In the current Participatory Design (PD) practice, paper-based approaches are commonly applied. However, the use of software tools can potentially enhance the PD process and outcome, given their flexibility for prototype presentation, data storage, retrieval and analysis. Driven by this assumption, we developed the specific-purpose PD online tool PDotCapturer. To evaluate the effectiveness of PDotCapturer, as compared with a paper-based approach, we conducted a within-subjects study where 33 participants were asked to provide feedback on e-learning prototypes, using either paper or PDotCapturer in one session and vice-versa in another session. The evaluation criteria were quantity and quality of the participants’ comments. For qualitative data analysis, we applied the refined coding scheme CAt+. Results show that using PDotCapturer partly led to feedback of higher quality, but the number of comments was higher for the paper-based approach. Our work contributes to the HCI community by augmenting the repertoire of the PD toolbox.