Dataset Information

Integrated Single-Cell Proteomics Analysis on an Active Matrix Digital Microfluidic Chip

ABSTRACT: We introduce and implement a comprehensive single-cell proteomics sample pre-treatment solution based on an active matrix digital microfluidics chip(AM-DMF-SCP). This platform accommodates high-throughput single-cell isolation and seamless, non-destructive sample pre-treatment, characterized by its efficiency, speed, stability, and ease of use, thereby overcoming the longstanding bottleneck in single-cell protein sample preparation.

ORGANISM(S): Homo Sapiens

SUBMITTER: Hu Zhou

PROVIDER: PXD048434 | iProX | Mon Apr 15 00:00:00 BST 2024

REPOSITORIES: iProX

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Publications

AM-DMF-SCP: Integrated Single-Cell Proteomics Analysis on an Active Matrix Digital Microfluidic Chip.

Yang Zhicheng Z Jin Kai K Chen Yimin Y Liu Qian Q Chen Hongxu H Hu Siyi S Wang Yuqiu Y Pan Zilu Z Feng Fang F Shi Mude M Xie Hua H Ma Hanbin H Zhou Hu H

JACS Au 20240326 5

Single-cell proteomics offers unparalleled insights into cellular diversity and molecular mechanisms, enabling a deeper understanding of complex biological processes at the individual cell level. Here, we develop an integrated sample processing on an active-matrix digital microfluidic chip for single-cell proteomics (AM-DMF-SCP). Employing the AM-DMF-SCP approach and data-independent acquisition (DIA), we identify an average of 2258 protein groups in single HeLa cells within 15 min of the liquid ...[more]

PMID: 38818059

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Project description:The analysis of single cell proteomes has recently become a viable complement to transcript and genomics studies. Proteins are the main driver of cellular functionality and mRNA levels are often an unreliable proxy of such. Therefore, the global analysis of the proteome is essential to study cellular identities. Both multiplexed and label-free mass spectrometry-based approaches with single cell resolution have lately attributed surprising heterogeneity to believed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lacks behind. Here, we introduce the proteoCHIP, a universal option for single cell proteomics sample preparation at surprising sensitivity and throughput. The automated processing using a commercial system combining single cell isolation and picoliter dispensing, the cellenONE®, allows to reduce final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error prone manual sample handling and overcoming evaporation. With this specialized workflow we achieved around 1,000 protein groups per analytical run at remarkable reporter ion signal to noise while reducing or eliminating the carrier proteome. We identified close to 2,000 protein groups across 158 multiplexed single cells from two highly similar human cell types and clustered them based on their proteome. In-depth investigation of regulated proteins readily identified one of the main drivers for tumorigenicity in this cell type. Our workflow is compatible with all labeling reagents, can be easily adapted to custom workflows and is a viable option for label-free sample preparation. The specialized proteoCHIP design allows for the direct injection of label-free single cells via a standard autosampler resulting in the recovery of 30% more protein groups compared to samples transferred to PEG coated vials. We therefore are confident that our versatile, sensitive, and automated sample preparation workflow will be easily adoptable by non-specialized groups and will drive biological applications of single cell proteomics.

Dataset Information

Integrated Single-Cell Proteomics Analysis on an Active Matrix Digital Microfluidic Chip

Publications

AM-DMF-SCP: Integrated Single-Cell Proteomics Analysis on an Active Matrix Digital Microfluidic Chip.

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