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Proteomics Mass Spectrometry

Sandy Bay Campus, Chemistry Building, Level 3, Room 334
Contact: Dr Richard Wilson (Senior Research Fellow and Officer in charge)

The University of Tasmania proteomics facility is equipped with a Q-Exactive HF Orbitrap mass spectrometer, installed in June 2018, coupled with Ultimate 3000 high performance liquid chromatography systems for analytical, capillary and nano flow applications. The primary use of these instruments is label-free quantitative proteomic analysis of complex protein samples using either "single-shot" or 2-D HPLC peptide separation. Depth of proteome coverage is sample-dependent; however, this advanced system is capable of identification and quantitation of several thousand protein groups using 90minute LC/MS gradients.

We support you throughout the complete proteomics experimental workflow. This includes guidance on protein extraction protocols and development of novel sample preparation approaches if required, advice on sample quality control and robust methods for peptide digest preparation. In addition to large-scale proteome analysis, we offer protein separation by gradient gel SDS-PAGE (NuPAGE), gel imaging and protein identification by in-gel digestion.

MS/MS data is processed using MaxQuant and the Andromeda search engine for protein identification, and relative protein expression is based on normalized peptide intensities matched between LC/MS runs. We provide training in the statistical and bioinformatics analysis of proteomics datasets using Perseus software (www.perseus-framework.org) and on-line resources to identify significant biochemical pathways (KEGG), interaction networks (STRING) and enrichment of functionally-related proteins (DAVID).

Non-targeted analysis of small molecules, including metabolomics, is also supported using a dedicated Ultimate 3000 UHPLC system for high-flow separations. We can provide advice on experimental design, suggest methods for metabolite extraction and help with the identification of unknowns using targeted MS/MS and matching fragmentation data with spectral libraries (https://metlin.scripps.edu/index.php).

Licenced software from ThermoFisher Scientific (Proteome Discoverer and Compound Discoverer) for advanced processing and visualization of proteomics and metabolomics data is also available to experienced users of the facility. Prior to booking sample analysis using the Q-Exactive Orbitrap, please contact Dr Richard Wilson so we can discuss your requirements.