Protein Identification and Quantification

The Protein Identification and Quantification capability uses mass spectrometry to detect, identify and quantify protein biomarkers in complex biological samples, for example, to distinguish proteins on cancer cells from those on healthy cells. It also offers quality control services for recombinant proteins and peptides.

Mass spectrometry is used across a range of science disciplines to characterise proteins of interest from all organisms (e.g. viruses, bacteria, fungi, plants and animals), and as an analytical tool with many applications in pharmaceutical, biomedical, agricultural and environmental research, to name a few.


This capability is home to a range of instrumentation listed here

Thermo Scientific Orbitrap Eclipse™ Tribrid™ Mass Spectrometer (with ETD and FAIMS) - represents the latest ‘top of the line’ technology in liquid chromatography mass spectrometry. It features important advancements that offer unprecedented depth of analysis, especially for highly complex, low abundance, or difficult-to-analyse biological samples. It will enable identification and quantification of proteins in mixtures at much higher resolution than existing instrumentation in the facility, even enabling the characterisation of proteins within a single cell.

Thermo Scientific Q-Exactive HF with Ultimate 3000 RSLCnano - for protein, peptide and small molecule applications, it takes identification and quantitation to a new level with respect to speed, sensitivity and resolution.

Thermo Scientific LTQ Orbitrap Elite ETD Mass Spectrometer - provides excellent mass accuracy and resolution of proteins in high complexity samples (such as cell lysates, plasma and tissue homogenates) and the characterization of posttranslational modifications (such as phosphorylation and glycosylation).

Dionex UltiMate 3000 Intelligent LC System - enables the separation of complex mixtures of proteins and biomolecules (such as cell lysates, plasma and tissue homogenates).

Bruker Daltonics HCT ultra PTM Discovery System Ion-Trap Mass Spectrometer -  identification of proteins and mapping of post translational modifications of proteomic samples with low complexity (e.g. gel bands).


There is a broad range of applications that this capability can assist you with including:

  • Accurate mass determination of purified proteins (e.g. over-expressed recombinant products)
  • Proteome profiling
  • Label-free quantification
  • Label-dependent quantification (e.g. SILAC)
  • Phosphoproteomics

We provide advice on experimental design and methodology. Contact us to discuss your research applications.


There are a number of ways that you can access the services provided by this capability:

  1. Annual subscriptions for internal and external academic users:
    • Bronze (up to 50 samples per annum)
    • Silver (up to 110 samples per annum)
    • Gold (up to 240 samples per annum)
  2. Fee-for-service
  3. Research Contracts for bespoke projects

Contact Us

For more information and to discuss your requirements please email or contact a team member:

Dr Rohan Lowe, Bioinformatician in Proteomics

Dr Bushra Amin, Mass Spectrometry (Proteomics) Specialist

  • T: +61 3 9479 5006