Hydrogen exchange protection factors can be extracted from sparse HDX-MS data

Hydrogen/deuterium exchange (HDX) monitored by mass spectrometry (MS) is a promising technique for rapidly fingerprinting structural and dynamical properties of proteins. The time dependent change in mass of any fragment of the polypeptide chain depends uniquely on the rate of exchange of its amide hydrogens but determining the latter from the former is generally not possible. Here we show that, if time-resolved measurements are available for a number of overlapping peptides that cover the whole sequence, rate constants for each amide hydrogen exchange (or equivalently, their protection factors) can be predicted. In most cases, the solution may not be unique, so a number of solutions have to be considered. Such analysis always provides meaningful constraints on protection factors and thus can be used in situations where obtaining more refined data is impractical, e.g., high throughput structure and interaction fingerprinting. It also provides a systematic way to improve data collection strategies in order to obtain unambiguous information at single residue level, e.g. for assessing protein structure predictions at atomistic level.