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

Recent research by Ctortecka et. al 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 characterisation 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 Rapid75 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

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