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Doing The Time Warp, Biennial Siena Proteomics Meeting Looks to the Past for Hope in the Future

SIENA, Italy — Organizers of the 7th Siena Conference on Proteomics may have titled this year’s event “From Genome to Proteome: Back to the Future” in acknowledgement of previous work in the field that continues to resonate today.
But among some of the speakers and attendees at this week’s meeting that title may have well been a reference to how time seems to be standing still when it comes to significant progress in the field.
Over the course of the five-day conference, more than 70 lectures and presentations covered a wide swath of topics — from the nucleopore-promoter interaction of genes in yeast, which kicked off the conference, to the outlook for the UniProt consortium, which closed the conference.
But even as presenters and authors enthusiastically elucidated their research to an audience hungry for new information and techniques, there was a sense that research in the field has hit a wall.
While this sentiment was far from pervasive, some attendees were clearly disappointed with the state of the field.
Ruedi Aebersold, a professor at the University of Zurich and the Federal Technical University in Zurich, put it bluntly, saying that despite all the work that has been devoted to identifying proteins, the number of fully characterized proteins for a typical experiment is stuck somewhere between 1,000 and 2,000. He added that while proteomics has led to some interesting observations, most research has not progressed beyond that, and many of the goals of the field — including the global analysis of the proteome of any species — have yet to be achieved [see Proteomics Pioneer, this issue, for interview with Aebersold].
To overcome these hurdles, Aebersold suggested a new strategy based on mapping out the whole proteomic space with statistical analysis to validate the quality of the data. He also is pushing for a targeted analysis of information-rich peptides. Such peptides, he said, would have to be observable by mass spectrometry.
To many, the lack of progress is due not to a shortage of imagination or aspirations, but to the limitations of technology. Daniele Perini, a PhD student in biotechnology at the University of Siena, said that it is currently impossible to study the entire proteome of a research subject. Only partial sections of it can be viewed at a time.
"Even if you want to look at the whole protein you'd have to have 10 different technologies," he said. Not many labs are that well-equipped, he added, "so in this sense it is still frustrating."
During a wine and hors d'oeuvres gathering hosted by conference sponsor Waters, one researcher said that the field is currently stymied by the same people doing the same research with the same tools. Instrument-makers, she added, have not responded to of scientists’ needs.
To be sure, advances have been made in instrumentation. Denis Hochstrasser, a professor at the University of Geneva and a conference organizer, said in his opening remarks that “mass spectrometry has grown tremendously and modified the way we do our work.”
But some, like Aebersold, while acknowledging the improvements in technology, nonetheless say that it is not progressing quickly enough to keep pace with the demands of proteomics research.
"The core question of proteomics, mainly how proteomes behave under certain conditions, vigorously can not be answered right now because of technical limitations,” he said, and until technology catches up with the goals of the scientists, proteomics will always remain a science of unfulfilled potential.
Regardless, the Siena conference remains one of the prime venues to catch up on the latest work being done in proteomics and to mingle with those who have made their mark in the field and those about to do so.
Of course it doesn’t hurt that the meeting is held in the heart of Italy’s Tuscany region in a town where the cobblestone streets and dark, brick houses bring to mind the Italian Renaissance.

"The core question of proteomics, mainly how proteomes behave under certain conditions … can not be answered right now because of technical limitations.”

Held every two years, the Siena conference is one of the most respected in the proteomic field and since the first meeting in 1994, attendance has grown from about 120 to 700. Since that first conference, it has been moved to a bigger site to accommodate a bigger crowd, and organizers said that the number of attendees would be even larger if they did not put a cap on it.
At this week's event, the list of speakers included luminaries of the field such as Aebersold, Mathias Uhlen of Sweden’s Royal Institute of Technology, and Ulrich Laemmli of the University of Geneva. There were also ground-level researchers, PhD students, and post-doctoral candidates, as well as vendors trying to sell their wares.
Organizers, however, remain strict about maintaining the purity of the conference's emphasis on the science. Any business deals being forged were done so discreetly and on-site mention of the conference's sponsors is limited to a single display.
The pace of the conference was brisk. Topic sessions were scheduled one on top of the other with speakers being hurried along by hosts who often limited audience to one or two questions, in order to keep to the schedule. In many cases, a session ended without any time for questions afterward.
Sara Zanivan, a PhD student at the University of Turin in a multi-discipline program combining bioinformatics, biology, math, and physics, hopes to do post-doc research on cell activity. While she didn’t see much work being discussed in that area in Siena, she had the chance to see the different techniques being used by proteomics researchers.
“I just want to understand what are the differences and then I will choose in the future [which ones to use],” she said.

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