What does La Trobe's Proteomics Platform do? (Matt Perugini)

Proteomics at La Trobe
The Comprehensive Proteomics Platform provides postgraduate students and senior researchers with priority access to contemporary technologies for identifying and quantifying proteins, determining protein structure, and looking at how proteins interact.

Essentially, it is a “one stop, proteomics shop” that brings together specialised technologies and expertise in gas, solution and crystal phase protein analyses that complement the La Trobe Genomics and Biostatistics platforms.

In this week's blog, Matt Perugini (Platform Director) shares with us his work on the Proteomics platforms, and some of the experiences of researchers who've used it so far.

The RED Alert will feature posts on the experiences of each of the new research platforms over the coming weeks.

These have been created to bring together capabilities, expertise and technology from across the university under defined structures to enhance how La Trobe researchers do their work, so we hope you enjoy learning about them!
The Comprehensive Proteomics Platform, or CPP for short, is a specialist multi-capability facility housed in the $100 million La Trobe Institute for Molecular Science (LIMS) at Bundoora. It is comprised of multi-million dollar mass spectrometry instrumentation for identifying proteins in blood, urine or cell lysates; as well as technologies for determining the structure of biomolecules; and a suite of contemporary instruments for quantifying biomolecular interactions. The CPP also contains access to high performance computing facilities for advanced bioinformatics analyses and molecular dynamics simulations.

It supports basic and translational research initiatives from all molecular science disciplines, including agricultural science, biochemistry, genetics, health science, physiology and psychology.

Many of the projects the CPP supports focus on understanding the molecular mechanisms of health and disease, phenotypes from animal models, cell culture models, transgenic plants and even clinical samples. For example, it has projects aimed at identifying gene products (or proteins) that are more or less abundant in diseases, such as cancer, cachexia, stroke and Alzheimer’s disease.

These projects often yield a list of differentially abundant proteins that allow researchers to identify disease mechanisms and even new targets for the development of novel drugs or intervention strategies.

The platform also has projects where researchers are interested in determining the structure of proteins functioning in important cellular processes, such as apoptosis, cell-cell communication, metabolism, muscle contraction and neural networks. Some researchers have used the CPP simply to quantify the binding of a ligand (such as a drug) to a protein target of interest, or determine if a protein has the propensity to homo- or hetero-associate to form oligomers that are important for function.

Dr David Greening has been using the technologies offered by the platform to examine exosomes. Malignant mesothelioma cells can secrete tiny vesicles containing a variety of proteins that educate the tumour microenvironment and lead to disease progression. In a recent study published in Scientific Reports, researchers identified the proteins that are commonly secreted inside these vesicles, 'exosomes'. The study, “Secreted primary human malignant mesothelioma exosome signature reflects oncogenic cargo,” developed at LIMS, may provide a new source of much-needed diagnostic markers for mesothelioma, as well as new targets for future therapeutic approaches.

Dr Tatiana Soares da Costa, a Capability Manager of the Proteomics platform, says the CPP:
has been instrumental in getting pre-commercial data, which is the subject of provisional patents in preparation. Excitingly, we are in the process of negotiating with industry partners to work collaboratively on the development of this intellectual property facilitated by the platform.
For more information about the Proteomics Platform, please visit cpphub.latrobe.edu.au or contact the Director of the LTU-CPP, A/Prof Matthew Perugini: M.Perugini@latrobe.edu.au / +61 3 9479 6570).


Matt Perugini completed both his undergraduate degrees at the University of Melbourne, and then his PhD in 2002 on the ‘Characterisation of Human Apolipoprotein E3 and E4 Isoforms’ supervised by A/Prof Geoff Howlett in the Department of Biochemistry & Molecular Biology, University of Melbourne.

In 2005, Matt was awarded an Australian Postdoctoral Fellowship (APD) by the Australian Research Council (ARC), and in the same year, moved to the new Bio21 Molecular Science and Biotechnology Institute (Bio21 Institute) at the University of Melbourne. During his tenure at the Bio21 Institute, Matt was awarded the 2007 Applied Biosystems Edman Award by the Australian Society for Biochemistry and Molecular Biology, an inaugural ARC Future Fellowship in September 2009, and was promoted to Reader at the beginning of 2010.

In January 2012, Matt then moved his laboratory to the new $100 million La Trobe Institute for Molecular Science (LIMS). At La Trobe, he heads a 10-member lab. His current research initiatives focus on (i) the development of novel antibiotics & herbicides targeting an essential enzyme from bacteria & plants, and (ii) unravelling the molecular mechanism underpinning the link between apolipoprotein E and Alzheimer’s disease. He is also Director of the Comprehensive Proteomics Platform.