Here we present MS data of ERα-NTD protein samples exposed to 0-50 ms of X-ray beam at the Advanced Light Source (Berkeley, CA). Irradiated protein samples were digested with two sets of proteases, Asp-N and Lys-C, and pepsin. LC-MS/MS data was utilized to identify 16 sites of modification listed in table S3. LC-MS data were used to quantify the extent of oxidative modifications for these 16 residues. Quantification of oxidative modification for all sites has been done manually.