On analyzing data of biochemical reaction dynamics monitored by time-resolved spectroscopy, one faces the problem that the concentration time courses of the involved components are not directly observed, but the superposition of their absorption spectra. Furthermore the single spectra are often unknown, because the corresponding reagents cannot be isolated. We propose a method based on Bock's multiple shooting algorithm to estimate the rate constants and individual spectra simultaneously. Applying this procedure to a biochemical reaction we identify the specific rate constants characterizing the reaction dynamics as well as the nonobservable absorption spectra. The results lead to a better understanding of the kinetics of a novel modification reaction which was used as trapping reaction in disulfide bond mediated protein folding reactions.