Recent research by Ctortecka et al. pre-published in BioRxiv from Steve Carr’s laboratory at the Broad Institute has unveiled an automated workflow for single-cell proteomics (SCP) analysis, aiming to provide a high-throughput and sensitive process for deep characterization of single cells. This innovative approach marks a significant leap forward in the field of SCP, enabling a deeper understanding of cellular behavior at the single-cell level.

The study’s workflow demonstrated the use of a fully automated single cell preparation using a dedicated chip, the proteoCHIP EVO 96, designed for the cellenONE dispensing robot. Following digestion, the proteoCHIP EVO 96 was directly interfaced with the Evosep One before analysis using a timsTOF SCP and timsTOF Ultra. Key to the success of the study were IonOpticks’ Aurora Elite and Rapid 5×75 columns, which ensured precise peptide separation and enhanced data quality.

The advanced workflow allowed for the consistent detection of up to 4,000 proteins in single HEK-293T cells, without relying on carrier proteins or match-between runs. This comprehensive approach has opened up new avenues for exploring cellular biology at the single-cell level, providing researchers with a powerful toolset to uncover the complexities of cellular behavior.

IonOpticks column used in Single-Cell Proteomics Workflow contributed to the study’s success by advancing SCP, making significant strides in enhancing data acquisition and interpretation.

BioRxiv –  January 22, 2024

Authors

C. Ctortecka; N. M. Clark; B. Boyle; A. Seth; D. R. Mani; N. D. Udeshi & S A. Carr

Title

Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications