Systems and methods for radiation treatment planning in proton therapy using pencil beam scanning (“PBS”) are described. More particularly, the systems and methods described in the present disclosure related to quantifying the output from a proton therapy system implementing PBS. The systems and methods described in the present disclosure can therefore be implemented when commissioning a new proton therapy system, or when performing quality assurance (“QA”) on a proton therapy system. A spot delivery pattern that includes a spiral out pattern is used for beam delivery. A number of control points along the spot delivery pattern define a beam pause time during which delivery of the proton beam is paused. Radiation measurements are obtained at the control points and at the end of the spot delivery pattern, and these radiation measurements are used to compute field size factors for field sized associated with the segments of the spot delivery pattern.