Since lattice strain and charge density affect various material properties of graphene, a reliable and efficient method is required for quantification of the two variables. While Raman spectroscopy is sensitive and non-destructive, its validity towards precise quantification of chemical charge doping has not been tested. In this work, we quantified in-situ the fractional frequency change of 2D and G peaks in response of charge density induced by sulfuric acid solution as well as native lattice strain. Based on the experimental data and theoretical corroboration, we presented an optical method that simultaneously determines strain and chemically-induced charge density for three popular excitation wavelengths of 457, 514 and 633 nm. In order to expedite intercalation of dopant species through the graphene-SiO2 substrates, dense arrays of nanopores were precisely generated in graphene by thermal oxidation. The nano-perforated graphene membrane system was robust for multiple cycles of doping and undoping processes, and will be useful in studying various types of chemical interactions with graphene.