When teaching STEM courses, it is important to introduce state-of-the-art techniques. Students need to learn how to conduct experiments, analyse data and choose the most effective approaches to address meaningful situations. Here we present the assessment of the implementation of a structured inquiry-based activity aimed at teaching students about protein mass and size. This activity emerges as an intervention in our educational module, designed to create a cognitive conflict that effectively drives a conceptual change. To evaluate the efficacy of this module, we collected data on students' perceived and actual knowledge through pre- and post-class surveys (n = 36 and 34, respectively, mean age 26 ± 2). Additionally, we evaluated lab reports using a detailed rubric. Results indicate that the practical innovation we propose is a challenging activity that promotes the accomplishment of our learning objectives. The activity led to improvements both in confidence and in actual mastery of theoretical concepts and techniques. After completing the activity, students were able to choose the most appropriate technique to solve specific problems. Furthermore, we found that the use of a structured questionnaire in lab reports helped students to accurately analyse and process experimental data. It also allows them to demonstrate understanding of technical limitations, while integrating the knowledge and skills acquired during the module. Overall, this activity provides notions that are conceivable and profitable, thus leading to successful conceptual changes.