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Australasian Biotechnology (backfiles)
ISSN: 1036-7128
Vol. 6, Num. 3, 1996
Australasian Biotechnology,
Volume 6 Number 3, May/June 1996,pp.178-180

APAF : the Australian Proteome Analysis Facility

By Keith L Williams,
Macquarie University Centre for Analytical Biotechnology (MUCAB) and
Bradley J. Walsh,
Australian Proteome Analysis Facility (APAF), School of Biological Sciences, Macquarie University, Sydney, NSW, Australia 2109. ph 61-2-98508212, fax 61-2-98508174 email

Code Number: AU96005
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Technological developments in protein science, combined with ready access to DNA sequence databases and bioinformatics have opened up a new field in biology: Proteome studies. The federal Australian government has funded APAF as a major national facility for Proteome analysis. This article outlines the origins of APAF and how it is expected to impact on Australian science and particularly biotechnology.


The combination of two dimensional gel electrophoresis using immobilised pH gradients, preparative loading (mg protein/gel), and new microanalytical techniques have revolutionised protein science to such an extent that the new field of Proteome research is emerging. It is not surprising that Australia is strongly represented in this new field as there is a long tradition of protein chemistry in this country. Indeed the first protein sequencer was built and operated by Pehr Edman and Geoff Begg in Melbourne. There is however a Swiss connection to the inception of APAF. In Spring of 1993 Denis Hochstrasser from the Medical Hospital in Geneva visited Sydney. Denis laboratory is at the forefront of 2D-gel technology and he had solved the two key problems which had held back the field for two decades. These were the ability to make highly reproducible 2D-maps and being able to load sufficient protein so that individual proteins purified by the 2D-gel separation could be studied chemically (Bjellqvist et al.1993). There remained however the problem of how to study the proteins. Denis had thousands of pure protein spots but each protein sequencer, the traditional means by which proteins are identified, has the capacity of studying perhaps 10 proteins in a week. Wherever he went Denis spoke with protein sequencing laboratories to get some of his samples studied. When Denis visited MUCAB and outlined this dilemma, we decided that there must be a quicker and cheaper way, and so research in the MUCAB laboratories began to focus on this. Three years later we have a suite of new instruments and the capacity not only to identify proteins, but also to study their post-translational modifications.

The politics of major national facilities

When the APAF application was finally submitted, a colleague who had been involved in a recent CRC application said to me "now the work begins!". How right he was. Money is always tight and with the prospect of perhaps half a dozen $10 million facilities, the competition was interesting. APAF had the advantage of being very new, hence it fitted the innovative concept of the major facilities program. On the other hand being at the leading edge of a technology also involves some risk, and so some thought it better to stay with well established technolgies that had a proven track record internationally. Fortunately, we had extremely strong support from our international scientific colleagues as well as from both local and international equipment manufacturers. At the end of the day the decision was political and we (and several others) benefitted at the expense of a major expediture on the European Southern Observatory's very large telescope in Chile (Swinbanks 1995). The outcome for the biological sciences community was excellent, with $10 million being made available for the establishment of AGRF (Australian Genome Research Facility) and $7 million for establishing APAF (Australian Proteome Analysis Facility).

How APAF is structured

The Major National Facilities funding is for the physical aspects of the facility only, ie bricks and mortar and equipment. We are left with the issue of funding the staff and consumables. A strategy must also be developed to allow renewal of the facility as new instruments become available. This is a major challenge as the pace of change in this emerging technology is such that investment in equipment in 1996 is unlikely to remain state of the art beyond 3-5 years at most. In our application we envisaged that this would be done by partnering with industry in research and development of the next generation of Proteome technology. Currently we are discussing partnerships with a number of companies involved with 2D gel technology, HPLC, glycobiology, mass spectrometry and robotics.

