Introduction
Plasma proteomics using mass spectrometry remains one of the leading methods to establish disease biomarkers. However, for any large-scale proteomics studies, a robust LCMS setup is required, without compromising on peptide and protein coverage and analysis precision. On the other hand, proteins in plasma are expressed at a wide dynamic range and most analytical methods are not yet capable of covering the full proteome. Here we present a high-throughput, plasma proteomics workflow with Orbitrap Exploris 480 mass spectrometer coupled to a High-Field Asymmetric Waveform with Ion Mobility Spectrometry (FAIMS) as a robust analytical setup for in-depth analysis of neat plasma and plasma samples processed with Seer’s ProteographTM Product Suite utilizing a multi-nanoparticle-based approach for an unbiased and deep plasma proteomics analysis at scale.
Methods
The neat and processed plasma with Proteograph Assay were prepared on Seer’s Proteograph Product Suite. Samples were analyzed using a few different high-throughput workflows enabling the user to choose a workflow optimized for their projects. EasySpray PepMap Neo and µPAC-Neo columns were utilized with a Vanquish Neo UHPLC system coupled to an Orbitrap Exploris 480 mass spectrometer. Data analysis was done using Proteome Discoverer software 3.1 and Seer’s Proteograph Analysis Suite.
Results
Neat plasma suffers from dynamic range issues resulting in lower coverage. The Fully automated plasma sample processing with the Proteograph workflow offers an enhanced depth of coverage while balancing the need for high throughput analysis. Preliminary results show over 600 protein groups in neat plasma and more than 3000 protein groups in plasma samples enriched with a Proteograph XT Assay kit.
Regardless of the sample preparation method chosen for plasma proteomics, the Orbitrap Exploris 480 mass spectrometer delivers a high proteome coverage and throughput for plasma proteomics.