Several of the most well-known proteomics scientists in the US last week formed a national branch of HUPO called USHUPO. The national branch, along with a regional South American branch and an eventual national Canadian branch, will take the place of a previously envisioned HUPO Americas that would have spanned the entire Western Hemisphere, newly elected USHUPO president Catherine Fenselau told ProteoMonitor (see PM 11-28-03).
“We continue to interact under the international umbrella, but we thought it would be more effective to have the regional in the case of South America and the national in the case of the US,” for convenience and ease of communication reasons, Fenselau, a professor of chemistry at the University of Maryland, said.
The move came during an informational meeting of the HUPO Plasma Proteome Project at the NIH held on April 22. It was a big week for other HUPO initiatives as well: The HUPO Brain Proteome Project and the Proteomics Standards Initiative both met last week in France for their annual workshops. HPPP will hold its own workshop in June (see PM 10-17-03, 1-23-04).
In addition to naming Fenselau as president, the new organization elected Gil Omenn and John Yates as vice presidents; and Brian Chait, Al Burlingame, Sam Hanash, and Paul Tempst as members of the executive committee. Council members were also chosen but a complete list was not immediately available.
USHUPO’s mission will be to “engage in scientific and educational activities to encourage the spread of proteomics technologies and to disseminate knowledge pertaining to the human proteome and that of model organisms,” Fenselau said. This will likely include the coordination of US-based proteomics initiatives, she added. “Clearly the [HPPP] is one of the preeminent American initiatives. But there was also the prospect of an antibody initiative, and some of the folks were interested in more functionally focused initiatives,” Fenselau said. “So we’ll see what comes up — we certainly have opened the floor.”
At its founding meeting, the new group discussed potential collaborations with other American scientific bodies such as the Association of Biomolecular Resource Facilities and the American Association for Clinical Chemistry, Fenselau said. It also developed its mission statement and made plans for soliciting new members. Unlike international HUPO, USHUPO will solicit paid memberships, the money from which will go towards funding the organization’s activities. Fenselau anticipated that membership rolls would be opened in early summer. The first national conference will likely take place “within the next 10 to 12 months,” she said.
HBPP Struggles for Funding
In other HUPO news, the HBPP met in Paris last week to discuss strategies for the initiative’s pilot phase, which began in January (see PM 9-12-03). Joachim Klose, vice-chair of HBPP, said that mouse and human brain samples have been distributed to participating laboratories, and that results of the pilot studies on these samples should be in by the end of this year — but that a lack of funding for HBPP remains a huge problem.
About 80 participants — including industry representatives from such companies as Amersham (now GE Healthcare) and Applied Biosystems, as well as from several pharmas — participated in the workshop, but Klose said he feared that many of the participants were taking a wait-and-see approach before becoming active members of the project. “The number of participants … was relatively high, but sometimes I think that people just look at what happens, and if it’s not really attractive, maybe we’re out of luck,” he said.
He added that he thought a similar and potentially serious problem was at the root of the difficulty the organization was experiencing in winning grants or commercial deals. To date, no company or government organization has pledged funds to the HBPP. In the case of pharma in particular, “all this [work] seems to take too long” to interest them, Klose said. As for government funding agencies such as the European Union, “we have to offer already excellent results and show that the cooperation works, like the [Human] Genome Project — and this is very difficult,” he said.
Still, Klose is holding out hope that things might turn around once the pilot phase begins to bring in results. By participating in the pilot phase, labs “can do something immediately, and of course they are interested in what other people are doing,” he said.
As HBPP treasurer Michael Hamacher said in September, the participating pilot phase labs looking at the mouse brains — there are currently 10 to 15 labs involved — are searching for differences among brains from three stages of development: 16-day embryos, those from seven days after birth, and eight weeks after birth. “These laboratories should investigate these brains in the best way they can do. So if one is an expert in mass spectrometry, he would use this method; if other people use 2D electrophoresis or protein-protein interaction,” they use that, he said. The labs are responsible for securing their own funding.
HBPP’s next workshop will take place at the international HUPO Congress in Beijing in October.
HUPO PSI Looks Beyond Nature Biotech
The HUPO PSI met in Carros, France last week as participants in three different tracks worked separately to define the next phase of the PSI’s molecular interaction standards, lay out plans for finalizing the first version of its mass spec standards, and develop definitive standards for its submission of proteomics experimental data to a journal (see PM 10-24-03).
“Hopefully we will in the end unite all of these aspects and have one common model — but that’s still quite awhile away,” Henning Hermjakob, head of the PSI Molecular Interactions track, told ProteoMonitor.
For now, however, Hermjakob’s PSI-MI track is leading the way, having already published its first XML-based standardized format for molecular interactions in Nature Biotechnology in February (see PM 2-6-04). PSI-MI is now on its way to releasing a second version on Sept. 15, “just in time so that people have time to look at it before the HUPO meeting in Beijing,” Hermjakob said. He added that PSI-MI would try to get the updated format published in a journal before then. Major changes from the first version of the format include an expansion of interaction data to include protein interactions with DNA, RNA, and small molecules in addition to other proteins; an emphasis on using both UniProt and NCBI data for every protein; and the addition of BIND and MIPS to the group of databases that have agreed to release data in the new standard format.
The mass spec data standards track, led by Weimin Zhu, plans to finalize changes to the m/z data format within the next month, and has made a deal with “one or two of the vendors … [to] implement the m/z data format as their native output format, and we will then import this directly into the search engine,” Hermjakob said. He would not say which vendors have agreed to do this, but did say they were among the industry representatives at the workshop — which included Bruker Biosciences, Shimadzu, MDS Sciex, and Thermo Electron. Hermjakob added that more information about this collaboration would be released at the ASMS meeting in Nashville next month.
The experimental data submission track, led by Chris Taylor, is at the earliest stage in its development, but it has now officially adopted MIAPE — or minimum information about a proteomics experiment — as its model. MIAPE is based on a similar standard already in place for microarray data, called MIAME (see PM 10-24-03). Specific standards have not yet been established, but Hermjakob said that specific standards were now in the development process, and that preliminary results should be ready for HUPO Beijing in October.
HUPO PSI will hold its next major workshop in a year.