As leaders and members of the Human Proteome Organization’s Proteomics Standards Initiatives convened for their annual fall workshop, initial feedback from reviewers of PSI’s plan to develop and issue reporting standards revealed deep skepticism and anxiety.
During a session held at the three-day workshop, comments by scientists who reviewed PSI’s minimum information about a proteomics experiment’s “parent paper” — a broad overview of the goals of PSI’s standardization efforts — suggested that the real work may be in convincing others in the proteomic field that standards even need to be created.
According to PSI leader Chris Taylor, the underlying principle of the parent paper — and indeed the whole of PSI’s work — is to facilitate the understanding of how proteomic experiments are conducted and to create standards of reporting so that researchers can recreate each others’ work.
It was submitted to the journal Nature Biotechnology, which is planning an issue focusing specifically on standards in the scientific community.
Some of the comments made by reviewers about the parent paper commended PSI for its efforts, saying that as the amount of proteomic data approaches the amount of gene expression data, the ability to query that information efficiently will become increasingly necessary. Others praised PSI for its balance in its approach.
But many reviewers also questioned the wisdom of PSI’s work. Some wanted to know why HUPO is trying to create standards since they see no great clamoring for them. Others wanted to know what MIAPE would enable them to do that they currently can’t do already. Still others complained that writing rules is easier than complying with them, and that MIAPE standards will ultimately create a burden to labs that don’t have the informatics capability to implement the standards.
Members of PSI responded to some of the criticism by saying that the group had either already addressed or was in the process of addressing the concerns.
— Tony Fong
PATENT WATCH
US Patent 7,112,446. Method for analyzing protein or peptide. Inventors: Hirotaka Minagawa, Ichiro Ishida, Akira Tsugita, and Takuji Nabetani. Assignees: Tokyo Rikakikai and NEC Corporation. Issued: September 26, 2006.
This invention relates to a method for analyzing a protein or peptide and, more particularly, to a method for structural analysis of a post-translational modification of a protein or peptide without the use of an enzyme.
US Patent 7,117,098. Machine-readable storage medium for analyzing distribution of macromolecules between the cell membrane and the cell cytoplasm. Inventors: R. Terry Dunlay, Lansing Taylor, Albert Gough, and Kenneth Giuliano. Assignee: Cellomics. Issued: October 3, 2006.
According to the patent’s abstract, this invention provides systems, methods, and screens for an optical system analysis of cells to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect biological functions.
SHORT READS
At a session during the UBS Life Sciences Conference, Bruker BioSciences CEO Frank Laukien told attendees that the rate of growth at which drug makers invest in life science tools and technologies may never reach the levels seen during the 2000 or 2001 “boom.”
Protagen, a German protein biochip company, expanded its operations into the United States with a new office to handle sales and distribution in Chester, NJ. The new office, Protagen’s first overseas facility, will initially focus its distribution efforts on the East Coast and will be headed up by Howard Jacobsen.
Ludesi, a bioinformatics company based in Lund, Sweden, raised $3.4 million from venture capital firm InnovationsKapital to ramp up sales of its current offering, a 2D gel-analysis service, and support development of a second product line.
The Brain Research Centre in Vancouver opened a new proteomic core facility. The 50,000-square-foot Peptide Proteomic Core Facility, which opened Sept. 1, offers custom peptide synthesis along with peptide array services including epitope mapping, peptide library screening, and peptide substitution screening assays.
The Flanders government has extended a grant to Peakadilly to speed up development of its biomarker discovery platform. The company plans to use the funds to expand relationships with pharma and diagnostic companies and to accelerate development of its own diagnostic products.
DATAPOINT
$104 million
Amount of the Clinical Proteomic Technologies Initiative for Cancer unveiled this fall by the National Cancer Institute. Of that, $35.5 million was awarded in grants to establish a Clinical Proteomic Technology Assessment for Cancer network.