Protocols for monitoring and avoiding radiation damage: A new method for X-ray absorption spectroscopy data, multiple datasets and fitting of X-ray absorption spectroscopy measurements with propagated uncertainties

X-ray Absorption Fine Structure (XAFS) is a powerful tool to characterize local structural information around an element of many chemically sensitive materials including bio-samples, inter-metallic clusters, metal–organic compounds and polymers. However, radiation damage is a major challenge for all X-ray-based spectroscopic techniques, including XAFS. Some of the X-ray absorption spectroscopy (XAS) experiments require high-intensity radiation that gives rise to photo-damage even in cryogenic conditions. This may lead to inaccurate structural determinations, highlighting the necessity of investigating the effect of radiation damage. Furthermore, EXAFS fittings for complex biological systems are challenging due to the numerous independent parameters involved in the model. This work explains both qualitative and quantitative understanding and identification of the radiation damage in the process of structural determination of N-truncated amyloid- β peptides, both in solution with a flow-cell and in frozen cryogenic samples. Multiple data refinements in XAFS analysis allow us to fit measurements to a structural model with more independent parameters. Standard XAFS analysis explores coordination geometry and local structure. However, absolute structural determination and reliable hypothesis testing are hindered by the exclusion of estimated experimental uncertainties. The eFEFFit package incorporates experimentally propagated uncertainties to determine reliable structural information. We develop eFEFFit to perform multiple data refinements for many applications such as bio-samples.