Mapping the Human Proteome
Team one: ProteomicsDB catalogues more than 18,000 human proteins – or 92 percent of the human proteome
In February 2001, scientists celebrated the initial sequencing of the human genome by two competing groups. Now, not one but two draft human proteomes form the next logical link in a chain. Bernhard Kuster, who led the Technische Universitat Munchen (TUM) research team’s effort (1), says that the initial spark of inspiration for the work was a desire to generate a database that could potentially have a big impact on proteomics. “A common problem in science is the sheer amount of data produced. Unfortunately, we do not always have the capabilities or the right tools to mine this information,” explains Kuster. “This project was the result of a joint venture between TUM and the software company SAP – technology was key to developing an intellectually clear, useable database.”
Kuster and colleagues compiled raw mass spectrometry data from various public databases, as well as generating their own data from human tissue, bodily fluids and cancer cell lines to help fill the gaps. Overall, the team catalogued more than 18,000 human proteins, which is about 92 percent of the human proteome – the work clearly isn’t finished yet. The group intends to continue profiling human tissue and will also be using the data to examine how cancer drugs interact with proteins and signaling pathways.
The data has been made publicly available in ProteomicsDB, a “high-performance, in-memory database for real-time analysis of terabytes of big data,” which includes information on the types, distribution and abundance of proteins in various cells, tissues and bodily fluids.
“Proteomics and genomics aren’t science fiction anymore,” says Kuster, “We have shown that it can be done. Many advances were made after it was demonstrated that the human genome could be mapped, so we hope our work will spur other researchers into action, benefiting the field of proteomics.”
Parallel Proteomes (set link) explores the efforts of the second team of researchers at Johns Hopkins University in Baltimore, US, and the Institute of Bioinformatics in Bangalore, India.
- Mathias Wilhelm et al., “Mass-spectrometry- based Draft of the Human Proteome”, Nature 509, 582–587 (2014).
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