The atlas would help researchers in determining the molecular basis of diseases such as cancer and will provide important insights into the function of different proteins and how changes in the distribution of proteins could lead to diseases as grave as cancer.
"We are trying to map the building blocks of life," said Professor Mathias Uhlen of the Royal Institute of Technology in Stockholm, leader of the project.
The hugely ambitious project has involved the development of a massive infrastructure to enable the proteins to be identified in a realistic period of time.
The way, in which genes and their products, proteins, interact together in complex networks in living cells, is called functional genomics. If these interactions are abnormal, it can lead to diseases.
Firstly, the researchers used the human genome, the sequence of all the 20000 or so genes in human cells, to encode individual proteins. Later, they developed 'antibodies', protein molecules that recognise specific targets, against each of these proteins.
The antibody that recognises a given protein was then labelled with a marker to make it visible under a microscope and is exposed to samples of different tissues and cells. The antibody binds to the proteins and in this way the location of the protein can be detected.
"To do this systematically requires a lot of automation and robotics. We have six software engineers writing codes just to keep track on the samples. The project is generating 400 gigabytes of data every day," said Uhlen.
A 100-strong team is working on the project, with a site due to be set up soon in India, and with antibody-producing sites in Korea and China.
"To get an idea of how far we have come, in our first year we produced on antibody. This year we are hoping we can make 3000," said Uhlen.
He believes that the programme, launched in 2003, along with sufficient funding the first full version of the atlas could be available by 2014.
The team has so far mapped the location of around 5000 proteins in human cells and tissues. They are also investigating whether certain common cancers, colon, prostate, lung and breast, have different protein profiles to normal tissue.
In this way, new 'biomarkers' could be identified, molecules which indicate that a tissue or cell is in a diseased state, which could alert doctors to the early stages of a disease.
The human protein atlas was presented at the European Science Foundation's 3rd Functional Genomics Conference in Innsbruck, Austria.