Coupling the structural sensitivity of vibrational spectroscopics, such as Raman scattering and Raman optical activity (ROA), with the analytical insight provided by 2D generalized correlation analysis provides a new and exciting set of tools for structural biology. These new tools of 2DCos Raman and 2DCos ROA have the potential to provide new information on the mechanisms of conformational transitions of proteins and ribonucleic acids (RNA), such as those for folding and misfolding. However, the complexity of biomolecular transitions and the practicalities of spectroscopic data collection can make the analysis of 2DCos Raman and 2DCos ROA contour plots difficult. In this paper we present it summary of our methodology for obtaining reliable 2DCos contour maps and for their interpretation for folding and misfolding transitions in polypeptides, proteins and RNA. We demonstrate that our protocols for data pre-treatment greatly improve the quality of 2DCos contour maps, revealing the large amount of structural information that they contain, and then show that a moving window analysis is required to adequately follow biomolecular conformational transitions in detail. (C) 2007 Elsevier B.V. All rights reserved.