## 3 Results and Discussion  
Figure 3a shows Auger spectra of fragmenting thymine ions as a function of kinetic energy. The different spectra are measured at various time delays between the UV ionization and X-ray probe pulse as given in the figure. At negative delays, the ultra-short X-ray pulses hit molecules before the ultraviolet photoionization, thus, those spectra reflect the core hole decay of thymine in its electronic ground state. The spectrum is only weakly structured, centered around 504 eV photon energy, and possesses a width of around 10 eV. The Auger spectra of thymine have been published by us in another context, however, we realized during the work on this publication, that the energy calibration in [17] must be shifted up by 3 eV. The ADC(2) theory in [17] was too high in energy by about 1.5 eV; now it is too low compared to the experimental thymine spectrum by about the same amount. The overlap of UV and X-ray pulses in the pump-probe experiment manifests itself by a strong bleach of the main Auger line due to the removal of the population from the electronic ground state of neutral thymine [17]. This feature has also been used to set the zero-delay time for this experiment. As shown in Figure 3a, the Auger spectrum broadens considerably and develops a pronounced wing towards lower kinetic energies after the UV pulse excitation. The underlying reason for this wing are additional states newly populated by absorption of the UV pump pulse. In part, this is the desired, dissociative cationic state. Since the photoionization efficiency is enhanced by resonant excited states in the neutral molecule, there are certainly additional contributions from population in those states. From our previous study [17], we know that photoexcitation to the lowest valence state of the neutral results in a shift of the Auger spectrum to lower energies by about 5 eV within 500 fs. We can expect the Auger electron spectrum of the cationic state to shift more strongly in the same direction, simply based on the argument that Auger electron emission must work against one more charge in the molecular ion compared to the case of Auger decay from a core-ionized neutral molecule. The combination of energy shifts to the spectrum from excited and ionized states can explain unambiguously the appearance of a broad signature at lower electron kinetic energies. Two new features, having a width smaller than the broad underlying band, appear in the spectrum after about 400 fs. At a UV-X-ray delay of 600 fs, three features stand out in the lower kinetic energy wing. They continue to sharpen and shift towards higher kinetic energies as the delay progresses. At 1200 fs after UV excitation, the features have reached a steady state. We now compare the time-resolved spectra with steady-state Auger spectra of HNCO. The red dotted line in Figure 3b is the steady-state spectrum of HNCO as taken at the PLEIADES beamline of SOLEIL. The spectrum is characterized by 4 dominant peaks in the region between 494 and 508 eV. To further understand the character of these signatures, we also calculated the Auger decay features using the ADC(2) method. The method has been described in the context of thymine in [17]. The result of the calculation is shown as the solid blue spectrum on top of Figure 3b. The simulation reproduces the essential features of the steady-state experimental spectrum. The four lower energy maxima are  
Figure 3: Results of the transient Auger studies on fragmenting thymine ions. (**a**) The Auger spectra of the UV-fragmented molecules are shown as a function of delay between the UV and soft X-ray pulse. Narrow lines appear on a broadening baseline with increasing delay. The three vertical grey lines indicate the position of peak maxima for long delays, showing that the narrow lines shift towards higher energies with increasing delay. The time-resolved data is synthesized from single FEL shots.