The Seer Proteograph platform facilitates exploration of the proteome by compressing the dynamic range of protein abundance in a sample while automating digestion, cleanup and reconstitution of plasma and serum samples. This dynamic range compression is achieved through a nanoparticle assay whose physicochemical properties promote the equalisation of protein abundance in the generated protein corona [1]. Following MS analysis of the reconstituted peptides, data analysis can either be performed on Seer’s cloud-based software, Proteograph Analysis Suite (PAS), or can be exported for analysis on third party platforms, e.g. Spectronaut.
Here we compare ovarian cancer samples prepared by Seer Proteograph followed by LC-MS/MS to top14 depletion followed by LC-MS/MS, with subsequent data analysis on Spectronaut software. Samples prepared on the Seer Proteograph platform showed a greater identification of proteins than top14 depletion with over 5100 proteins identified across 9 orders of magnitude with substantially more proteins detected at concentrations below 1ng/mL than samples prepared by top14 depletion.
Furthermore, due to the automation provided by the Seer Proteograph platform, these results were generated from samples requiring only a total of two hours for instrument and sample loading across all stages of sample preparation, fluorometric assay, sample dry-down and subsequent reconstitution.
Further analysis of the data generated in this study will be used to identify potential biomarkers of ovarian cancer to be further investigated by targeted analysis. To date members of the University of South Australia’s Mass Spectrometry and Proteomics group have used this valuable technology in other studies for investigations of protein regulation of ectopic pregnancy, pre-type 2 diabetes treatments, and chronic pain conditions.
[1] Blume, J.E., Manning, W.C., Troiano, G. et al. Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. Nat Commun 11, 3662 (2020)