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With No New Deals, GeneProt to Close Its Doors


After failing to negotiate new deals in 2004, Geneva-based proteomics outfit GeneProt has decided to close its doors. Keith Rose, the company’s former CSO, says GeneProt had not run out of cash but was shutting its doors “because closing down was seen as the best way to preserve and not squander the remaining resources.”

Rose, who left GeneProt last June but kept his CSO title and continued consulting with the company until Jan. 1, says GeneProt has already sold off virtually all of its mass spectrometers to “some sort of reseller or surplus warehouse,” and the company is currently selling off more of its equipment.

Bertrand Damour, the CEO of GeneProt, declined to comment.

At its peak, in 2002, GeneProt employed 117 people, Rose says. That was about two years after the company was founded, and a year and a half after GeneProt signed a pivotal, $91-million discovery deal with Novartis. Under that deal, GeneProt agreed to analyze proteomes relating to three disease states in order to identify potential diagnostic markers or therapeutic proteins. In return, Novartis agreed to pay GeneProt $41 million in fees and make a $50 million equity investment.

Rose says that part of the reason no additional major deals were ever signed was because investors began to realize that proteomics wasn’t “delivering” in the way they had thought it would. GeneProt’s business model of taking a biological sample, analyzing it, and delivering a list of the most important proteins began to suffer when investors realized that the important proteins were not necessarily going to lead to blockbuster drugs, Rose postulates.

A few years later, when it became clear that blockbluster protein therapeutics were not in line with what proteomics was likely to deliver, proteomic companies, including GeneProt, began to focus on finding biomarkers. This was of less interest to investors because they were less likely to bring in large amounts of money, Rose said.

Other proteomic companies that had platforms similar to GeneProt’s have suffered as well. The Netherlands-based Glaucus Proteomics closed down; Large Scale Biology closed its contract proteomic business; MDS ceased investing in its daughter company MDS Proteomics; and Oxford Glycosciences was bought by Celltech, which decided not to maintain the proteomic services part of the company.

—Tien-Shun Lee



In His Own Words: Aaron Timperman

Aaron Timperman recently was awarded a half-million dollar grant from the National Science Foundation for his project on “Seawater Proteomics.” ProteoMonitor caught up with Timperman to find out what seawater proteomics involves, and how he got into the uncommon field.

Position: Assistant professor of chemistry, West Virginia University, since 1999.

Background: Postdoc, Ruedi Aebersold’s laboratory of molecular biotechnology, University of Washington, 1997-1999.

Postdoc, Paula Coble’s laboratory of marine chemistry, University of South Florida, 1995-1997.

PhD in analytical chemistry, University of Illinois, 1995.


What is the idea behind separating proteins from ocean water?

I have a big interest in molecular characterization of dissolved organic matter. The whole reason is we really don’t know how dissolved organic matter cycles. So there’s a lot of fundamental questions about dissolved organic matter cycling that really need to be answered. We know that we’re putting a lot of carbon dioxide into the atmosphere, and other gases, and we really don’t know how the earth as a climate system is going to change and to adjust to that. There’s already ample evidence of global climate change, and dissolved organic matter is surely important in that cycle, because there’s about as much carbon in dissolved organic matter in the ocean as there is total carbon in the atmosphere. The question then is how carbon from the atmosphere moves through the ocean — some of it is extremely stable and builds up to relatively high concentrations. What is it about those molecules, their structure, their environment that allows them to really accumulate? All those transformations of molecules as they go through dissolved organic matter are really unknown.

In the past, people have done a lot of ‘class’ sorts of analyses, looking at are there different reactive groups present, or if I treat it by such a method, what will happen to it? Our focus is much more at the molecular level. We know how to sequence proteins and peptides from gels and other things, so if we’re going to look at dissolved organic matter at the molecular level, it makes the most sense to start with proteins, because they are so well characterized, and they’re somewhat predictable as biopolymers.

If you really want to try to find out how dissolved proteins cycle, and you want to find out how dissolved organic matter in general cycles, you need to have some idea of what proteins are there, and how they change. It’s hard to say how they change if you don’t have any structural information at the molecular level.



