Design science research (DESRIST) is a research process based on the activities of design (development). Prototyping method, in which an IT artifact is usually created, can be used as a vehicle for research. But it is different from a normal development work.
In design science research, there are a number of stages involved in the process: awareness of the problem, suggestion, development, evaluation, and conclusion (see http://desrist.org/design-research-in-information-systems/). There are two major activities in the prototyping based development stage: prototyping and knowledge creation (see the figure below).
First, there are a lot of normal system development (prototyping) activities, such as requirement analysis, design, programming, debugging, testing, etc. Second, it is also a knowledge creation process. In this process, conceptual components of the system were identified and defined; the relationships among them were also defined. The prototyping process is the underlying activity to provide raw materials for conceptual thinking and abstraction. Concepts are abstracted from the prototyping. At the same time, new theoretical developments are implemented into the prototyping process. These cycles of abstraction and implementation continue as both the knowledge and prototype are modified and improved. Eventually, the prototype becomes functionally complete and stable, and the theoretical model matures. Periodically, formative evaluations are conducted to confirm the design and demonstrate utility or usability, at same time to get external feedback for continuing research. Then formal evaluation would take place to conclude the project. During the development stage, there are multiple sources that contribute to the development of both processes: prior design experience, existing knowledge (literature), external feedback (exploratory interviews, and some other informal discussions with other people), and creativity (sudden idea pop-up).
The prototyping method used in the development is not different from normal information system development methodologies in practice. What makes the prototyping work different in a research, particularly design science research, is the knowledge creation process. Here, the prototype instantiation is not the only objective of the development. The knowledge, abstracted, representative, and generalized (to a certain degree), is another important objective for research. In this sense, prototyping is used as a vehicle to learn the problem domain, seek and refine the solution, and finally create knowledge. This process usually takes a lot of time and effort. The original design could be significantly changed, incorporating new discoveries and generating new ideas.
[Note: these thoughts (and the diagram) are based on my design research experience in my dissertation work. To cite:
Zheng, Guangzhi, “A Multidimensional and Visual Exploration Approach to Project Portfolio Management,” Ph.D Dissertation, Robinson College of Business, Georgia State University, 2009.