Finally a complete ‘Human Proteome Project’ is in the pipeline. It aims the tissue-level complete knowledge of the human proteome revealing “which proteins are present in each tissue, where in the cell each of those proteins is located and which other proteins each is interacting with”. Keep in mind also that around 21′000 human genes encode 1 million different proteins and that the effort cannot localize exactly which cell types in a given tissue is producing which protein. According to Nature’s Helen Pearson: Biologists initiate plan to map human proteome

“Those involved in the draft plan say that a human proteome project is now feasible partly because estimates of the number of protein-coding genes have shrunk. It was once thought that there might be around 50,000 or 100,000, but now, just 21,000 or so are thought to exist, making the scale of human proteomics more manageable. And the group plans to focus on only a single protein produced from each gene, rather than its many forms.

The plan is to tackle this with three different experimental approaches. One would use mass spectrometry to identify proteins and their quantities in tissue samples; another would generate antibodies to each protein and use these to show its location in tissues and cells; and the third would systematically identify, for each protein, which others it interacts with in protein complexes. The project would also involve a massive bioinformatics effort to ensure that the data could be pooled and accessed, and the production of shared reagents.”

The idea is to analyze and list all the proteins manufactured by chromosome 21 within 3 years as a pilot study and then finish the whole project within 10 years. Chromosome 21 is the smallest child in the family and likely contains between 200 and 400 genes, so the pilot study can yield us a couple hundreds proteins. Another powerful idea is to start with the human mitochondrial proteome which is around 1000-1500 proteins as far as I know, that is at least 3 times as many as encoded by chromosome 21.

“Steven Carr, director of proteomics at the Broad Institute in Cambridge, Massachusetts, says there is likely to be broad support for a large-scale proteomics effort, but much debate about how best to do it. Rather than analyse the proteome of one chromosome, he says it may be better to tackle the proteome of mitochondria or the cell membrane because it would reveal more about biology and diseases related to those structures. “It’s time to think about something in a systematic fashion — whether this is the project is a different question,” he says.”

Source:

Helen Pearson: Biologists initiate plan to map human proteome Published online 23 April 2008 | Nature | doi:10.1038/452920a http://www.nature.com/news/2008/080423/full/452920a.html
Human proteome project: 21000 genes/1 protein, 10 years, $1 billion? http://pimm.wordpress.com/2008/04/23/human-proteome-project-21000-genes1-protein-10-years-1-billion/#more-1462