00048 J Silva Proteo Monitor 2005 1104

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Profiling proteins in complex mixtures for relative abundance and stoichiometry

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00048 J Silva Proteo Monitor 2005 1104

  1. 1. 11/4/2005 | Volume: 5 | number 42 in this issue Features Waters Develops New Label-Free, Mass Spec- Based Method for Absolute Quantification The new method relies on an "unexpected" relationship between the average MS signal response for the three most intense tryptic peptides and protein concentration. However, so far the method can only be performed using the Waters Q-TOF Premier instrument, because the tool has a special data-collection strategy that toggles back and forth between acquisition of low-energy precursor ion information and elevated energy fragmentation data. EMBL Researchers Develop High-Throughput Method for Producing Monoclonal Antibodies The method was able to generate 68 monoclonal antibodies within six weeks after immunizing eight mice with 10 antigens each. Proteomics Pioneer NIH's Glen Hortin on Translating New Biomarkers into Clinical Laboratory Tests Industry Briefs Caprion, AstraZeneca, Beckman Coulter, Consorta, Beckman Coulter, PerkinElmer, EU, Compugen New Products/Movers & Shakers International School of Advanced BioMedicine and Bioinformatics, Lipari International School for Computer Science Researchers, Sebastian Meyer-Plath, Jizhong Zhou Charts Recent Proteomics Papers of Note (K-Z)* Copyright Notice The newsletter subscription is for a single individual user. Passwords and user logins may not be shared. You may print and retain one copy of each issue of this newsletter during the term of your subscription. Copying, photocopying, forwarding or duplicating this newletter in any form is prohibited. If multiple individuals need to access this newsletter online, you need an affordable, multi-user site license. Contact Allan Nixon at +1-212-651-5623 or anixon@genomeweb.com. If you have received this file under a GenomeWeb site license, your rights to forward, copy or otherwise distribute this file are governed by the provisions of that site license. Contact your site license administrator for details. 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 1 of 16
  2. 2. Features Waters Develops New Label-Free, Mass Spec- Based Method for Absolute Quantification Waters has developed a new label-free, mass spectrometer-based method for absolute quantification of proteins. The new method, published in the Oct. 11 issue of Molecular & Cellular Proteomics, relies on an "unexpected" relationship between protein concentration and the average MS signal response for the three most intense tryptic peptides, according to Jeff Silva, the first author of the study who is a senior research and development scientist in Waters' Core Technologies/Proteomics department. There is one important caveat to the method, Silva noted: So far, the method can only be performed using the Waters Q-TOF Premier mass spec, because the instrument has a special data-collection strategy that toggles back and forth between acquisition of low-energy precursor ion information and elevated energy fragmentation data. Normally, the relative quantitation of a peptide as compared to another peptide can not be determined by comparing MS intensities because peptides ionize at different efficiencies, Silva explained. The new absolute quantification method is based upon a relationship that was discovered between absolute concentrations of proteins and the [MS signal] "response factor" of the three highest ionizing peptides of a given protein. "It turns out that at equimolar concentration, the average intensity measurement of those top ionizing peptides are the same," said Silva. "So there's a counts-per-mole equivalent for any given protein." Silva's research team tested the method of absolute quantification by first working with five proteins of known concentrations that varied "It seems simple. They've in size from 15 to 98 kilodaltons, then carrying out the same noticed a trend where if you calculations with a subset of human serum proteins of unknown look at the most abundant concentrations. ions, you can generate a universal factor that you can The researchers calculated the average signal response from the top three tryptic peptides for each of the proteins, which varied in multiply everything with. You concentration from six picomoles to 15 pmoles. They showed that find your scaling factor, and each of those proteins had the same response factor, such that the you can go back and actually signal response is a fixed number of counts per picomole of protein. figure out micromolar Once they had the response factor for their Waters Q-TOF Premier amounts." instrument, the researchers used that factor to calculate the absolute quantity of 11 proteins in human serum. The concentrations of the proteins as determined by the new method correlated with concentrations of the proteins that had been previously published in other studies. "It seems simple," said Minerva Hughes, a recent PhD graduate in Craig Townsend's laboratory at Johns Hopkins University who has been using the Waters Protein Expression system to do relative protein quantitation. "They've noticed a trend where if you look at the most abundant ions, you can generate a universal factor that you can multiply everything with. You find your scaling factor, and you can go back and actually figure out micromolar amounts." The reason that only Waters Q-TOF Premier instruments work with this method is that so far, only those instruments collect data in an alternating fashion, such that there are three data points — mass, retention 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 2 of 16
