Proteomics Mass Spectrometry

Proteomics server

Sandy Bay Campus, Chemistry Building, Room 334

The UTAS proteomics facility is equipped with a Thermo Scientific LTQ Orbitrap high resolution tandem Mass Spectrometer with APCI, electrospray and nanospray flex 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 UPLC system installed in July 2015.

We provide support for the complete proteomics workflow, including guidance on appropriate protein extraction protocols, 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 band identification by in-gel protein digestion.

MS/MS data is analyzed using MaxQuant software that includes the Andromeda search engine for protein identification.  Relative protein expression is based on normalized peptide intensities matched between LC-MS runs.  We provide training in the statistical analysis of proteomics datasets using the MaxQuant Perseus module (

Non-targeted analysis of small molecules using the LTQ-Orbitrap, including metabolomics, is also supported and we can provide advice on the design of your experiments and methods for sample preparation. Targeted MS/MS of selected compounds is used to acquire structural information and we can help with identification of unknowns by matching fragmentation data with spectral libraries (

To book samples for analysis by the LTQ Orbitrap please contact Dr Richard Wilson at the Central Science Laboratory so we can discuss your requirements.