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Purpose/objective(s): The purpose of this study is to present the root-cause analysis on failed patient-specific quality assurance (QA) measurements of pencil-beam-scanning (PBS) protons; referred to as PBS-QA measurement.Materials/methods: A criterion to fail a PBS-QA measurement is having a < 95% passing-rate in a 3.0%-3.0mm Gamma-index analysis. The 2D Gamma-index analysis toolkit was clinically used to obtain the passing-rate. A 2D detection array with finite-size ionization-chamber was utilized.Results: A total 2488 PBS-QA measurements were catalogued. The percentage of measurements for the sites of Head/Neck, Breast, Prostate, and Other are 53.3%, 22.7%, 10.5%, and 13.5% respectively. The percentage of measurements with a passing rate of 100%-to-95%, 94%-to-89%, and < 89% were 93.6%, 5.6%, and 0.8% respectively. The percentage of failed measurements with a < 95% passing rate was 10.9%. 8.1% became acceptable by either re-measurement or re-analysis to remove the setup or user errors. A feature of > 3% per-mm dose gradient along depth of beam path was observed on the failed measurements. To study the effect of depth dose gradient, a 3D Gamma-index analysis toolkit was used. 43.1% of measurements improved using this 3D toolkit. A feature among measurements that remained sub-optimal was a sharp > 3% per-mm lateral dose gradient that may not be well handled by using the detector size of 5.0mm in-diameter. An analysis of the sampling of finite-size detectors using 1D error function showed a large dose deviation at locations of low doses in a valley between two plateaus. User error, large depth dose gradient, and the effect of detector-size are identified.Conclusion: With an understanding and mitigation of these root causes, the goals of patient-specific QA, specifically detecting actual deviation of beam delivery or identifying limitations of dose calculation algorithm in used treatment planning system, can be directly related to the failure of PBS-QA measurements. [ABSTRACT FROM AUTHOR]