05:15pm Sunday 24 September 2017

Mathematicians solving today’s problems of ‘systems biology’

Australian bioinformaticians have now created clever software that allows exactly this kind of processing, enabling analysis of the vast quantity of data produced by an exquisitely sensitive new generation of mass spectrometers.

The new software will even allow the re-processing of older data run in the lab, identifying at least 25% more proteins than have been identified in the past. In the not-so-exact science of systems biology, which sometimes struggles to ascertain whether or not a molecule is present or not in a sample, this is a giant leap forward.

PhD student Pengyi Yang and Dr Jean Yee-Hwa Yang, from Sydney’s Garvan Institute of Medical Research and the University of Sydney respectively, have developed an algorithm that will allow scientists to identify specific proteins out of the hundreds of thousands of protein fragments in a sample. Details of the project are published online today in the Journal of Proteome Research.

Prior to being processed by a mass spectrometer, a tissue sample is ‘digested’ by an enzyme, which breaks down the proteins into a peptide soup. Until now, it was only possible to ‘reassemble’ them (in a virtual sense) as members of protein groups. That is because over 2 million peptides are shared between two or more proteins within the 89,486 proteins recorded in the International Protein Index.

The new software enhances protein identification and will enable scientists to investigate complex diseases (such as Type 2 diabetes) as entire systems operating through time, by monitoring the thousands of protein changes that take place.

“It’s now necessary to combine the disciplines of mathematics, computer science and biology to cope with the data being produced in systems biology,” said Pengyi Yang.

“Previously, the majority of labs were focused on their favourite genes or proteins. Now you need to look at all proteins, all genes, in a cell. When you try to do that you need a computational methodology to analyse the information.”

“For this project we created a mathematical model and implemented it using a computational approach – applied to the biology.”

The Garvan Institute of Medical Research was founded in 1963. Initially a research department of St Vincent’s Hospital in Sydney, it is now one of Australia’s largest medical research institutions with over 500 scientists, students and support staff. Garvan’s main research programs are: Cancer, Diabetes & Obesity, Immunology and Inflammation and Neuroscience. Garvan’s mission is to make significant contributions to medical science that will change the directions of science and medicine and have major impacts on human health. The outcome of Garvan’s discoveries is the development of better methods of diagnosis, treatment, and ultimately, prevention of disease.


All media enquiries should be directed to:
Alison Heather
Science Communications Manager

M: + 61 434 071 326
P: +61 2 9295 8128
E: a.heather “a” garvan.org.au

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