Abstract-Scientific community is one of the major driving forces for developing and utilizing IT technologies such as Supercomputers and Grid. Although, the main race has always been for bigger and faster infrastructures, an easier access to such infrastructures in recent years created a demand for more customizable and scalable environments. However, introducing new technologies and paradigms such as Cloud computing requires a comprehensive analysis of its benefits before the actual implementation.In this paper we introduce the TimeCap, a methodology for comparing IT infrastructures based on time requirements and resource capacity wastage. We go beyond comparing just the execution time by introducing the Time Complexity as part of TimeCap, a methodology used for comparing arbitrary time related tasks required for completing a procedure, i.e., obtaining the scientific results. Moreover, a resource capacity wastage is compared using the Discrete Capacity, a second methodology as part of TimeCap used for analyzing resource assignment and utilization. We evaluate our methodology by comparing a traditional physical infrastructure and a Cloud infrastructure using our local IT resources. We use a real world scientific application for calculating plasma instabilities for analyzing time and capacity required for computation.