Formative assessment has long been identified as a critical element to teaching for conceptual development in science. It is therefore important for university instructors to have an arsenal of formative assessment tools at their disposal which enable them to effectively uncover and diagnose all students' thinking, not just the most vocal or assertive. We illustrate the utility of one type of formative assessment prompt (reading question assignment) in producing high-quality evidence of student thinking (student-generated reading questions). Specifically, we characterized student assessment data using three distinct analytic frames to exemplify their effectiveness in diagnosing student learning in relationship to three sample learning outcomes. Our data will be useful for university faculty, particularly those engaged in teaching upper-level biochemistry courses and their prerequisites, as they provide an alternative mechanism for uncovering and diagnosing student understanding.