1 setup at the Mainz Microtron by studying the $e p to e p gamma$ reaction. The article focuses on selected aspects of the analysis. Method: The experiment extracted the $P_{LL} -P_{TT} / epsilon$ and $P_{LT}$ structure functions, as well as the electric and magnetic GPs of the proton, at three new values of the four-momentum transfer squared $Q^2$: 0.10, 0.20 and 0.45 GeV$^2$. Results: We emphasize the importance of the calibration of experimental parameters. The behavior of the measured $e p to e p gamma$ cross section is presented and compared to the theory. A detailed investigation of the polarizability fits reveals part of their complexity, in connection with the higher-order terms of the low-energy expansion. Conclusions: The presented aspects are elements which contribute to minimize the systematic uncertainties and improve the precision of the physics results.