Electrospray-ionization (ESI) mss spectrometry is used to monitor higher order structural changes of polypeptide induced by alteration of the pH or organic solvent composition in the protein solution environment. A bimodal charge-state disribution is observed in the ESI mass spectrometry of ubiquitin (relative molecualr mass 8565) in solution containing small amounts (<20%) of organic solvents. The distribution of peaks at high m/z (low-charge state) is found to represent the protein in its native, globular state; the higher-charge-state distribution is characteristic for a more extended conformation. Addition of methanol denaturant in excess of 40% v/v is needed to eliminate the low-charge-state distribution completely. Lesser amounts of acetonitrile, acetone, or isopropanol (∼20%) are reqiored to denature the ubiquitin protein. Other proteins showing conformational efects in their ESI mass spectra are also illustrated. While the ESI spectra are related to solution phase structure, ESI-tandem mass spectrometry of multiply charged molecular ions of different conformation is suggested as a probe of gas-phase protein three-dimensional structure.