Label-free LC-MS based proteomics quantification correlates to gene expression and pathway analysis results

I’m following up my promise to try and get hold of some posters from ASMS showing how users are applying Progenesis LC-MS to their research. I’m pleased to say the first, of what I hope will be a final list of about five, is available to download and view via our website.

This poster was presented by Ben Collins from the School of Medicine and Medical Science, University College Dublin in Ireland. You may have seen Ben in the news recently when Agilent Technologies and UCD appointed him as the Agilent Technologies Newman Fellow in Quantitative Proteomics at the UCD Conway Institute of Biomolecular and Biomedical Research?

Anyway, the poster was a continuation of work  presented at the 2009 BSPR meeting in Cambridge, UK. The group have used Progenesis LC-MS to perform label-free LC-MS proteomics as part of a combined ’omics approach, alongside conventional toxicology methods, as a strategy for evaluating preclinical safety. What the poster nicely highlighted was,

  • The method demonstrated excellent analytical reproducibility with a mean CV of 10.9% from quantifying over 19,000 features
  • There was good proteome coverage with 809 proteins identified at a 3.1% false identification rate
  • It only used modest instrument time

In the latest poster presented at ASMS Ben had added some new results to these headlines showing they had determined 90 proteins to be differentially expressed with fold change >1.5 and ANOVA p-value <0.05, which are all things you can easily measure using Progenesis LC-MS.

Another result added to the latest version of the poster was the finding that protein fold changes reported from label-free LC-MS analysis mapped, although weakly, to corresponding mRNA fold changes and had strong agreement at the pathway level.

This is a great example of putting label-free LC-MS analysis in context and validating it with other complimentary results; it’s something I’ve never seen one of our users do before. That doesn’t mean it’s not happening of course! If you’re doing anything similar we’d love to hear about it or anything else you’re doing with Progenesis LC-MS.

In the meantime if you haven’t got Progenesis LC-MS and need it for differential expression analysis then try a demonstration on your data today.

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