  3. 3. time, and signal intensity — per time interval, Silva said. Other instruments acquire data through only a fraction of the peak list, until they have gathered enough information to identify that peptide. "The alternate scanning mode of acquisition allow you to get a true sense of what's there in terms of peak area to a given protein," said Silva. "Because we were able to see the true 3D peptide mass fingerprint, without partial peak sampling, the correlations fell right out of the data." Silva and Hughes noted that absolute quantitation is important for determining the stoichiometry of molecules that make up a complex. Paul Skipp, the manager of the Center of Proteomics Research at the University of Sussex in the U.K., added that absolute quantitation is "I think the way that [mass important for understanding signaling pathways. spec] technology is going to move in the future is to move "In a signaling pathway, you tend to have a small signal that starts away from labeling." that causes a protein to bring other proteins to it — that may require 10 molecules, and those 10 molecules may signal to another protein," he said. "If you know a cell in its normal state has so many molecules of Y and so many molecules of Z, you start to understand how that cell's working. Also, if one of those molecules starts to produce a larger number of molecules, that could be an indicator of an onset of disease." Skipp currently uses a technique called AQUA to do absolute quantitation. The method relies on using a 13 C-labeled molecule as an internal standard. Skipp had not heard of Waters' new method of absolute quantitation, which does not require protein labeling, but said that he was pleased with the way Waters' Protein Expression system had worked for relative quantitation. "I think the way that [mass spec] technology is going to move in the future is to move away from labeling," said Skipp. "The beauty of the Protein Expression is that you don't have to label, and you can compare more than four conditions, and you can compare different experiments to each other." Silva said Waters is currently integrating the new absolute quantification relationships into their software so that it will be easy to calculate the average intensities of the top three ionizing peptides. He noted that the reason for using the top three ionizing peptides, as opposed to another number, was a function of the size of the protein. For small proteins, the top two might work better, and for large proteins the top four might work better, he said. "You could make it a function of molecular weight, but three worked in this demonstration," he said. — Tien Shun Lee (tlee@genomeweb.com) 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 3 of 16
  4. 4. EMBL Researchers Develop High-Throughput Method for Producing Monoclonal Antibodies Using antigen arrays, researchers at the European Molecular Biology Laboratory have developed a high-throughput method for producing monoclonal antibodies. In a study published in the Oct. 27 issue of Proteomics, researchers led by Federico De Masi and Alan Sawyer showed that the method was able to generate 68 monoclonal antibodies within six weeks after immunizing eight mice with 10 antigens each. "Normal antibody production takes five to nine months for a single antibody, depending on how immunogenic the antigen is," said De Masi, who is now a postdoc in Martha Bulyk's laboratory at Brigham & Women's Hospital. "By using antigen microarrays, we can basically detect the antibody of the animal at a much earlier stage, and the screening is faster than with an ELISA or Western blot." The EMBL's patented antibody production method has been commercialized by Taiwan-based Abnova, which signed a collaboration agreement with EMBL in December 2004. As with many other antibody production methods, the EMBL method begins with immunizing a mouse with an antigen of interest. Researchers then wait four weeks for the mouse to generate an immune response before sacrificing it. After B-cells have been harvested from the spleen of the mouse, researchers generate a library of thousands of hybridoma cell lines — immortal cell lines that produce one type of monoclonal antibody each — by fusing the B cells with cells from a mouse cancer cell line. The key to the new antibody production method is that screening of hybridoma cell lines is done using a chemically modified glass slide "The greatest challenge in coated with the antigen of interest. Because this array method is more creating the array is that we sensitive for detecting antibodies than ELISA or Western blot had to find the right methods, researchers do not have to wait as long for mice to generate concentration of the antigens, an antibody response before sacrificing the animals. and the right chemical While traditional monoclonal antibody