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False Positives Adventures in Technology, SciFi and Culture from Toronto

Thursday, March 24, 2005

Mass spectrometry analysis with field-programmable gate arrays for for genomics and proteomics diagnoses

A article hightlighting the use of mass spectrometry analysis with field-programmable gate arrays (FPGAs) is in todays Globe and Mail and applying it to the problem of processing gene (genomics) and protein (proteomics) data.

The Blueprint Initiative at Mount Sinai Hospital working with the University of Toronto's Department of Electrical and Computer Engineering, replaced a $80,000 computer cluter and staff, with a prototype build for ~ $7,000.

The Blueprint Initiative team had a lofty goal: Find a method of comparing a sample from a patient to these three billion pairs in less than a second on a single computer, so that doctors can identify signs of abnormality or disease..

Dr. Hogue explains that ordinary blood tests usually use techniques that look for signs of a specific disease, such as enzymes that might indicate a liver problem. Unfortunately, that means that while a sample from a patient might hold an important clue to an underlying health issue, it could go undetected unless the doctor ordered a specific test designed to check for that type of ailment.

Mass spectrometers can do a much more detailed analysis looking for any abnormalities in a sample, but they aren't used for blood tests today because they produce too much data to process easily.
A paper on the project, to appear in the March 30 issue of Rapid Communications in Mass Spectrometry, but for those of us with out access the press release will have to do. (PMID: 15723443 :"Hardware-accelerated protein identification for mass spectrometry".)

They are also planning to spin off a company, Watershed Devices Ltd, that will concentrate on commercializing the FPGA technology for use in mass spectrometers.

See , , , and for more background.

How soon before we can do home diagnoses of this sort or at least in your Doctor's Office? What improvments are happening in mass spectrometry?

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update: a related story on Slashdot: Using proteomic spectral pattern recognition software, as a way to diagnose Multiple Sclerosis from a blood sample. Anyone have a copy of the January 2005 Journal of Molecular Neuroscience so I can read : A Distinctive Molecular Signature of Multiple Sclerosis Derived from MALDI-TOF/MS and Serum Proteomic Pattern Analysis: Detection of Three Biomarkers


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