Nanoparticles: the key to unlocking low-level abundance proteins
Nanoparticles are known for their intrinsic ability to bind proteins. Seer’s Proteograph Product Suite platform for plasma proteomics relies on a library of proprietary engineered nanoparticles to enrich low-abundance proteins. The elegance of this technique relies on the highly reproducible, yet non-specific protein-nanoparticle interactions. Unlike aptamer and antibody-based plasma proteomics methods, the Proteograph’s plasma fractionation system is species agnostic and can be used for biomarker discovery experiments in non-human samples.
How does it work?
Proteins in the plasma sample are attracted to the nanoparticles to form what is called a “protein corona”. The composition of the protein corona is affected by different parameters, such as the size, shape, porosity, charge, and the surface chemistry of the nanoparticles and the proteins themselves. By using a magnetic core and various surface chemistries, the Proteograph assembles and isolates different protein coronas that span the entire range of protein concentration in plasma. These proteins are then digested into peptides and are ready for analysis using LC-MS/MS. You can learn more about Seer’s technology on their website.
Fig. 1 Illustration of a protein corona
Plasma protein fractionation and DIA for in-depth plasma biomarker discovery
Data independent acquisition (DIA) offers unparalleled power in label-free quantitative proteomics. However, the depth of analysis one can get from a DIA workflow is highly dependent on two factors: the dynamic range of the protein concentrations in the sample and the quality of the ion library. The fractionation power of the Proteograph instrument enables our team to drastically compress the dynamic range of protein concentrations to reproducibly quantify upwards of 1500 proteins in plasma. For even more flexibility, we offer gradient options which translate into different yields in total number of quantified proteins.
Data analysis and report
Results from our plasma biomarker discovery using label-free quantitative proteomics experiments are delivered to customers in a user-friendly data report or through Proteograph Analysis Suite. We provide both basic statistics such as average, standard deviation, and %CV and fold change for each protein to allow direct group comparisons. Additional advanced statistics such as PCAs, volcano plots, heatmap clustering, gene ontology and more, are also available.