production methods require modification of the slide to waiting six weeks to three months before sacrificing the immunized get the microarray functional. mouse, the EMBL method requires only four weeks of waiting. Then each sample that we spot has a different density After hybridomas have been spotted onto the antigen-coated slide, the slide is washed, incubated with a fluorescent secondary antibody that and viscosity, so there was a recognizes mouse antibodies, then washed again. If an antibody has lot of tweaking that had to be stuck to the antigen-coated slide, then it can be visualized through the done. It took some time to fluorescent secondary antibody. find the right conditions that were highly reproducible for "The greatest challenge in creating the array is that we had to find the right concentration of the antigens, and the right chemical the whole spectrum of modification of the slide to get the microarray functional," said De antibodies." Masi. "Then each sample that we spot has a different density and viscosity, so there was a lot of tweaking that had to be done. It took some time to find the right conditions that were highly reproducible for the whole spectrum of antibodies." To make the monoclonal antibody production process even more high throughput, EMBL researchers decided to immunize mice with more than one antigen at a time. They first tried two antigens per mouse, 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 4 of 16
  5. 5. then five, then 10. In a large-scale experiment, De Masi and his colleagues immunized eight mice with 10 antigens each. After the mice were sacrificed and hybridomas were created, the researchers screened the hybridomas on 10 slides that were coated with one antigen each. In the end, the researchers were able to generate antibodies against 68, or 85 percent, of the antigen targets, within six weeks of primary immunization. Aside from using the arrays to cut down on antibody production time, EMBL researchers also saved on time by using custom-built robots to automate the hybridoma production process. "The robots take care of changing cell medium, fusion of B-cells, plating onto plates, [and] incubation," said De Masi. "Otherwise, we'd have to have somebody 24 hours per day taking care of these cells." Currently, the EMBL's monoclonal antibody core facility will produce monoclonal antibodies to an antigen for about 2,500 ($3,017) per antigen, De Masi said. Monoclonal antibodies against peptides cost a little more — 3,000 ($3,591) per peptide — because it is harder to raise a good immune response against a peptide, which is generally shorter than an antigen. The EMBL generally leaves quality testing of antibodies up to the researchers who have requested them, De Masi said. "Generally what's done is we obtain five to 10 strong affinity hybridomas and we send it to the investigator so that he or she can choose the one that he or she likes," said De Masi. "Depending on what the investigator needs the antibody for, the antibody might be fantastic for one application, but useless for another. For example, with some of our antibodies that we did test, they gave some signal on the microarray, a beautiful Western blot band, but no signal on an ELISA." Abnova president and CEO Wilber Huang said that his company's collaboration with EMBL furthers its effort to become a leader in high-throughput antibody production. "Custom service and partnership now form the core of our business. We are concurrently developing a comprehensive antibody bio-tool catalog for the drug discovery and diagnostic industry," said Huang, following the formation of the collaboration agreement. "As such, we are focusing on several key areas of human proteins: kinase, apoptosis, receptors, stem cell and plasma proteome. The collaboration with EMBL is the latest step in our effort to realize these goals." — Tien-Shun Lee (tlee@genomeweb.com) 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 5 of 16
  6. 6. Proteomics Pioneer NIH's Glen Hortin on Translating New Biomarkers into Clinical Laboratory Tests At A Glance Name: Glen Hortin Position: Chief of clinical chemistry, Department of Laboratory Medicine at the National Institutes of Health, since 2000. Acting, assistant chief of clinical chemistry, since 1997. Background: Associate professor of pathology, University of Alabama at Birmingham's clinical chemistry section, 1993-1997. Glen Hortin Assistant professor in pediatrics and pathology, Washington University, 1989-1992. Chief of clinical chemistry, Department of Laboratory Medicine National Institutes ofLast week, Glen Hortin gave a talk on "Translating New Biomarkers into Clinical Health Laboratory Tests" during an American Association for Clinical Chemistry meeting in Washington, DC. ProteoMonitor caught up with Hortin to find out about his advice on this issue, and about his research background. How did you get into developing biomarkers and clinical tests? Originally, I was interested mostly in protein chemistry. I started in the 1970s looking at protein biosynthesis. As an undergraduate and graduate student, I was looking at processing events like the processing of secretory proteins and glycosylation of proteins. As a graduate student I worked on the basic aspects of a signal hypothesis in terms of how secretory