Western Australian Proteomics Facility

Label Free Quantitative Proteomics

Label free relative quantitation of protein abundances offers a simple and accurate means to compare the abundance of thousands of proteins between samples. This affordable methodology is suitable for both large and small sample numbers and serves to both identify the proteins present in a sample and to measure their relative abundance. Proteins present in each sample are subjected to tryptic digestion followed by individual injection onto our state-of-the-art Orbitap instruments. We offer two gradient lengths with more complex samples such as whole tissue lysates being ideally suited to longer analysis to allow greater depth of coverage of proteins present and a shorter gradient for less complex samples such as immunoprecipitations and subcellular fractions. This service includes sample digestion, cleanup and mass spec analysis followed by data processing to supply a spreadsheet of proteins present and their normalised relative abundances across samples. This service can be extended to include a detailed statistical analysis of the data generated along with data visualisation.

Our protein identification service offers a cut price entry to the world of proteomics and is suitable for routine protein identification and sample quality control tasks. Analysed on a short gradient on one of our Orbitrap instruments, this service can provide an extensive list of the protein(s) present in a sample and make estimates as to the relative proportion each protein constitutes of the total sample.

Our targeted proteomics service allows researchers to track the abundance of a smaller number of specific proteins across multiple samples. This analysis has the advantage of allowing the highest confidence measurements of relative abundance available in proteomics as well as the ability to show that the specified proteins are absent (below the limit of detection of the instrumentation). This technique is commonly described as a mass Western but is much faster, more quantitative, not prone to cross reactivity and can generally be tailored to specific isoforms of proteins. This service includes sample digestion, cleanup and mass spec analysis followed by data processing to supply a spreadsheet of proteins present and their normalised relative abundances across samples.

Protein flux analysis offers the opportunity to understand how much of which proteins are being translated and degraded in your experimental system. These measurements allow a much more detailed understanding of the dynamics of protein biology than simple abundance measurements. In this methodology a pulse of stable isotope labeled substrate is fed into the experimental system which is metabolically incorporated into the amino acid pool and subsequently into newly synthesised protein. By tracking the rate of accumulation of protein with incorporated stable isotopes relative to the preexisting unlabelled protein, both the rate of translation and degradation can be derived from a set of samples. This service includes help to design the labelling strategy, analyse the samples and process data to supply relative synthesis and degradation rates for abundant proteins in your samples.

Sample Submission

Meet the team

With several decades of dedicated proteomics research combined, our scientists can help you get the most out of your experiment. The WA proteomics team at UWA consists of Dr Elke Stroeher (left), our Operations Manager, Professor Harvey Millar (centre) our Platform Lead and Dr Owen Duncan (right), our Scientific Lead.