SCIEX has announced collaborators in the OneOmics™ project, an exclusive partnership between Illumina and SCIEX that integrates SWATH™ Acquisition based next-generation proteomics (NGP) and next-generation sequencing (NGS) data on the BaseSpace® cloud computing environment. Advaita Bioinformatics, The Institute for Systems Biology (ISB) and researchers at Yale University have each developed cloud-based applications and libraries that utilize SWATH Proteomics data in novel ways allowing researchers to analyze and compare proteomics and genomics data. This effort furthers the OneOmics project’s goal of eliminating the informatics barriers that exist between different Omics disciplines.
Rob Moritz, Associate Professor, and his team from ISB developed the SWATHAtlas Ion Library Generator Application that enables fast and simplified access to ISB libraries for use in NGP experiments with SWATH Acquisition. Currently, ISB hosts ion libraries for the Human, Yeast and Mycobacterium tuberculosis (Mtb) proteomes.
Moritz, who was influential in establishing the partnership said, "We are delighted to be part of this project SCIEX and Illumina. Collectively, our tools developed at ISB and in the wider academic community will provide a powerful solution that will impact the way that proteomics research and systems biology will be conducted in the future".
Deriving biological insight from genomics and proteomics data is at the cutting edge of bioinformatics. Advaita Bioinformatics, a leader in the development of analytic solutions for high-throughput biological data, has developed the iPathwayGuide App, for the BaseSpace® platform. The App performs biochemical pathway analysis, gene ontology analysis, miRNA prediction, and drug and disease analyses of SWATH Proteomics and Illumina RNASeq data. The App simplifies the process of finding real biological insights from integrated proteomics and transcriptomics data sets, and will help to advance biomarker discovery and disease research.
Dr. Chris Colangelo (proteomics) and Dr. Rob Kitchen (genomics bioinformatics) from Yale University collaborated to develop the RNASeq Translator Application for the BaseSpace® platform that translates the output from an Illumina RNASeq experiment into a protein database that can be used to create ion libraries to mine SCIEX SWATH Acquisition data. The application enables a more targeted approach to proteomics analysis within the context of identifying splice variants, which can be critically important to researchers seeking to understand the genetics of a particular disease. This serial workflow is a common requirement for systems biology research, but until now has required complex bioinformatics protocols that are beyond the reach of all but a few specialized laboratories.
“SWATH Acquisition enables researchers to accurately and reproducibly quantify several thousand proteins across hundreds of samples, leading to meaningful conclusions about how the proteome changes in response to perturbation”, said Aaron Hudson, Senior Director of Academic and Clinical Research Business of SCIEX. “The next logical step is to integrate those proteomic conclusions with other omics results, such as genomics and transcriptomics. Our collaborators at ISB, Yale University, and Advaita Bioinformatics, have all launched complimentary applications that expand the workflow and provide general access and standardization of data analysis across two of the largest fields in life science."
Released earlier this month, the SCIEX SWATH Proteomics Cloud Tool Kit suite of applications is hosted on Illumina’s BaseSpace® cloud computing environment, creating a single location for genomics and proteomics “big data,” and enabling fast, secure, and streamlined analysis of complex multi-omics data sets. By providing simplified informatics within a web-based environment, the solution is designed to help advance biomarker discovery and the development of new drugs for diseases such as cancer, diabetes, Alzheimer’s and heart disease.