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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 UTAS proteomics facility is equipped with a Thermo Scientific LTQ Orbitrap high resolution tandem Mass Spectrometer with APCI, electrospray and nanospray ion sources.  The primary application of this instrument is label-free quantitative proteomics of complex protein samples.  Orthogonal and "single-shot" peptide separations are achieved using an Ultimate 3000 nanoflow UHPLC system, which was upgraded in 2016 to enable peptide sample microfractionation by capillary LC.

We support you throughout the complete proteomics 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 analyzed using the Andromeda search engine for protein identification within the MaxQuant data processing pipeline.  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 ( and on-line software for pathway (KEGG), interaction network (STRING) and gene set enrichment (DAVID) analysis.

Non-targeted analysis of small molecules using the LTQ-Orbitrap, including metabolomics, is also supported and a second Ultimate 3000 UHPLC system dedicated to metabolomics and other applications that require high-flow separations was installed in 2017.  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 (

Prior to booking sample analysis using the LTQ Orbitrap, please contact Dr Richard Wilson at the Central Science Laboratory so we can discuss your requirements.

Proteomics server