Purpose: The purpose of this study is to evaluate the impact of two methods of reporting planned dose distributions on the Gamma analysis pass rates for comparison with measured 2D film dose and simulated delivered 3D dose for proton pencil beam scanning treatment of the Imaging and Radiation Oncology Core (IROC) proton lung and liver mobile phantoms. Methods and materials: Four-dimensional (4D) computed-tomography (CT) image sets were acquired for IROC proton lung and liver mobile phantoms, which include dosimetry inserts that contains targets, thermoluminescent dosimeters and EBT2 films for plan dose verification. 4DCT measured fixed motion magnitudes were 1.3 and 1.0 cm for the lung and liver phantoms, respectively. To study the effects of motion magnitude on the Gamma analysis pass rate, three motion magnitudes for each phantom were simulated by creating virtual 4DCT image sets with motion magnitudes scaled from the scanned phantom motion by 50, 100, and 200%. The internal target volumes were contoured on the maximum intensity projection CTs of the 4DCTs for the lung phantom and on the minimum intensity projection CTs of the 4DCTs for the liver phantom. Treatment plans were optimized on the average intensity projection (AVE) CTs of the 4DCTs using the RayStation treatment planning system. Plan doses were calculated on the AVE CTs, which was defined as the planned AVE dose (method one). Plan doses were also calculated on all 10 phase CTs of the 4DCTs and were registered using target alignment to and equal-weight-summed on the 50% phase (T50) CT, which was defined as the planned 4D dose (method two). The planned AVE doses and 4D doses for phantom treatment were reported to IROC, and the 2D-2D Gamma analysis pass rates for measured film dose relative to the planned AVE and 4D doses were compared. To evaluate motion interplay effects, simulated delivered doses were calculated for each plan by sorting spots into corresponding respiratory phases using spot delivery time recorded in the log files by the beam delivery system to calculate each phase dose and accumulate dose to the T50 CTs. Ten random beam starting phases were used for each beam to obtain the range of the simulated delivered dose distributions. 3D-3D Gamma analyses were performed to compare the planned 4D/AVE doses with simulated delivered doses. Results: The planned 4D dose matched better with the measured 2D film dose and simulated delivered 3D dose than the planned AVE dose. Using planned 4D dose as institution reported planned dose to IROC improved IROC film dose 2D-2D Gamma analysis pass rate from 92 to 96% on average for three films for the lung phantom (7% 5 mm), and from 92 to 94% in the sagittal plane for the liver phantom (7% 4 mm), respectively, compared with using the planned AVE dose. The 3D-3D Gamma analysis (3% 3 mm) pass rate showed that the simulated delivered doses for lung and liver phantoms using 10 random beam starting phases for each delivered beam matched the planned 4D dose significantly better than the planned AVE dose for phantom motions larger than 1 cm (p ≤ 0.04). Conclusions: It is recommended to use the planned 4D dose as the institution reported planned dose to IROC to compare with the measured film dose for proton mobile phantoms to improve film Gamma analysis pass rate in the IROC credentialing process.