proteins are processed. Then I was interested generally in the issues of protein processing — post-translational modifications and molecular recognition between proteins, how various proteases or substrates would find their right substrates or protease to inhibit — how they got together. Simultaneously I was getting interested in clinical chemistry. Those are interests of mine that go back about 20 years. Which laboratory were you working in? I was working with Irving Boime at Washington University in St. Louis. I continued on as a faculty person. Arnie Strauss helped me get going — he had done a lot of work in the protein processing area. He was a pediatric cardiologist, but also did basic science. Before I got started on my graduate work also, I had the good fortune to work with Donald Steiner at the University of Chicago — he was the fellow who discovered proinsulin. At the time, he was studying the precursors of proinsulin. I spent a couple of summers in his lab as a student. It was an interesting entré into protein chemistry. I went to medical school, and I did a residency from 1983 to 1987 in clinical pathology. My main interest was in the clinical chemistry end of the laboratory. What types of problems were you working on? 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 6 of 16
  7. 7. In clinical chemistry, you tend to get interested in a wide range of problems — whatever problems come up in the laboratory. It's really kind of problem solving and problem focused. In the clinical chemistry area, probably half of the assays we deal with relate to protein measurement — some of them are enzyme assays, some of them are immunoassays, some of them are simple electrophoretic assays. Basically, in the clinical laboratory, a major portion of the protein assays are really kind of within the subspecialty of clinical chemistry. Another section is the immunology section. Were you working on enzyme assays? Well, I did a fair amount of work in looking at protease specificity. From a practical standpoint, you're often in a problem solving mode in the clinical lab to address the patient needs. In general, I've had a more basic research lab effort that's kind of gone in parallel. Part of that effort was directed at studying post-translational processing of proteins. I spent a fair amount of work on sulfation of proteins. Where did you go after Washington University? I stayed on as faculty there for about five years, and then I went to the University of Alabama in Birmingham. A greater amount of my time there was spent doing clinical work — helping to run a clinical laboratory. I got involved fairly actively in terms of point-of-care testing, which is a lot of the testing done at the patient's bedside. The things done at the bedside are usually things like glucose testing, electrolytes, things like that. Then eight years ago, I came to the NIH, where I had a little bit more time for doing research work. I really became interested in some of the issues with protein analysis. With new developments in mass spectrometry and new tools, I could go back and look at some of the issues I had been interested in years before. I suppose I was basically interested in proteomics 15 or 20 years ago, but we didn't have the tools to do it. I remember 15 years or so ago being interested in 2D electrophoresis and how you might use it for diagnostic purposes. But it wasn't well enough developed then. You would get lots of spots, but you really couldn't identify what most of the spots were. It's really over about the last five years or so that with new mass spectrometry tools, and with completion of the human genome that basically defines all the protein sequences, you can go back and identify whatever protein or peptide you want, and you have a lot more of a solid basis for doing these things. Another thing is that detection limits have become much more practical to work with. The scale of samples that you would get in a clinical lab before — you might have had to draw much larger volumes of blood than would be routinely practical, and kind of go through many steps to get down to what you need. This is starting to really enable things to be more approachable on true clinical samples. Did you start to work with biomarkers at the NIH? Well, 'biomarkers' is in a sense a nonsense term. I've been working with biomarkers for 30 years, though people didn't call them that back then. All the lab tests that we deal with pretty much are measuring biomarkers. Biomarkers is such a vague term, it's practically a nonsense term. I don't know why people use it. It's just kind of a catchy term that for some reason people think means something special. Every test that we use in the clinical lab is basically measuring a biomarker — it may be an enzyme activity. If you look at the current definition, it's basically anything that you can currently measure that might be related to a physiological response that you might be interested in following. We've had biomarker labs for many years — they're called clinical labs. It is a very interesting time in that you can sort through possibilities much faster in terms of doing discovery 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 7 of 16
