A challenge for real-time monitoring of biochemical processes, such as cells, is detection of biologically relevant molecules. This is due to the fact that spectroscopy methods for detection may perturb the cellular environment. One approach to overcome this problem is coupled microfluidic-spectroscopy, where a microfluidic output channel is introduced in order to observe biologically relevant molecules. This approach allows for non-passive spectroscopy methods, such as mass spectrometry, to identify the structure of molecules released by the cell. Due to the non-negligible length of the microfluidic channel, when a sequence of stimuli are applied to a cell it is not straightforward to determine which spectroscopy samples correspond to a given stimulus. In this paper, we propose a solution to this problem by taking a molecular communication (MC) perspective on the coupled microfluidic-spectroscopy system. In particular, assignment of samples to a stimulus is viewed as a synchronization problem. We develop two new algorithms for synchronization in this context and carry out a detailed theoretical and numerical study of their performance. Our results show improvements over maximum-likelihood synchronization algorithms in terms of detection performance when there are uncertainties in the composition of the microfluidic channel.