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At IBC, Difficulties with Plasma Proteome Abound


A series of speakers at the IBC international protein arrays conference in September highlighted problems in working with the human plasma proteome, including a decline in success in finding proteins suitable for clinical diagnostic tests, a lack of validation following identification of potential biomarkers, and high costs for developing immunoassays.

“In the last 10 years the number of new proteins per year approved [by the US Food and Drug Administration] for clinical diagnostic tests has declined to almost zero,” said Leigh Anderson, the CEO of the Plasma Proteome Institute in Washington, DC, who gave a keynote speech at the conference. “We are discovering more proteins, so why is the curve going down?”

Anderson said that although proteomics researchers are finding markers, they’re not being validated in part because the cost for validation is too high. Also, the role of validation has not been taken up by, or designated to, specific companies or institutions.

“Immunoassays would be good, but it takes $2 million to $4 million to make a sandwich assay, per protein,” Anderson said. “Who is going to take these candidate proteins and attempt to figure out which of the hundreds are useful markers?”

Standardizing methods for processing plasma is one of the primary initial goals of the Human Plasma Proteome Project, a Human Proteome Organization initiative that was started about a year ago. As part of the pilot phase, 12 reference specimens collected from three different ethnic populations were sent to 46 different labs in 14 different countries. Each of the labs used their own proteomics techniques to analyze the reference specimens. Results from the 46 labs were expected to be presented at the HUPO conference in Beijing during the last week of October.

—Tien-Shun Lee



US Patent No. 6,787,760. Method for increasing the dynamic range of mass spectrometers. Inventors: Mikhail Belov, Richard Smith, Harold Udseth. Assignee: Battelle Memorial Institute. Issued: September 7, 2004.

The patent covers a method for enhancing the dynamic range of a mass spectrometer by first passing a sample of ions through a mass spectrometer having a quadrupole ion filter, whereupon the intensities of the mass spectrum of the sample are measured and ions are chosen for study. Further sampling introduces more ions into the mass spectrometer, and the appropriate radio frequency voltages are applied to a quadrupole ion filter, thereby selectively ejecting the undesired ions previously identified and allowing the desired ions to be collected for longer periods of time in an ion trap.


US Patent No. 6,799,121. Sequencing of peptides by mass spectrometry. Inventors: Ivan Chu, Tai-Chu Lau, K.W. Siu. Assignee: York University. Issued: September 28, 2004.

The patent describes a strategy for the semiautomatic sequencing of argentinated oligopeptides. The method of sequencing is based on a search algorithm that identifies a triplet peak relationship in a product ion spectrum of the [M+Ag].sup.+ ion of an oligopeptide. The ions that constitute a triplet are [b.sub.n +OH+Ag].sup.+, [b.sub.n -H+Ag].sup.+, and [a.sub.n -H+Ag].sup.+. The difference in the m/z values of adjacent triplets identifies the residue that is “cleaved.” Observation of the [y.sub.n +H+Ag].sup.+ ion containing the cleaved residue confirms the assignment.




Number of entries in UniProt Release 2.5, the latest catalog of information on proteins published by the UniProt consortium, which consists of the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, and the Protein Information Resource. The database can be accessed at


After an $18.1 million court victory against Waters in March, Applied Biosystems and MDS Sciex file suit against Thermo Electron for the alleged infringement of US patent number 4,963,736 — the same patent involving the company’s triple quadrupole mass spectrometers that Waters was found to have infringed upon in 2002.


Oxford GlycoSciences’ proteomics division has a new lease on life. Members of the OGS proteomics team, who were laid off after OGS was acquired by Celltech in December 2003, are launching a company of their own called Oxford Genome Sciences.


ProteoGenix and Bruker Daltonics sign a pact to develop a high-throughput protein biomarker discovery and mass spectrometry-based multi-analyte assay platform.


Celera Genomics and Genentech sign a multi-year agreement to develop new cancer drugs based on targets derived from Celera’s proteomics platform. Genentech will validate these further and develop drugs against them.


Medibic, a Japanese pharmaceutical consulting company, will work with partners including Strand Genomics of India and SurroMed to provide an advanced proteome analysis service.


Cell Signaling Technology signs an agreement with Aventis to conduct a pilot study in which CST will identify phosphorylation sites of protein tyrosine kinase targets.


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