Proteins play essential roles in every cellular process including the catalysis of biochemical reactions, structural functions to maintain cell shape, and cell signaling. Therefore, the analysis of proteins are essential to the understanding of biological systems and the mechanism of disease progression. Specific proteins are being discovered as biomarkers or therapeutic targets to improve disease diagnosis, prognosis, or treatment outcomes. Studies on proteins include the level of protein expression in a cell type or tissue, post-translational modifications, the functions of protein and their modified forms, as well as protein-protein interactions. The association of a specific protein and its modified form could be used for diagnosis, prognosis, or treatment of diseases. Investigations of interesting questions about proteins rely on sensitive methods for efficient protein isolation, detection, and quantification.

 

The field of “proteomics” has emerged and grown since the global analyses of structures and functions of proteins almost two decades ago following progress on the Human Genome Project. Advances in proteomics research have been facilitated with new technological breakthroughs in mass spectrometry instrumentation, as well as high-throughput protein production and array technologies. Proteomics research has three developmental phases. The first phase is the rapid development in mass spectrometry instruments, protein isolation and separation technologies, computational tools for protein identification, quantification and bioinformatic analysis. The second phase is the application of proteomic technologies for cataloging and quantitative analysis of proteomes such as different cells, tissues, body fluids, organs, and simple organisms like bacteria, yeast, and drosophila, as well as subproteomic analyses such as organelle proteomics, phosphoproteomics, glycoproteomics, acetylated proteomics, and other types of modified forms of proteomics, as well as interactive proteomics. As a result of these efforts, a number of protein databases have been established to document these characterizations and provide repositories to store new protein identifications. Analyses of the databases using statistical and bioinformatic tools have identified a number of potential disease biomarkers. The third phase of proteomics is the accurate, reproducible, and high throughput quantitative proteomics for verification and validation of targeted proteins identified from genomic and proteomic discovery with the purpose of developing new disease-associated proteins for personalized medicine. The result of this development is the creation of “Clinical Proteomics” with special emphasis of the application of proteomic technologies to all aspects of clinical investigations including academic, clinical laboratory, pharmaceutical, and diagnostic settings.

 

We are one of five Proteome Characterization Centers (PCCs) funded by the National Cancer Institute (NCI). The primary goal of the PCCs is to comprehensively characterize tumors and biospecimens in order to systematically identify, prioritize, and verify cancer-related proteins for the development of biomarkers. The proteomic technologies for cancer proteome characterization include protein microarray, immunoassays, and mass-spectrometry-based methods. The aim is to bridge genomic and proteomic discoveries to medicine using proteomic technologies. Our Center is equipped with a number of proteomic instruments including six mass spectrometers, five liquid chromatography systems, and a protein array platform for proteomic characterizations. In addition, we have two liquid handlers for automated sample processing and protein chemistry and molecular biology platforms for biological and clinical validation of disease-associated proteins.

 

Finally, the overall goals of the Center for Biomarker Discovery and Translation are to develop, validate, and translate multiplex test systems to enable the measurement of multiple proteins simultaneously and quantitatively with improved sensitivity and specificity.