Each protein adopts a particular, well-defined, unique three-dimensional (3D) structure, which is directed to do certain functions. 3D structures of proteins can be well-determined at atomic level resolutions using x-ray crystallography and nuclear magnetic resonance (NMR) techniques. These high resolution structures of proteins are essential for understanding their structurefunction relationships. However, there is a divergent correlation between these experimental outcomes and requirements of current research in structural biology. In this background, ProCOOP algorithm was developed to predict population of secondary structures in proteins based on molecular mass of their deuterated-forms. By taking into consideration of many different structural and environmental factors, the ProCOOP validates its outputs and gives suggestion to improve experimental conditions for better predictions. The applications of ProCOOP for the data analysis in proteomics and genomics have also been brought into fore in detail.