  8. 8. work, and the whole pace of discovery has been speeded up a lot. Some of the techniques allow you to look at hundreds of components at a time. That's really a new dimension in terms of looking at things. In the past, most of the things that we've done in the clinical lab have been done one test at a time. That's not the case 100 percent [of the time], but the majority of them have been. A few things we've looked at [involved more than one thing at a time] — a profile on electrophoresis, or some things looked at an entire pathway, or perhaps 10 or more components. But we now have a new tool set to look at these things, and I think it is opening up new possibilities, particularly to look at molecular variation and some of the post-translational modifications. What kind of tests are you working on developing currently? Mainly I'm interested at the moment in trying to characterize a diversity of smaller peptide components in biological fluids — mainly plasma and urine samples. By traditional tools, that was one area that we did not see in very great detail. The new tool sets have really expanded quite a bit our ability to look at these. Mass spec is very good for looking at peptides. The older tools like 2D electrophoresis — the peptides fall off the bottom, so they're kind of invisible. We probably had underaccounted for them some. So that's the area I'm interested in looking at the moment. What issues do researchers have to deal with in translating a biomarker into a clinical test? There are many steps in going from a basic biomarker to a useful laboratory test. Particularly in some of the profiling techniques that have been used for the MALDI-TOF or SELDI-TOF techniques have not applied the usual types of standards that we use in the clinical laboratory. To start to figure out how to standardize these types of assays better — you have to define some of the things that you usually do for any clinical test in terms of evaluating reproducibility, linearity of responses. You have to figure out how the intensity of various peaks relate to the concentration of what you're trying to measure. I think that to move some of these techniques to clinical lab tests, you have to come up with approaches that deal with these things. Otherwise you would not be meeting the usual standards that we would apply in a clinical lab. What's the biggest challenge in moving something into a clinical test? There are so many steps in this that it's a little bit hard to know where to begin. There are really probably a half dozen or more important steps. There are whole issues in terms of having adequate specimens to validate the test in the first place, and to kind of serve as a database. There are so many issues related to the specimen selection, and how you perform those studies. And then people are still trying to grapple with specimen collection issues. Often times they haven't paid quite enough attention in terms of pre-analytical variables — the patient preparation, and how to standardize the collection processes and things. There's also the issue of marker selection. Many markers are not going to be suitable if they're too variable or unstable. Most of what we're doing at the moment is method and technology development rather than specific test development. It's a little premature to try to develop a test until you really have your methods optimized more. A lot of our efforts now are really towards trying to get the most information possible about peptide repertoires in different samples and stability issues so that we can figure out how to handle the samples before we even get to the point of doing a test. Once we do that, I think then we'll be able to move forward fairly quickly and a little bit more rigorously in terms of doing tests. We have analyzed some clinical sets and things, but those were a little bit more discovery efforts in terms of finding peptides that might be discriminatory for certain things. We weren't really to the point of doing tests yet. Some people think as soon as they get some peaks showing up in a pattern, they have a test, but I think in 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 8 of 16
  9. 9. general there's a fairly big gap in terms of finding a few peaks in a pattern and figuring out how you can use that meaningfully in a test. What kind of advice would you give to someone who has found some biomarkers and is looking to develop them into a clinical test? Generally, I feel it's important to be able to identify what your peaks are, and to understand the biology and what they represent. Is there really any physiological basis that they should be related to what you're trying to understand? The second thing is you have to optimize your methods so you get good reproducibility. Your ability to get accurate measurements in general kind of depends on your ability to get high signal to noise. If you're dealing with very weak signals, in general you're not going to be able to get very robust tests out of it. 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 9 of 16
