Laboratory courses are often designed using step-by-step protocols which encourage students to conduct experiments without thinking about what they are doing or why they are doing it. Such course design limits the growth of our students as scientists and can make it more difficult for a student to transition to the expectations of a research laboratory experience. To facilitate student growth in the process skills necessary to transition from the teaching laboratory to the research laboratory, an advanced biochemistry laboratory was redesigned to be team-taught and project-based culminating in a 7 week group research project in which the students worked collaboratively to propose, design, and troubleshoot their own experiments. Here, we report perceived student learning gains which provide additional evidence that inquiry- and research-based pedagogies impact student confidence with respect to the process skills required for self-directed research.