A system for commissioning a machine such as an internal combustion engine includes commissioning probes, and a user interface having a computer receiving test data from the commissioning probes. The computer is structured to store a commissioning profile for the machine on a memory, and to populate the commissioning profile based on a compensation factor that depends on a difference between a performance response of ancillary equipment connected with the machine and an expected response. The computer outputs a commissioning suitability signal based on comparing the commissioning profile to a target profile.