  10. 10. Industry Briefs Caprion Partners with AstraZeneca on Prostate Cancer Targets Caprion and AstraZeneca will collaborate to develop therapies for prostate cancer, Caprion Pharmaceuticals said this week. Under the agreement, AstraZeneca will evaluate prostate cancer drug targets discovered by Caprion and obtain exclusive, worldwide rights to develop and commercialize therapeutic applications for selected targets. Caprion will retain rights to other targets. AstraZeneca will pay Caprion an unspecified amount for up-front payment and license fees. The company will make additional payments contingent on its meeting certain development and commercialization milestones. Beckman Coulter Licenses Clinical Lab Tests to Consorta; Deals Worth $105M Over Five Years Beckman Coulter will provide Consorta its chemistry, immunoassay, hematology, and automation product lines, the company said this week. The three contracts are worth approximately $105 million over the next five years to Beckman. Consorta also extended its hematology agreement with Beckman, valued at $10 million a year, for two more years, Beckman said. The contract provisions include the company's new line of UniCel systems, such as the DxC 600 and 800 chemistry analyzers, the DxI 800 Access immunoassay system, and the Power Processor automation system, said Robert Kleinert, an executive vice-president at Beckman Coulter, in a statement. Consorta will also have access to nearly 200 different reagent kits. Beckman Coulter Q3 Revenues Grow 2 Percent as Income Drops Nearly 40 Percent Beckman Coulter this week said that its third-quarter sales grew by a 2 percent, while net income fell 38 percent. Total worldwide sales for the three months ended Sept. 30 inched up to $593.4 million from $581.2 million in the same quarter last year. The company reported that $591.7 million of total sales for the quarter were organic, while $1.7 million could be attributed to currency. The Fullerton, Calif.-based company also said that sales in the US remained even compared to last year, but that international sales grew by 3.8 percent. Net income in the third quarter fell to $36.2 million from $57.2 million year over year, the company said, resulting in basing earnings being reduced to $0.58 per share from $0.93 per share. Beckman Coulter said that the company incurred $19.2 million in special charges during the quarter, mostly due to "impaired receivables and leased equipment" related to Hurricane Katrina — which cost the company 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 10 of 16
  11. 11. $4.9 million — and "the non-cash write off of intangible assets of discontinued robotic automation product" from the discontinuation of the Bovine Spongiform Encephalopathy testing initiative, which cost Beckman $13.4 million. The company added specifics to a plan to reorganize the company, as reported by ProteoMonitor's sister publication GenomeWeb News on July 22, signaling its intent to "close at least three facilities, sell two parcels of real estate, harvest or discontinue mature product lines," reduce 350 positions, and streamline the company's physical distribution. Beckman Coulter president and CEO Scott Garrett said in a statement that he expects the lay-offs will result in a benefit of up to $2 million in the fourth quarter of this year, as well as "$15 million of annual savings in 2006, growing to $20 million of annual savings in 2007 and beyond." Garrett also offered a preliminary outlook on 2006. Beckman is now expecting total 2006 sales to be $2.5-$2.6 billion. He added that the company's decision to favor operating-type leases over sales-type leases for instrument placements may reduce sales over 2005 and 2006 as the change in policy is implemented. "Our original range for the impact of the leasing policy change on sales through 2006 was $200 to $220 million," Garrett said. "We now expect the change to reduce revenues by $190 to 200 million over the implementation period, which will be split about evenly between 2005 and 2006." Beckman Coulter spent $51.6 million on R&D in the quarter, compared to $51.5 million in the same quarter last year. As of Sept. 30, the company held cash, cash equivalents, short-term investments, and restricted cash totaling $59.3 million. PerkinElmer Obtains $350M Revolving Loan; Cash Could Fund M&A, Alliances PerkinElmer obtained a $350-million unsecured revolving credit facility, the company said this week. The five-year loan, which replaces a previous $100 million facility, will be used for "general corporate purposes," such as working capital, refinancing, capital expenditures, share repurchases, acquisitions, and strategic alliance, said PerkinElmer. The facility was jointly made with Banc of America Securities and Citigroup Global Markets. EU Awards $10.8M to Form Network of Excellence on Biological Research The Commission of the European Union awarded 9 million ($10.8 million) to establish a virtual institute for biological research, the European Bioinformatics Institute said this week. ENFIN, or the Experimental Network for Functional INtegration, will combine 20 computational and experimental biology labs across 17 institutions in 13 counties to make computational systems biology accessible to European scientists. While applicable to any area of biological research, the network will focus on the regulation of cell division. While there's an open-access database for almost every type of biological information, the average biologist struggles to access the data, the institute said. 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 11 of 16
