Synchrotron radiation (SR) has become a preferred technique for the analysis of a wide range of archeological samples, artwork, and museum specimens. While SR is called a nondestructive technique, its effect on proteinaceous specimens has not been fully investigated at the molecular level. To investigate the molecular level effects of synchrotron X-ray on proteinaceous specimens, we propose a methodology where four variables are considered: (1) type of specimen: samples ranging from amino acids to proteinaceous objects such as silk, wool, parchment, and rabbit skin glue were irradiated; (2) synchrotron X-ray energy; (3) beam intensity; (4) irradiation time. Irradiated specimens were examined for both macroscopic and molecular effects. At macroscopic levels, color change, brittleness, and solubility enhancement were observed for several samples within 100 s of irradiation. At molecular levels, the method allowed one to quantify significant amino acid modifications. Aspartic acid (Asp), wool, parchment, and rabbit skin glue showed a significant increase in Asp racemization upon increasing irradiation time with rabbit skin glue showing the greatest increase in d-Asp formation. In contrast, Asp in silk, pure cystine (dimer of cysteine), and asparagine (Asn) did not show signs of racemization at the irradiation times studied; however, the latter two compounds showed significant signs of decomposition. Parchment and rabbit skin glue exhibited racemization of Asp, as well as racemization of isoleucine (Ile) and phenylalanine (Phe) after 100 s of irradiation with a focused beam. Under the experimental conditions and sample type and dimensions used here, more change was observed for focused and low energy (8 keV) beams than unfocused or higher energy (22 keV) beams. These results allow quantification of the change induced at the molecular level on proteinaceous specimens by synchrotron X-ray radiation and help to define accurate thresholds to minimize the probability of damage occurring to cultural heritage specimens. For most samples, damage was usually observed in the 1-10 s time scale, which is about an order of magnitude longer than SR studies of cultural heritage under X-ray fluorescence (XRF) mode; however, it is consistent with the duration of X-ray absorption spectroscopy (XAS) and microcomputed tomography (μCT) measurements.