The operation of APAF will be under the guidance of a board which will have the brief of providing strategic advice. In the planning stage this will involve decisions about how quickly projects can be started and the balance of short term vs long term goals. APAF can start immediately in a labour intensive fashion, but we must also invest some effort in automating our technologies so that large scale projects can be initiated.

What will APAF do?

While DNA genome sequencing is a major undertaking that is unlikely to be completed on more than a small group of eukaryotic organisms, the proteins of hundreds or even thousands of organisms can be readily displayed using 2D gel technology. Hence the way is open for Proteome studies on any organism or tissue. Since a subcellular fraction, cell type, or tissue can be displayed on a 2D gel, it is possible to get a complete picture of both normal and diseased states. The implications for both basic research and biotechnological applications are major.

The components of Proteome research are the technology for protein separation (using 2D gels), protein identification and the means to study post-translational modifications to the proteins, all at the level of a single 2D gel spot (ie at mg amounts of protein). We have reviewed these advances recently (Wilkins et al. 1995). Our approach to Proteome research is to use a hierarchy of techniques such that many proteins are screened quickly and cheaply, followed by more intensive (and expensive) work on a small group of proteins of special interest. Therefore, Proteome studies can be viewed as a sequence of stepwise operations.

Relationship to the Australian scientific community

APAF is a national facility, hence it is owned by the national community. It is our intention that access to APAF be as wide as possible. Rather than sending samples to be processed, we anticipate that many researchers will send someone from their laboratory (or even come themselves) to be involved with the Proteome processing. We are discussing with Macquarie University affordable accommodation for visitors to the facility. This will take a little while to organise, but we expect many visitors to the facility to partake of our high level training courses or to pursue projects.

The research centres which underpin APAF will have a major influence on how it develops. In particular, MUCAB (Macquarie University Centre for Analytical Biotechnology) will continue research programs to provide the new technologies which APAF will adopt. Precedents for this are already apparent from several research projects that have had commercial outcomes. For example APAF will use the GBC Scientific Equipment "AminoMate" for amino acid analysis, the Beckman Instruments "GlycoSite" for glycosylation site identification and the Gradipore Ltd "Gradiflow" for protein prefractionation and concentration. MUCAB had a role in the development of all three instruments.

Ultimately Australia's role in the development of the new field of Proteome research will be influenced by the success of APAF, but all protein researchers around the country have a role to play. We anticipate that many researchers will choose to participate in these exciting times by conducting projects in the new facility.

International linkages

An advantage of designating a national facility is that it enables high level interactions with other countries. There is much to be done in this area, but already discussions are well in hand for making the facility a mirror site for the Swiss ExPaSy database system. Discussions are also going on with Adrian Gibbs (RSBS, ANU) and Professor Gojobori who heads the DDBJ national database in Japan. As well as forging links with databases these connections are already having concrete outcomes.

For example, the close interactions with the Swiss laboratories is not only productive in the area of basic research, but also in database strcuture and searching. Recent modifications to ExPaSy simplify the means of identifying proteins by being able to search on a string of different parameters (eg amino acid composition, pI, MW, N-terminal sequence tag) and this has been driven by collaborative work between MUCAB and Switzerland.

We are setting up structures around which the vitality of the facility can be maintained, while at the same time supporting efficient execution of national proteome projects. There is much planning to be done and we welcome input from all stakeholders in the scientific and business community (email


Bjellqvist,B., Sanchez, J-C., Pasquali, C., Ravier, F., Paquet, N., Frutiger, S., Hughes, G.J. and Hochstrasser, D.F. (1993b). Micropreparative 2-D electrophoresis allowing the separation of milligram amounts of proteins. Electrophoresis 14.1375-1378

Swinbanks,D. 1995. Australia backs innovation, shuns telescope. Nature 378:653

Wilkins, M.R., Sanchez, J-C., Gooley, A.A., Appel, R.D., Humphery-Smith, I., Hochstrasser, D.F. & Williams, K.L. (1995). Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev.. 13:19-50.

Copyright 1996 Australian Biotechnology Association Ltd.

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