  12. 12. "Researchers will be able to go straight to the public data that they want, combine it with their own unpublished data and perform truly integrated analyses using data from different types of experiments," said the institute's Ewan Birney, who will coordinate ENFIN. ENFIN will incorporate both "wet" and "dry" biologists whose expertise spans database architecture, data analysis tools, and experimental molecular biology. Compugen Reports 22-Percent Slide in Q3 Revenue, Names New CEO Compugen said this week that revenues for the third quarter declined 22 percent while net losses remained flat. The company also said it has named Alex Kotzer president and CEO. He started on Sept. 1. Total revenues for the three months ended Sept. 30 fell to $761,000 from $971,000 year over year. About 87.5 percent of the amount, or $666,000, came from "governmental and other grants," said Compugen Third quarter R&D spending increased slightly to $3 million from $2.8 million in the previous year. The company reported that net loss remained flat for the quarter, at approximately $3.6 million, or $.13 per share. As of Sept. 30, the company had $29.9 million in cash and cash equivalents. 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 12 of 16
  13. 13. New Products/Movers & Shakers New Products The International School of Advanced BioMedicine and Bioinformatics and the Lipari International School for Computer Science Researchers are jointly organizing a two-week course on "Proteomes and Proteins." The course will be held on Lipari — an island off the coast of Eastern Sicily — from July 9 to July 22, 2006. It will focus on describing knowledge of proteomes, their dynamic changes during the life cycle of cells and organisms, and their modifications in disease states. More information on the course is available at http://lipari.cs.unict.it/lipari/currentedition.htm. Movers & Shakers Sebastian Meyer-Plath returned to Bruker Daltonics as vice president for its nuclear, biological, and chemical business and as a managing director of Bruker Daltonik GmbH, the Bruker Daltonik operation in Leipzig, Germany, the company said this week. He originally joined Bruker in 1993, and held several project- and product-management positions in the company. He left in 2002 for Germany's Advalytix AG and joined Smiths Detection as vice president of sales & marketing in 2003. At its Oct. 25 meeting, University of Oklahoma's Board of Regents decided to bring Jizhong Zhou to the university as a functional genomics researcher, said Lee Williams, vice president of research. Zhou's genomics laboratory on campus is expected to be fully operational by January 2006. Prior to his OU appointment, Zhou was in Oak Ridge, Tenn. at Oak Ridge National Laboratory. 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 13 of 16
  14. 14. Charts Recent Proteomics Papers of Note (K-Z)* Journal Title Authors Molecular & Cellular Absolute quantification of Proteomics. Silva JC, Gorenstein MV, Li GZ, Vissers JP, proteins by LCMSE: A virtue 2005 Oct 11; Geromanos SJ. of parallel MS acquisition. [Epub ahead of print] Molecular & Cellular Biomarker discovery from Gronborg M, Kristiansen TZ, Iwahori A, Proteomics. pancreatic cancer secretome Chang R, Reddy R, Sato N, Molina H, 2005 Oct 8; using a differential proteomics Jensen ON, Hruban RH, Goggins MG, Maitra [Epub ahead of print] approach. A, Pandey A. High throughput quantitative Molecular & Cellular glycomics and Uematsu R, Furukawa JI, Nakagawa H, Proteomics. glycoform-focused proteomics Shinohara Y, Deguchi K, Monde K, 2005 Sep 16; of murine dermis and Nishimura SI [Epub ahead of print] epidermis. Molecular & Cellular Comparative proteomics Proteomics. analysis of intra- and Hu Y, Malone JP, Fagan AM, Townsend RR, 2005 Sep 30; inter-individual variation in Holtzman DM. [Epub ahead of print] human cerebrospinal fluid. Differential protein expression Molecular Psychiatry. in the prefrontal white matter Alexander-Kaufman K, James G, Sheedy D, 2005 Sep 20; of human alcoholics: a Harper C, Matsumoto I. [Epub ahead of print] proteomics study. Liver tumors in wild flatfish: a Stentiford GD, Viant MR, Ward DG, Johnson OMICS. histopathological, proteomic, PJ, Martin A, Wenbin W, Cooper HJ, Lyons 2005 Fall;9(3):281-99. and metabolomic study. BP, Feist SW. Proceedings. Biological Behavioural manipulation in a Sciences/The Royal grasshopper harbouring Biron DG, Marche L, Ponton F, Loxdale HD, Society. hairworm: a proteomics Galeotti N, Renault L, Joly C, Thomas F. 2005 Oct approach. 22;272(1577):2117-26. Proceedings of the National Academy of An evolutionary proteomics Sciences of the United approach identifies substrates Budovskaya YV, Stephan JS, Deminoff SJ, States of America. of the cAMP-dependent Herman PK. 2005 Sep protein kinase. 27;102(39):13933-8. Epub 2005 Sep 19. Proteomics. Proteomics-based consensus 2005 Oct 11; prediction of protein retention Tjalsma H, van Dijl JM. [Epub ahead of print] in a bacterial membrane. Functional proteomics and correlated signaling pathway Proteomics. of the thermophilic bacterium Topanurak S, Sinchaikul S, Sookkheo B, 2005 Oct 13; Bacillus stearothermophilus Phutrakul S, Chen ST. [Epub ahead of print] TLS33 under cold-shock 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 14 of 16
