Reference dosimetry measurement in a pencil beam scanning system can exhibit dose fluctuation due to intra-spill spot positional drift. This results in a noisy reference dosimetry measurement against energy which could introduce errors in monitor unit calibration. The aim of this study is to investigate the impact of smoothing the reference dosimetry measurements on the type A uncertainty. Methods: The reference dosimetry measurement (D_w/MU) with a PTW 34045 advanced Markus chamber placed at 2 cm depth and a 10 x 10 cm^2 scanned field are performed for 98 energy layers on five non-consecutive days using a water tank. The PTW 34089 large area ionization chamber (LAIC) is placed at the same depth and the charges are measured with a single spot irradiation (M_spot^LAIC). (D_w/MU) and M_spot^LAIC are fitted with a linear and quadratic function to obtain a smooth plot of (D_w/MU) against the proton energy (reference dosimetry curve). Type A uncertainty of the measured reference dosimetry curve is compared against the de-noised fitted curve. Results: The repeatability of reference dosimetry measurement shows relative difference of up to 2.3% across the five days. The linear and quadratic fits between LAIC charges and the (D_w/MU) from PTW 34045 show a high R^2 values of more than 0.95. The maximum type A uncertainty of the de-noised reference dosimetry curve is lower (0.69% at 70.2 MeV) compared to the measured one (0.88% at 77.5 MeV). However, the average type A uncertainty of the denoised curve across all energies is higher compared to the measurements (0.50% versus 0.43%). Conclusion: We have presented the physical basis and procedure for fitting the charges measured with a LAIC to the reference dosimetry curve. The fitted reference dosimetry curve avoids large error in any energy layer but increases the average type A uncertainty across energies and should be used with caution. 
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Keywords: dosimetry; pencil beam scanning; proton therapy.
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