Cardiac Organellar Protein Atlas Knowledgebase (COPaKB) -- COPa Library

The COPa knowledgebase is a resource of proteome biology configured specially for cardiovascular investigators. This project is developed under NHLBI proteomics center program with the partnership of Beijing Genomics Institute (BGI), European Bioinformatic Institute (EBI), Royal Institute of Technology (KTH), The Scripps Research Institute (TSRI), the Zhejiang University (ZJU) and UCLA. We hope it will serve as a useful tool for advancing cardiovascular biology and medicine.

The innovations in proteome biology offer unprecedented opportunities towards translational medicine. Advancing cardiovascular medicine requires an understanding of cardiac function at the systems level but with sufficient molecular details at the same time. Proteomics technologies are large scale in nature and their datasets come in various forms. The integration of these resources inspires innovative insights and bridges data-driven discoveries with hypothesis-driven investigations. The effective and comprehensive characterization of proteome biology holds the promise to advance cardiovascular medicine.

Nevertheless, there remain challenges in characterizing cardiac proteome biology. These include the requirements on specialized expertise, high investments in hardware and software, integration of proteomic data with biological mechanisms, data memory, and synergistic interaction among isolated investigators. Our objective is to build a specialized protein knowledgebase to address these challenges in cardiovascular proteomics. In this knowledgebase, we envision orthogonal sets of proteomic knowledge are integrated, including mass spectra datasets, image datasets, gene-based datasets and clinical datasets. In a data federation framework, knowledgebase users can access all these datasets from a single web server.

This proteome knowledgebase takes a modular structure based on the subcellular residency of individual proteins, which were originated from large scale proteomic surveys of cardiac tissues conducted previously. This modular schema enables in depth proteomic assay with a subcellular resolution. In the first release of the COPa library knowledgebase, four modules are released, i.e. human mitochondrial module, human 20S proteasome module, mouse mitochondria module and mouse 20S proteasome module. Additional subcellular specific modules are under construction, and will be released soon.

The long term goal of delineating the dynamics of cardiovascular proteome properties is beyond the capacity of individual or a small group of investigators. In addition to provide tools and annotated resources, specialized infrastructure is also implemented to invite, welcome and encourage scientists with diverse expertise to participate the synergistic development of the COPa knowledgebase for the mutual benefit of all. The contributing scientists and their publications will be clearly highlighted in the COPa knowledgebase. A COPa-Wiki component is integrated to each data entry within the knowledgebase to welcome inputs at the protein level, peptide level and spectrum level without any restrictions.

In short, COPa knowledgebase provides annotated peptide spectra, their association knowledge on proteome properties, cardiovascular biology, as well as tools to access this resource. With input of Raw spectra, biological phenotype, protein ID or peptide sequence, relevant knowledge is retrievable from the COPa knowledgebase. The knowledge is contextualized to facilitate in-depth analyses. In a joint effort with EBI, KTH and TSRI, we wish to contribute bioinformatic supports to the cardiovascular research community.