Proteomics: Analysis of spectral data

The goal of disease-related proteogenomic research is a complete description of the unfolding of the disease process from its origin to its cure. With a properly selected patient cohort and correctly collected, processed, analyzed data, large scale proteomic spectra may be able to provide much of the information necessary for achieving this goal. Protein spectra, which are one way of representing protein expression, can be extremely useful clinically since they can be generated from blood rather than from dis eased tissue. At the same time, the analysis of circulating proteins in blood presents unique challenges because of their heterogenei ty, blood contains a large number of different abundance proteins generated by tissues throughout the body. Another challenge is that pro tein spectra are massively parallel information. One can choose to perform top-down analysis, where the entire spectra is examined and candidate peaks are selected for further assessment. Or one can choose a bottom-up analysis, where, via hypothesis testing, individual proteins are identified in the spectra and related to the disease process. Each approach has advantages and disadvantages that must be understood if protein spectral data are to be properly analyzed. With either approach, several levels of information must be in tegrated into a predictive model. This model will allow us to detect disease and it will allow us to discover therapeutic interventions that reduce the risk of disease in at-risk individuals and effectively treat newly diagnosed disease.