I am reading some articles about use of ion mobility-mass spectrometry for determination of dynamics of proteins. I am not able to understand how to convert mass data to the structure of any state of the protein. If you have some references and/or data about this, please share it with me.
Are you asking about "Hydrogen exchange mass spectrometry for the analysis of protein dynamics" e.g. http://www.ncbi.nlm.nih.gov/pubmed/16208684
Basically, the speed of hydrogen-deuterium exchange of protein amide protons is dependent both on the static and the dynamic solvent accessibility of the different amide protons. Mass spectrometry can be used to measure the time course of hydrogen exchange, while NMR is used to determine exactly which protons exchange in which timeframe.
You can also refer to this JoVE article to gain a visual intuition of HD exchange mass spectrometry in understanding protein dynamics.
http://www.jove.com/video/50839/analyzing-protein-dynamics-using-hydrogen-exchange-mass-spectrometry
Other articles include, but are not limited to,
http://www.ncbi.nlm.nih.gov/pubmed/21173980
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279949/
Carol Robinson at Oxford University has done a lot of work on studying protein dynamics using MS-HDX. Much of it was done in collaboration with Chris Dobson on lysozymes but a lot more has been published in recent years as well.
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