We study the 1S-3S two-photon transition of hydrogen in a thermal atomic beam, using a homemade cw laser source at 205 nm. The experimental method is described, leading in 2017 to the measurement of the 1S-3S transition frequency in hydrogen atom with a relative uncertainty of 9 × 10 −13. This result contributes to the "proton puzzle" resolution but is in disagreement with the ones of some others experiments. We have recently improved our setup with the aim of carrying out the same measurement in deuterium. With the improved detection system, we have observed a broadened fluorescence signal, superimposed on the narrow signal studied so far, and due to the stray accumulation of atoms in the vacuum chamber. The possible resulting systematic effect is discussed.