Industrial purification of biomolecules is commonly based on a sequence of chromatographic processes, which are adapted slightly to new target components, as the time to market is crucial. To improve time and material efficiency, modeling is increasingly used to determine optimal operating conditions, thus providing new challenges for current and future bioengineers. At the Karlsruhe Institute of Technology (KIT), mechanistic modeling of protein chromatography has long been part of the curriculum of the Bioengineering master's degree program, supported by exercises using simulation software. Emphasis lies on nonlinear preparative chromatography, where the result strongly depends on the sample concentration. For undergraduate students to gain hands-on experience in model-based optimization, a three-week, in-depth laboratory course was designed on the purification of a ternary mixture of proteins using ion-exchange chromatography and mechanistic modeling. Students apply in-house software ChromX, which is made available for download, together with tutorials on numerics and practical applications. This article presents the working principle of ChromX and results of the laboratory course for undergraduate students.