Proteomics Center Devises Method for Assigning Probabilities to Human Protein InteractionsJanuary 25, 2008The Stowers Institute's Proteomics Center has published a novel method of using normalized spectral counts derived from a series of affinity purifications analyzed by mass spectrometry (APMS) to generate a probabilistic measure of the preference of proteins to associate with one another. The work - which allows for the assignment of probabilities not only to the interactions within well-defined protein assemblies, but also to interactions between complexes - was posted today to the Web site of the Proceedings of the National Academy of Sciences (PNAS). Large-scale APMS studies have played important roles in the assembly and analysis of comprehensive protein interaction networks for lower eukaryotes, such as yeast. But the development of such networks for human proteins has been slowed by the high cost and significant technical challenges associated with systematic studies of protein interaction. The Stowers Institute's Proteomics Center has addressed this challenge by developing a method for building local and focused protein networks. With this computational approach, the probability for two proteins to associate is calculated from the bait-to-prey relationship alone, an improvement over other methods requiring systematic reciprocal bait-prey interactions or co-purification of preys by a third bait. "Previous protein interaction networks built using protein mass spectrometry data were largely based on binary 'yes/no' data, where a protein is present in a sample or it is not," explains Michael Washburn, Ph.D., Director of Proteomics and senior author on the paper. "We were interested in quantitative proteomics approaches. We were able to develop a method to generate more information-rich networks, where the preference of two proteins to associate within a defined complex or within a larger network assembly can be estimated using Baysian probabilities. The new approach adds more information to the analysis of protein complexes and networks, since not all proteins interact in the same way." The work not only provides a significant advancement in proteomic analysis, it also holds promise in facilitating the development of treatments for disease. "By having insight regarding the most probable contacts within a multiprotein complex, we can devise targeted strategies to disrupt specific interactions," said Mihaela Sardiu, Ph.D., Postdoctoral Research Associate and lead author on the paper. "This could be useful for developing new drugs for disrupting protein complexes involved in disease." The Proteomics Center is one of three technology development centers that support research at the Stowers Institute. In addition to collaborating with Stowers Institute independent research teams, the centers pursue cutting-edge solutions to the evolving s challenges of basic biomedical research. "The Stowers Institute's Proteomics Center is providing technology solutions that fundamentally change the way that Stowers researchers approach their work," said Robb Krumlauf, Ph.D., Scientific Director. "Because of the support provided by our technology development centers, Stowers research teams can approach long-standing problems in new and innovative ways, elevating their research and results." Additional contributing authors from the Stowers Institute include Yong Cai, Ph.D., Research Specialist I; Jingji Jin, Ph.D., Senior Research Associate; Selene Swanson, Research Specialist II; Ronald Conaway, Ph.D., Investigator; Joan Conaway, Ph.D., Investigator; and Laurence Florens, Ph.D., Managing Director of Proteomics. More information about the Stowers Institute's Proteomics Center is available at www.stowers-institute.org/labs/WashburnLab.asp. About the Stowers Institute Housed in a 600,000 square-foot state-of-the-art facility on a 10-acre campus in the heart of Kansas City, Missouri, the Stowers Institute for Medical Research conducts basic research on fundamental processes of cellular life. Through its commitment to collaborative research and the use of cutting-edge technology, the Institute seeks more effective means of preventing and curing disease. The Institute was founded by Jim and Virginia Stowers, two cancer survivors who have created combined endowments of $2 billion in support of basic research of the highest quality. Stowers Institute |
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| Related Proteomics Current Events and Proteomics News Articles Protein changes in heart strengthen link between Alzheimer's disease and chronic heart failure A team of U.S., Canadian and Italian scientists led by researchers at Johns Hopkins report evidence from studies in animals and humans supporting a link between Alzheimer's disease and chronic heart failure, two of the 10 leading causes of death in the United States. Will genomics help prevent the next pandemic? This week, the Public Library of Science, an open-access publisher, presents the "Genomics of Emerging Infectious Disease," a collection of essays, perspectives, and reviews that explores how genomics-with all its associated tools and techniques-can provide insights into our understanding of emerging infectious disease. How Proteins Talk to Each Other Investigators at Burnham Institute for Medical Research (Burnham) have identified novel cleavage sites for the enzyme caspase-3 (an enzyme that proteolytically cleaves target proteins). Drug discovery process more accurate, less expensive using novel mass spectrometry application Cancer and cell biology experts at the University of Cincinnati (UC) have developed a new mass spectrometry-based tool they say provides more precise, cost-effective data collection for drug discovery efforts. Weill Cornell Researchers Discover New Anti-Tuberculosis (TB) Compounds Attempts to eradicate tuberculosis (TB) are stymied by the fact that the disease-causing bacteria have a sophisticated mechanism for surviving dormant in infected cells. Scientists Use MicroRNAs to Track Evolutionary History for First Time The large group of segmented worms known as annelids, which includes earthworms, leeches and bristle worms, evolved millions of years ago and can be found in every corner of the world. Conaway Lab uncovers function of potential cancer-causing gene product The Stowers Institute's Conaway Lab has uncovered a previously unknown function of a gene product called Amplified in Liver Cancer 1 (Alc1), which may play a role in the onset of cancer. What makes stem cells tick? Investigators at the Burnham Institute for Medical Research (Burnham) and The Scripps Research Institute (TSRI) have made the first comparative, large-scale phosphoproteomic analysis of human embryonic stem cells (hESCs) and their differentiated derivatives. New Tool May Help with Early Detection of Deadly Pancreatic Cancer A new diagnostic tool developed by Van Andel Research Institute (VARI) scientists has shown promising results when used with patients of pancreatic cancer, one of the deadliest forms of cancer due to the difficulty of diagnosing it in its early stages. Preimplantation genetic diagnosis may pose neurological risks Preimplantation genetic diagnosis (PGD) has helped many couples conceive healthy children and is generally considered a safe practice. More Proteomics Current Events and Proteomics News Articles |
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