Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.

Propagation of transmissible spongiform encephalopathies is associated with the conversion of normal prion protein, PrP C , into a misfolded, oligomeric form, PrP Sc . Although the high-resolution structure of the PrP C is well characterized, the structural properties of PrP Sc remain elusive. Here we used MS analysis of H/D backbone amide exchange to examine the structure of amyloid fibrils formed by the recombinant human PrP corresponding to residues 90 -231 (PrP90 -231), a misfolded form recently reported to be infectious in transgenic mice overexpressing PrP C . Analysis of H/D exchange data allowed us to map the systematically H-bonded ␤-sheet core of PrP amyloid to the C-terminal region (staring at residue Ϸ169) that in the native structure of PrP monomer corresponds to ␣-helix 2, a major part of ␣-helix 3, and the loop between these two helices. No extensive hydrogen bonding (as indicated by the lack of significant protection of amide hydrogens) was detected in the N-terminal part of PrP90 -231 fibrils, arguing against the involvement of residues within this region in stable ␤-structure. These data provide long-sought experimentally derived constraints for high-resolution structural models of PrP amyloid fibrils.prion diseases ͉ transmissible spongiform encephalopathy ͉ amyloid structure ͉ mass spectrometry

The energetics of ubiquitin unfolding have been studied using differential scanning microcalorimetry. For the first time it has been shown directly that the enthalpy of protein unfolding is a nonlinear function of temperature. Thermodynamic parameters of ubiquitin unfolding were correlated with the structure of the protein. The enthalpy of hydrogen bonding in ubiquitin was calculated and compared to that obtained for other proteins. It appears that the energy of hydrogen bonding correlates with the average length of the hydrogen bond in a given protein structure.

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