LICR Melbourne Branch to Host a National Solution to Large-scale, Proteomics Mass Spectrometry Data Analysis
"Congratulations to the Melbourne Branch team, led by Drs. Tony Burgess and Robert Moritz, on the creation of the Australian Proteomics Computer Facility. In particular, Dr. Cassandra Thumwood, the Branch's Scientific Administrator, deserves praise for her hard work in negotiating and managing a complex network of agreements. The APCF is a great example of how vision and leadership can bring together academic and industry partners to create something that can be of great value for advancing our understanding of cancer."
Dr. Jonathan Skipper, Executive Director for Intellectual Property & Technology Licensing
Australia’s federal science and medicine funding body, the National Health and Medical Research Council (NH&MRC) has awarded AUD 2 million to enable the establishment of the Australian Proteomics Computer Facility (APCF), a large-scale computational solution for mass spectrometry-based proteomic analyses for researchers in Australia. The APCF will be hosted and led by the LICR Melbourne Branch.
Australian researchers are ranked highly in protein research, and the nation as a whole has considerable investment in high technology mass spectrometry equipment capable of identifying proteins important in health, medicine and agriculture. However, current mass spectrometry instrumentation produces more proteomics data than available laboratory-scale computer capabilities can analyze. This problem will be exacerbated by the increased installation of current technology instruments and new, even faster instruments to be released in the near future. The solution for the torrent of proteomics data, conceptualized by LICR’s Dr. Robert Moritz and Eugene Kapp, will provide scientists at the Melbourne Branch, as well as all other Australian researchers, access to a system that will provide proteomics-based informatics on a national scale. The system will be utilized primarily for the analysis of mass spectrometry data for protein identification. At the Melbourne Branch, Drs. Moritz, Kapp, Richard Simpson and Tony Burgess (Branch Director) will use the APCF’s services initially to identify potential colon cancer biomarkers in complex protein mixtures as part of the LICR’s Colon Cancer Initiative.
The APCF is being governed by a committee — chaired by Dr. Burgess — of Australian proteomics researchers from all states and territories. Dr. Moritz, the inaugural director of the APCF, is guiding both the setup of the facility and the establishment of its initial capabilities. The LICR Melbourne Branch has supplied the knowledge and space (through the kind co-operation of Melbourne Health, the Branch’s host institution) and will manage the APCF’s work. Microsoft, under an academic alliance, has donated Windows Server Cluster edition, an entirely new operating system for the solution, Intel has supplied the latest Quad-core processors prior to official release as well as donating software solutions and Dell Computers has donated a large amount of the hardware for this facility specifically for the benefit of human health.
Proteomics research is compromised when access to comprehensive databases, sophisticated software (particularly search algorithms) or computing power is inadequate. The APCF solution is seeking to address each of these issues. First,.multiple proteomic algorithms as well as truly non-redundant databases will be used. An example of the enormity of the diverse database is provided by a collaboration with Dr. Victor Jongeneel and his team (LICR Lausanne Branch), through which the Melbourne Branch obtains regularly updated databases containing all the identified proteins of a large number of organisms. At present, these databases can be used singly or as a concatenated non-redundant database containing the sequences of more than 4.5 million proteins. This non-redundant database — in constant use at the Melbourne Branch — has more than doubled in size over the last two years. In addition, a unique feature of the APCF will be to establish and provide a database repository for Australian proteomic data. With respect to software and other tools, it is anticipated that the creation of this database will enable the development of new proteomic analysis tools, particularly for proteomics data reduction and validation. Many laboratories struggle to utilize a number of proteomic informatics packages due to a lack of resources, but with the formation of the APCF — staffed by information technology professionals trained to assist researchers conduct state-of-the-art proteomics computational analysis — a major benefit in data analysis and reporting standards can be achieved. Finally, the APCF supercomputing cluster will provide 128 Quad-Core servers, providing 1024 processing cores in total. In 2007 the APCF computing power, state-of-the-art software and protein database will enable Australian researchers to perform reliable proteomic analyses in one-hundredth of the time it took in 2006.
The integrated approach to proteomics computing, the sharing of databases and the use of a 1000 processor computer cluster will put Australia at the forefront of the world's efforts to identify the proteins associated with the early detection of major human diseases. Examples in cancer research include the identification of proteins shed by tumor cells into proximal tissue, and the identification of differences in the intracellular and membrane protein complement of normal and tumor tissue. The APCF will also serve as a model for other national initiatives; interest in the use of this system has been expressed already by neighboring countries. Importantly, with the LICR/Walter and Eliza Hall Institute of Medical Research Joint Proteomics Laboratory contributing to both the Human Proteome Organization and the proteomics standards committees of major journals, the APCF’s work in proteomic identification — spear-headed by LICR — will contribute greatly to the world-wide efforts to define the proteome for a wide range of organisms, including humans.