Proteomics, as one ofthe disciplines of the "omics" cascade (genomics, transcriptomics, proteomics and metabolomics), is projected to have a profound impact on the clinical practice of oncology in the coming decades. Recent advances in proteomics have been hallmarked by orders of magnitude Increases in speed and sensitivity. These advances are driving bioinformatics efforts to facilitate and automate data interpretation and integration into the "omics" pipeline and application to translational medicine. The "data gathering" technologies for proteomics now have a firm, quantitative foundation and are being widely applied to biomarker development and hypothesis generation in cancer research. The SCCC Proteomics Core supports cancer research for biomarker development (discovery, verification and validation) and global molecular Investigations into cancer mechanisms. Both gel based (2D-DIGE) and quantitative label-free proteomics are available to researchers, the latter using high-resolution hybrid mass spectrometers (FTICR-MS and LTQ-Orbitrap-XL), Consultation in experimental design, feasibility, statistics, and customized sample preparation for proteomics studies is provided by the Director, a Bioinformaticist, and Mass Spectrometrist. Standardized proteomic workflows are executed by a skilled staff of senior research technicians. Assistance with proteomics data analysis is provided using advanced software tools for both gel (DeCyder (DIA, BVA and EDA modules), MASCOT and SCAFFOLD) and non-gel (Rosetta Elucidator, SORCERER-2) proteomics. The Core hosts greater than fifty terabytes of RAID array storage capacity for gel images, mass spectrographic, and meta data that have been acquired since the establishment of the Core in August, 2003. Since the last competitive renewal, the Core has worked with 58 SCCC members. The expertise and resources of the SCCC Proteomics Core are being applied to biomarker projects in pancreatic cancer (Dr. David Linehan), prostate cancer (Dr. Adam Kibel), breast cancer (Dr. Mathew Ellis), bladder cancer (Dr. Robert Grubb lllrd), cervical cancer (Dr. Janet Rader), and lung cancer (Dr. Issam El Naqa). In addition, the Core is currently supporting basic science projects in cell cycle regulation (Dr. Helen Piwnica Worms), mechanisms of CTL cell killing (Dr. Tim Ley), imaging apoptosis (Dr. David Piwnica-Worms), nucleoli proteomics and translational regulation (Dr. Jason Weber), telomere protein dynamics (Dr. Sheila Stewart), glycoprotein hormone (Dr. Jacques Baenziger), stromal contributions of glioma formation (Dr. Joshua Rubin), and molecular characterization of stage I lung cancer (Dr. Ming You). For biomarker development, customized immunometric services are provided which include both expertise and instrumentation to develop new assays for candidate protein biomarkers.
The Proteomics Core provides the research community with the technology and expertise to discover new proteins for the early detection of cancer and to understand mechanisms of cancer at the molecular level. Proteins are the product of information encoded in human genome.
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