A permanent magnet electron cyclotron resonance ion source PMECR II is used to generate proton ions for radio frequency quadrupole (RFQ) injection at Peking University (PKU). The proton fractions of the extracted beam were measured at the positions both after extraction system of ion source and the end of low energy beam transport line (LEBT). Experiments show that the proton fraction has a rise time within a beam pulse, and its value varies with pulse width and microwave power. The proton fractions measured at different positions are comparable.