Proteomics Projects
Technology and methods development are at the heart of the Interaction Proteome project, a European Union-funded collaboration of 14 research laboratories in 6 European countries. Franz Ulrich Hartl, the coordinator of the 2year-old project and a researcher at the Max Planck Institute of Biochemistry (Germany), explains, “We want to develop novel technology to establish a broadly applicable platform of routine methods for the analysis of protein interaction networks.” Already, tools are emerging from the efforts of the Interaction Proteome members. For example, Thermo Electron developed the Orbitrap mass spectrometer with partial funding from the project. Introduced in 2005, the Orbitrap was the first new type of mass spectrometer on the market in >20 years. The instrument achieves high resolution and high mass accuracy without using a magnet. The Interaction Proteome project is divided into four subprojects (SPs), with technology development denoted as SP1. Technologies currently in the SP1 pipeline include improved cryoelectron microscopy methods for mapping the locations of proteins throughout a cell and a method that combines light and fluorescence microscopy techniques to visualize posttransla-
tionally modified proteins in cells. The project is not just about developing technologies, however. The SP2 group searches for molecules that interact with protein domains and peptides. SP3 project members validate the instruments and methods produced by the SP1 group. Because SP3 research groups study chaperones and cell-signaling proteins in their own labs, these FRANZ ULRICH HARTL
Interaction Proteome: New tools for proteomics
Far-reaching network. A network diagram showing the collaborations (arrows) among Interaction Proteome research teams (circles and squares) across Europe.
molecules are used as model proteins for validation. SP4 members are bioinformatics gurus who are charged with determining the best ways to collect and store proteomics data. These researchers also develop models and simu lations of protein interaction networks.
One of the biggest challenges in leading a large project, says Hartl, is to ensure that members work together, harnessing the strengths of each laboratory. “We have achieved this [goal] by communicating intensively, and we have workshops and meetings together,” he explains. “These [interactions] are really working relationships that lead to common projects and publications.” Hartl and the other group leaders also plan to offer more opportunities for their students and postdocs to visit participating laboratories. He says, “Once this project ends, we want to have created additional expertise in the various countries to carry on with these methods, and the best way . . . is by training young people.” In the future, Hartl expects that the bioinformatics and experimental researchers in the Interaction Proteome project will interact to an even greater extent. For example, he says that project members will use some of the simulations developed by the SP4 researchers to study the protein– protein interactions of chaperones and signaling proteins, “because only then can we say that we really understand a cellular process properly.” He adds, “Clearly, this will not be something we will fully achieve within this 5-year project, but I hope that we can make a good start.” —Katie Cottingham
Government and Society
NIST upgrades MS database The National Institute of Standards and Technology (NIST), in collaboration with the U.S. Environmental Protection Agency (EPA) and the National Institutes of Health (NIH), has released a new version of the NIST/EPA/NIH Mass Spectral Library. The new edition, called NIST 05, adds ~20,000 MS spectra to the database, bringing the total number of spectra to >163,000. Each one has been critically evaluated to ensure the data are current. The upgraded database now includes >2000 MS/MS spectra, which could be of use to proteomics and metabolomics researchers. Gas-phase retention index data for >25,000 vola-
tile organic compounds have also been added to the library for use with GC. The NIST 05 library is available with version 2.0d of the NIST MS Search Program for Windows. More information can be obtained from the NIST Standard Reference Data Program at www. nist.gov/srd/nist1a.htm.
New proteomics center for Dana-Farber Cancer Institute The Dana-Farber Cancer Institute has announced plans to establish a new proteomics and computational biology facility. Called the Blais Proteomics Center, it will be funded by a recent $16.5 million donation from John (Jack) and Shelley Blais. The center, which will
470 Journal of Proteome Research • Vol. 5, No. 3, 2006
be led by Dana-Farber scientist Jarrod Marto, will be located within existing buildings at the institute’s site in Boston. The facility is part of a drive to increase the institute’s capabilities in the proteomics field. The gift will provide funding for the center to purchase high-throughput equipment, such as mass spectrometers, instrumentation for separations, and robotics. In addition, up to 25 new research positions for analytical scientists, bioinformaticists, and software developers will be created. Although the Blais Proteomics Center will serve primarily Dana-Farber researchers, it will also be open to scientists from other area institutions.
