One-Shot Single-Cell Proteome and Metabolome Analysis Strategy for the Same Single Cell

Area of Science:

• Biochemistry
• Molecular Biology
• Analytical Chemistry

Background:

• Single-cell multiomic studies require robust methods for simultaneous proteome and metabolome characterization.
• Current techniques often face limitations in throughput and sensitivity for dual-omic analysis at the single-cell level.

Purpose of the Study:

• To introduce a novel strategy, one-shot single-cell proteome and metabolome analysis (scPMA), for integrated proteomic and metabolomic profiling of individual cells.
• To establish a comprehensive workflow for single-cell capture, sample preparation, and dual-omic data acquisition via LC-MS/MS.

Main Methods:

• Development of the scPMA strategy for one-shot analysis of single cells.
• Implementation of a workflow including single-cell capture, nanoliter-scale pretreatment, and single LC-MS/MS injection.
• Utilizing dual-zone MS/MS detection for simultaneous proteome and metabolome profiling.

Main Results:

• Successfully applied scPMA to analyze single tumor cells (A549, HeLa, HepG2), quantifying an average of 816, 578, and 293 protein groups, respectively.
• Quantified an average of 72, 91, and 148 metabolites for A549, HeLa, and HepG2 cells, respectively.
• Demonstrated the utility of scPMA in a study of doxorubicin-induced antitumor effects at the proteome and metabolome levels.

Conclusions:

• The scPMA strategy provides a powerful tool for high-throughput, dual-omic analysis at the single-cell level.
• This method significantly advances single-cell multiomic research by enabling integrated proteome and metabolome characterization.
• scPMA opens new avenues for understanding cellular heterogeneity and responses to stimuli in complex biological systems.