Proteomics has revolutionized the field of biomarker discovery, offering unprecedented insights into cellular processes and disease mechanisms. However, as mass spectrometry (MS) technology advances, the bottleneck has shifted to the pre-analytical sample preparation phase. Evosep’s innovative solution addresses this challenge head-on with a fully automated, scalable workflow leveraging the Evotip platform. In collaboration with the Olsen group at University of Copenhagen, this has been evaluated and the findings detailed in the recent publication in Molecular & Cellular Proteomics.

Traditional sample preparation in proteomics involves multiple manual steps that are time-consuming, prone to variability, and costly. The new workflow developed by Evosep integrates sample digestion, cleanup, and loading onto Evotips in a fully automated manner using the Opentrons OT-2 robot. This approach not only streamlines the process but also significantly enhances throughput and reproducibility.

The key to this efficiency lies in the Evotip, that facilitates the direct loading of peptide samples onto the MS. By incorporating this with the OT-2 robot, up to 192 samples can be processed in just 6 hours, a dramatic improvement over traditional methods. This advancement is particularly beneficial for large-scale clinical studies, where hundreds of samples need to be analyzed quickly and consistently.

The automated workflow has been rigorously tested with HeLa cell samples, yielding impressive results. With a protein input of just 1 microgram, the workflow identified approximately 8,000 protein groups and 130,000 peptide precursors using the 100 SPD method in combination with the Orbitral Astral mass spectrometer. This level of sensitivity and reproducibility is crucial for detecting subtle changes in protein expression, which can be indicative of disease states or therapeutic responses.

Furthermore, the workflow demonstrated remarkable stability, with minimal sample degradation even after several days of storage. This flexibility allows for the seamless integration of sample preparation with subsequent MS analysis, reducing downtime and maximizing the use of instrumentation.

In addition to proteome analysis, the workflow can be extended to phosphoproteomics, a technique essential for studying cellular signaling pathways. By integrating an automated phosphopeptide enrichment step using magnetic Ti-IMAC beads, the system can process both proteomes and phosphoproteomes in parallel. This dual capability opens new avenues for investigating post-translational modifications, providing deeper insights into cellular dynamics and disease mechanisms.