ProteoRed

The specific objetives of the technological develoment are:

Allow a continuous improvement in the throughput and the performance of Proteomics Facilities of the Network.

Provide access for researchers to state-of-the-art Proteomics techniques.

Support new technical and scientific personnel contracted by ProteoRed nodes in the performance of proteomics technologies.

Coordinate and define the strategy for the acquisition of new equipment in order to optimize its utilization by research projects in Proteomics.

The specific objetives of the standardization of protocols are:

Collect and evaluate proteomics protocols used by ProtoeRed members to improve the quality of the data generated in their laboratories.

Define the minimum quality criteria that should be fulfilled by ProteoRed members.

Study the proteomics protocols and standards internationally accepted in order to distribute them to ProteoRed members and users.

Promote activities among ProteoRed members in order to guarantee the quality of the services.

Encourage the exchange of technical information among ProteoRed members.

Finally, one of the main goals will be the compilation and discussion of the new experimental approaches continuously being developed and, eventually, to encourage their use by ProteoRed for the improvement of service quality by all the members.

Current activities:

An increasingly common request for proteomics laboratories today is determining quantitative differences among samples in clinical matrices such as urine, plasma or CSF. The experiment often begins with a small set of pilot samples (case versus control) where putatively differentially expressed protein species are identified. Subsequently, further sample sets are provided for a more detailed examination of these proteins to determine if the initial observation of quantitative differences holds within a larger patient cohort. The major challenges associated with this type of analysis are detection and accurate quantification in these very complex matrices.
ProteoRed has encouraged to their members to participate in the contest organized by The Proteomics Research Group (PRG) of the Association of Biomolecular Resource Facilities (ABRF). This study will explore the use of different approaches for determining quantitative differences for several target proteins in six samples of human plasma.

The samples can be successfully characterized by scientists with different levels of experience using a wide variety of approaches and platforms. The primary goals of this study are to document the breadth of approaches used by the proteomics community and to highlight the type of information obtained. Participants will be asked to provide the following:

Relative quantification of three specified proteins in human plasma.
Information about methods used to analyze the samples.
Information about the experimental design used for quantification.

Sequence information on the three target proteins will be provided. At least two of the target proteins will be currently relevant human biomarkers. When submitting their results, participants will be asked to report the relative quantification for these target proteins in the plasma samples (two controls and four cases). The PRG will compile descriptions of the experimental methods that were used and highlight methods that successfully determined known differences in the sample sets. This information will be presented at the 2009 ABRF Meeting (February 7 – 10, 2009, Memphis, TN) and will be published on the ABRF website so that other researchers can compare results and adopt best practices.

The PRG expects to distribute the samples in October 2008 and requests that the resulting data be returned by December 1, 2008.