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International collaboration between McGill, the McGill University Health Centre and HUPO cooks up the right recipe

The winner of the chilli cook-off, usually has a key secret ingredient, which is hard to identify. Similarly, many diseases have crucial proteins, which change the dynamics of cells from benign to deadly. New findings from an international collaboration, involving McGill University, the Research Institute of the McGill University Health Centre (MUHC) and the Human Proteome Organisation (HUPO) just made identifying these changes one step easier. Their findings published in Nature Methods, show how to improve protein analysis to tease out relevant potential disease-causing molecules.

"Proteomics is the field that singles out the few significant proteins from the hundreds that may be present in a diagnostic sample," says co-author and recent new recruit of the Research Institute of the MUHC and of McGill Unversity, Dr. Tommy Nilsson. "It is important to associate the correct proteins with the correct condition. This process is incredibly complex. The aim of our study was to benchmark current analysis techniques worldwide and to identify potential bottlenecks."

Putting them to the test
Twenty-seven labs worldwide were sent a standard sample of proteins to analyse using their usual techniques. Only seven of the 27 participating labs were accurate in detecting all the proteins and in the more challenging part of the study, only one lab succeeded. However, further analysis of their raw data, showed that all the proteins had been initially detected by all the labs involved but they had been rejected in later analyses.

"Our centralized analysis showed us the problems encountered while conducting this type of testing," says Dr. John Bergeron, senior author from McGill University and HUPO. "We found that a major contributing factor to erroneous reporting is at the database level. We expect once databases and search engines improve, the accuracy of reporting will as well."

Importance of proteomics
The goal of proteomics is to characterise all the proteins that are encoded from human DNA, similar to how all genes were identified as a result of the Human Genome Project. It is expected that proteomics will accelerate the identification of cause of many human diseases and that improved diagnosis and therapy will emerge using proteomic techniques.

"The new technology described in our paper will potentially enable clinicians to determine the causes of disease," adds Dr. Bergeron.


Funding
This study was funded through grants the Canadian Institutes of Health Research, Genome Quebec and McGill University.

Dr Tommy Nilsson
Dr Tommy Nilsson is the Director of Proteomics and Systems Medicine at the Research Institute of the MUHC and Professor of Endocrinology and metabolism at McGill University.

Dr John Bergeron
Dr John Bergeron is the McGill chair of the Anatomy and Cell Biology Department, and a member of HUPO.

Partners

鈥淗UPO test sample study reveals common problems in mass spectrometry-based proteomics鈥�, was authored by Alexander Bell (McGill University), Eric Deutsch (Institute for Systems Biology, Seattle), Catherine Au (McGill University), Robert Kearney (McGill University), Ron Beavis (UBC, Vancouver), Salvatore Sechi (NIDDK (NIH)),听 Tommy Nilsson (Research Institute, MUHC), John Bergeron (McGill University) and the HUPO Test Sample Working Group.

You can find the press release published by the HUPO on the same topic at this address:

The Research Institute of the McGill University Health Centre (RI MUHC) is a world-renowned biomedical and health-care hospital research centre. Located in Montreal, Quebec, the institute is the research arm of the MUHC, the university health center affiliated with the Faculty of Medicine at McGill University. The institute supports over 600 researchers, nearly 1200 graduate and post-doctoral students and operates more than 300 laboratories devoted to a broad spectrum of fundamental and clinical research. The Research Institute operates at the forefront of knowledge, innovation and technology and is inextricably linked to the clinical programs of the MUHC, ensuring that patients benefit directly from the latest research-based knowledge.
The Research Institute of the MUHC is supported in part by the Fonds de la recherche en sant茅 du Qu茅bec.

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mark.shainblum [at] mcgill.ca