Pump probe spectroscopy techniques have enabled the direct observation of a variety of transient molecular species in both ground and excited electronic states. Time-resolved vibrational spectroscopy is becoming an indispensable tool for investigating photoinduced nuclear dynamics of chemical systems of all kinds. On the other hand, a complete picture of the chemical dynamics encoded in these spectra cannot be achieved without a full temporal description of the structural relaxation, including the explicit time-dependence of vibrational coordinates that are substantially displaced from equilibrium by electronic excitation. Here we present a transient vibrational analysis protocol combining ab initio direct molecular dynamics and time-integrated normal modes introduced in this work, relying on the recent development of analytic time-dependent density functional theory (TDDFT) second derivatives for excited states. Prototypical molecules will be used as test cases, showing the evolution of the vibrational signatures that follow electronic excitation. This protocol provides a direct route to assigning the vibrations implicated in the (photo)dynamics of several (photoactive) systems.