Fixing Proteomics Campaign

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The HUPO Reproducibility Study introduced by Jan Van Oostrum, one of the Fixing Proteomics founders

Large scale, in depth, proteomic studies of cells, tissues or body fluids, involving multiple laboratories, employing a variety of proteomics technologies have been executed in the past. Although the aim of these studies was not focused on achieving maximal reproducibility between the participating labs but rather to explore the deliverables of the individual technologies, it is apparent that different labs using different technologies on the same samples obtain rather different results. For any comparative study, i.e analysis of two or more different but related samples, such as healthy versus disease or different drug treatments, there is even more of a challenge to be investigated in such an experimental design.

The availability of internal or external standards in conjunction with comparative proteomics experiments are thought to be a major step forwards in obtaining data sets of such a quality that bioinformatics approaches can be applied productively. In order to take the next step forward it was deemed important by the HUPO-IAB (Industrial advisory board of the human proteome organization) to focus particular attention on analysis of the reproducibility of the various proteomics technologies.

A first study was initiated and was supported by 5 labs in a world-wide setting. The goal of this study was to demonstrate that cross lab experiments can be done, which would provide a very necessary leap forward in the ability to collect reliable data in proteomics. The study was of two different but related samples of H. Flu, one of which was treated with Actinonin. The study was a cross-lab 2-dimensional polyacrylamide gel electrophoresis analysis of the samples as it was believed by the organizers that that with the current technologies available and strict adherence to protocols, this would be possible, although a major challenge.

Ready to use samples were provided to the labs. Each participating lab ran two different but related samples on 2-D gels according to the supplied protocol, and then performed an analysis between the two samples using software provided to identify what are, in their opinion, the top 200 significantly changing spots. This of course includes newly appearing spots. The full analysis was uploaded to Nonlinear Dynamics (a HUPO-IAB member) for the comparison between labs and further analysis.

A publication is due out in 2008, but we are delighted to be able to report here that 2-D gel experiments can indeed be reproduced in different labs. This a major step forward for proteomics as a discipline.

Want to find out more?
Read more about the Reproducibility Study in this recent Proteomonitor article - Trying to Settle Ongoing Dispute, HUPO's IAB Finds 2D Gel Experiments are Reproducible

Have you heard the story about Fahrenheit and the cow?