US Patent 6,887,713. Bioactive chip mass spectrometry. Inventors: Randall Nelson, Dobrin Nedelkov. Assignee: Intrinsic Bioprobes. Issued: May 3, 2005.

The present invention covers a bioactive probe or chip that allows for the isolation of analytes, such as biomolecules, followed by modification or bioreaction on these said analytes. The invention also relates to various methods and apparatuses that include characterization and identification technologies, such as Bioactive Chip Mass Spectrometry. Preferably, the method involves capturing an analyte present within a sample by an interactive surface layer located in a separation site; washing unwanted portions of the sample from the surroundings of the captured analyte; transferring the captured analyte from the separation site to a modifying site; modifying or bioreacting the analyte to create a modified or bioreacted analyte. The modified analyte may then be characterized and/or identified by techniques such as mass spectrometry.



US Patent 6,887,701. Microarrays and their Manufacture. Inventors: Norman Anderson, Leigh Anderson. Assignee: Large Scale Proteomics. Issued: May 3, 2005.

The present invention relates to microarrays containing bioreactive molecules, their uses, and methods for their manufacture. The arrays are constructed by sectioning bundles of tubules or rods containing unique reactants to produce large numbers of identical arrays. The microarrays of the present invention are prepared by using a separate fiber for each compound being used in the microarray. The fibers are bundled and sectioned to form a thin microarray that is glued to a backing.



$500 million

According to Irish market research firm Research and Markets, the market for protein biochips will grow from $122 million in 2002 to more than $500 million in 2008.




At the 2005 international symposium on Computational Challenges in Systems Biology, the Institute for Systems Biology announced that its Human Proteome Folding Project launched on IBM’s World Community Grid in November 2004 has already predicted 50,000 protein structures.


Users of Waters’ ProteinLynx Global Server software now have the option to use either Matrix’s Mascot or Waters’ ProteinLynx search engine to identify and characterize proteins following mass spec analysis.


The Blueprint Initiative, a non-profit research program housed at the Samuel Lunenfeld Research Institute at Toronto’s Mt. Sinai Hospital, was forced to lay off 33 people, or around half its staff, as it faces a gap in its funding.


BD Diagnostics has acquired the technology and other assets of FFE Weber, a German company that specializes in the separation and fractionation of complex proteins using the Free Flow Electrophoresis protein-separation system.


Userspace has begun an evaluation of IPFlex’s DAPDNA-2, a reconfigurable processor, for use in an NIH-sponsored proteomics research project involving real-time tagging and data modeling of mass spectrometry data.


Millipore has signed an agreement under which its Immobilon-FL fluorescence membranes will be included in QDC’s Western blotting kits.


Invitrogen sued Bio-Rad Laboratories in April over gel electrophoresis technology, claiming that a number of Bio-Rad’s Criterion Bis-Tris gels infringe on three patents owned by Invitrogen, all entitled “System for pH-neutral stable electrophoresis gel.”


The National Institute of Diabetes and Digestive and Kidney Diseases has issued an RFP for an initiative designed to validate candidate biomarkers for various human diseases, including diseases of the liver, kidney, urological tract, digestive and hematologic systems, and endocrine and metabolic disorders. diabetes and its complications, and obesity.


With the help of technology developed by Vivascience for eluting biomarkers off high-concentration carrier proteins, PerkinElmer and Predictive Diagnostics have identified a panel of blood biomarkers that can distinguish Alzheimer’s patients from controls.


Abbott Laboratories has selected two antigen targets discovered by Celera Genomics using proteomics technologies for further investigation by Abbott for cancer therapeutic development.


The Blueprint Initiative has signed an agreement with Nature Publishing Group to have nine Nature-branded journals submit manuscripts containing biomolecular interaction data to Blueprint’s Biomolecular Interaction Network Database in advance of publication.


Agilent Technologies and Proteome Systems will collaborate on a combined platform for glycoprotein analysis that will make Proteome Systems’ GlycomIQ software compatible with Agilent’s XCT, XCT Plus and XCT Ultra ion-trap mass spectrometers.


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