  15. 15. stress. Proteomics. Proteomic dataset of mouse Mayr U, Mayr M, Yin X, Begum S, Tarelli E, 2005 Oct 20; aortic smooth muscle cells. Wait R, Xu Q. [Epub ahead of print] Proteomics. Proteomic dataset of Sca-1(+) Yin X, Mayr M, Xiao Q, Mayr U, Tarelli E, 2005 Oct 20; progenitor cells. Wait R, Wang W, Xu Q. [Epub ahead of print] Printing of protein Proteomics. microarrays via a Barron JA, Young HD, Dlott DD, Darfler MM, 2005 Sep 30; capillary-free fluid jetting Krizman DB, Ringeisen BR. [Epub ahead of print] mechanism. Proteomics. A proteomics approach to 2005 Sep 30; Wagg SK, Lee LE. identifying fish cell lines. [Epub ahead of print] A top-down proteomics Proteomics. approach for differentiating Williams TL, Monday SR, Edelson-Mammel 2005 Sep 30; thermal resistant strains of S, Buchanan R, Musser SM. [Epub ahead of print] Enterobacter sakazakii. Proteomics. Large-scale analysis of the Matsumoto M, Hatakeyama S, Oyamada K, 2005 Sep 30; human ubiquitin-related Oda Y, Nishimura T, Nakayama KI. [Epub ahead of print] proteome. Characterization of medium conditioned by irradiated cells Radiation Research. Springer DL, Ahram M, Adkins JN, Kathmann using proteome-wide, 2005 Nov;164(5):651-4. LE, Miller JH. high-throughput mass spectrometry. Differential expression profiling of membrane proteins by quantitative Stem Cells. Foster LJ, Zeemann PA, Li C, Mann M, proteomics in a human 2005 Oct;23(9):1367-77. Jensen ON, Kassem M. mesenchymal stem cell line undergoing osteoblast differentiation. *A-J were published in last week's ProteoMonitor 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 15 of 16
  16. 16. Copyright Notice - Subscription Terms and Conditions GenomeWeb Application-Focus Newsletters are copyrighted intellectual property. It is a violation of US and international copyright law to forward, copy or otherwise distribute a newsletter email bulletin or PDF file to non-subscribers or other unauthorized persons. Individual Subscriptions This newsletter subscription is for a single individual user. Passwords and user logins may not be shared. You may print and retain one copy of each issue of this newsletter during the term of your subscription. Copying, photocopying, forwarding or duplicating this newsletter in any form is prohibited. If multiple individuals need to access this newsletter online, you need an affordable, multi-user site license. Contact Allan Nixon at +1-212-651-5623 or anixon@genomeweb.com. Web Postings and Reprints Individual articles from this newsletter may not be posted on any website or redistributed in any print or electronic form except by specific arrangement with GenomeWeb LLC. Contact reprints@genomeweb.com for further information. Site Licenses If you have received this file under a GenomeWeb site license, your rights to forward, copy or otherwise distribute this file are governed by the provisions of that site license. Contact your site license administrator for details. ProteoMonitor SUBSCRIPTIONS REPRINTS AND WEB RIGHTS Tien-Shun Lee, Editor ISSN 1537-6079 +1.212.651.5618 tlee@genomeweb.com reprints@genomeweb.com ProteoMonitor is published Julia Karow, DPhil weekly (50 times annually) by GENOMEWEB LLC Contributing Editor GenomeWeb LLC 125 Maiden Lane jkarow@genomeweb.com Annual subscription rate: $985 Floor 2 New York NY 10038 Kirell Lakhman Allan Nixon Phone +1.212.269.4747 Editorial Director Director of Subscription Sales Fax +1.212.269.3686 klakhman@genomeweb.com +1.212.651.5623 www.GenomeWeb.com anixon@genomeweb.com Bernadette Toner Dennis P Waters PhD Deputy Editorial Director Chairman and Publisher ADVERTISING btoner@genomeweb.com Judy Block Elena Coronado Associate Publisher Senior Production Designer +1.212.651.5629 ecoronado@genomeweb.com Entire contents copyright © 2005 jblock@genomeweb.com GenomeWeb LLC. All rights reserved. Order a $95 12-week trial subscription* to these ___ YES, please begin my 12-week trial subscription(s) to GenomeWeb Application-Focus Newsletters the newsletter(s) indicated and bill my credit card for the amount below. __ BioArray News ___ BioCommerce Week Total number of newsletters: _____ x $95 = $______________ ___ BioInform ___ Cell-Based Assay News BILLING INFORMATION ___ Pharmacogenomics Reporter ___ ProteoMonitor ___ RNAi News Credit Card: ___ Visa ___ Mastercard ___ American Express Number ____________________________________________ Expiration __________________________________________ *Trial subscription offer available to new subscribers only Name on Card _______________________________________ Signature __________________________________________ Name ______________________________________________ Title _______________________________________________ Fax this page to +1-212-269-3686 or send via snail mail to: Organization ________________________________________ Address ____________________________________________ City ____________________________________ State______ GenomeWeb LLC ZIP/Postcode __________________ Country_______________ 125 Maiden Lane Floor 2 Phone _____________________________________________ New York NY 10038 Fax _______________________________________________ Email ______________________________________________ Phone +1-212-651-5623 Email circulation@genomeweb.com 11/4/2005 © 2005 GenomeWeb, LLC www.proteomonitor.com 16 of 16

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