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A novel in situ method was performed for measuring emissions and fuel consumption of transport refrigeration units (TRUs). The test matrix included two fuels, two exhaust configurations, and two TRU engine operating speeds. The test fuels were California ultra low sulfur diesel and gas-to-liquid (GTL) diesel. The exhaust configurations were a stock original equipment manufacturer (OEM) muffler and a Thermo King pDPF™ diesel particulate filter. The two TRU engine operating speeds were high and low, as controlled by the TRU user interface. Test results indicate that GTL diesel fuel reduces all regulated emissions at high and low engine operating speeds. Separately, the application of a Thermo King pDPF reduced regulated emissions, in some cases almost entirely. Finally, the application of both GTL diesel and a Thermo King pDPF reduced regulated emissions at high engine operating speed, but with an increase in oxides of nitrogen (NOx) at low engine speed.