We consider a capacitated job shop problem with order acceptance. This research is motivated by the management of a research and development project pipeline for a company in the agricultural industry whose success depends on regularly releasing new and innovative products. The setting requires the consideration of multiple problem characteristics not commonly considered in scheduling research. Each job has a given release and due date and requires the execution of an individual sequence of operations on different machines (job shop). There is a set of machines of fixed capacity, each of which can process multiple operations simultaneously. Given that typically only a small percentage of jobs yield a commercially viable product, the number of potential jobs to schedule is in the order of several thousands. Due to limited capacity, not all jobs can be started. Instead, the objective is to maximize the throughput. Namely, to start as many jobs as possible. We present a Mixed Integer Programming (MIP) formulation of this problem and study how resource capacity and the option to delay jobs can impact research and development throughput. We show that the MIP formulation can prove optimality even for very large instances with less restrictive capacity constraints, while instances with a tight capacity are more challenging to solve.