Proteomics: The human proteome projects

Richard Simpson came home from the second annual meeting of the Human Proteome Organisation in Montreal last month as the organisation's vice-president. But Simpson, of the Ludwig Institute for Cancer Research in Melbourne, has too much on his mind to be too carried away by the esteem of the role.

The Human Proteome Organisation -- HUPO -- has set itself the goal of discovering all human proteins. Simpson's charter as vice-president is to put in place a long-term planning strategy to try and link individual, national and regional interests in proteomics under the HUPO umbrella -- not a small task.

"I have definite ideas on how we should do this so that we have a level playing field," he says. "And we're off to a reasonable start. I am president of the Asia-Oceania HUPO so we already have a regional consortium of nations, their common interest being proteomics.

"I think what is evident with a lot of the countries in Asia-Oceania is that they don't want to miss out on the new wave of technology they felt that they lost out on with the [Human Genome Project], so they are pumping a lot of money into proteomics."

Technology -- particularly technical expertise and tech transfer -- is crucial, in Simpson's mind, to the success of HUPO's task. Well-trained protein chemists are not a common species, and Simpson and fellow committee members are setting up an exchange system to enable the transfer of people from one country to another so that others can learn about the use and application of the technology.

Simpson also chairs the HUPO committee on new technologies and resources, a role he has held since the organisation's inception three years ago. Here, his task is to coordinate resource and technology requirements for some of the major proteome initiatives, the key one at the moment being the human plasma proteome pilot project.

This committee also oversees standardisation of data to facilitate data comparison, exchange and verification. "There are a whole series of issues in terms of data interrogation and bioinformatics," says Simpson. "When you get a spectra from a mass spectrometer, if I analyse it in my lab using my algorithms and my informatics people, will we come up with the same [results] as someone else in Australia or around the world? It's a major issue and that all comes back to what sort of resources one needs to do this on an international level."

Plasma race

The human plasma proteome initiative is still in a pilot phase, but already it involves more than 50 labs around the world and a number of pharmaceutical companies. Australian involvement includes Simpson's group at the Ludwig, Mark Raftery's group at the Bioanalytical Mass Spectrometry Facility at UNSW, and Sydney-based bioseparations specialist Gradipore.

The ultimate aim of this project is to determine the proteins present in human plasma and, by comparing disease states to control states, identify potential biological markers for diagnostic tests. Blood serum is considered a rich source of biological markers for disease. These biomarkers may have application in the early detection of disease states such as cancer, the rapid detection of heart attack, and the early assessment of drug toxicity or drug efficacy.

HUPO is starting to get some of the data back from the groups involved in the pilot phase, which were all given the same sample to analyse. From these data, the best separation and analytical techniques will be determined for identifying proteins in human plasma, with a deadline of December 31. A subset of labs will then be chosen to continue their involvement with HUPO in the analysis of control or disease plasma samples.

According to Simpson, the work is already delivering some useful results. "At this stage, in terms of data interrogation, we need to use a number of different algorithms that are out there. There is no one algorithm, for instance, that will give you as definitive answer. And this will come to the surface from one of the publications from the plasma initiative," he says.

Reality check

"I guess proteomics is coming of age," Simpson says. "I think now there is a reality check happening in terms of what the technology can do. We need to be able to overcome the issue of the dynamic range of protein abundances which itself can vary by the order of 106, but once we start looking at plasma it could be in the order of 109 or 1010."

Simpson thinks the skills base in proteomics needs to move away from mass spectrometry to classical protein chemistry and protein fractionation, as he believes they are responsible for bottlenecks in the technology. HUPO's new technologies committee is using the plasma proteome project as a learning platform for such issues. "We are using the plasma proteome initiative as our first foray into the real world," Simpson says.

What the group learns from the plasma initiative will apply to other major proteome initiatives HUPO is undertaking -- the liver cancer proteome and the brain proteome. The brain proteome project was launched at the Montreal meeting and HUPO has chartered Germany to come back with a proposal on how the job can be done.

"The early years of proteomics haven't been helpful in the sense that we've overstated what the technology can do," Simpson says. "And that's not to say that it won't be able to do it, but I think we have to be really realistic in those goals and we need to put a lot more effort in."