EquiCP: Targeted Single-Cell Proteomics by Mass Spectrometry with Isobaric Labeled Multiplexing

Area of Science:

• Biochemistry
• Proteomics
• Mass Spectrometry

Background:

• Nontargeted single-cell proteomics often uses carrier proteomes for mass spectrometry with isobaric labeling.
• Carrier proteomes can complicate the identification and quantification of target proteins in complex biological samples.

Purpose of the Study:

• To develop a targeted proteomics protocol for single-cell analysis.
• To improve protein identification and quantification in single human cells by modifying existing mass spectrometry techniques.

Main Methods:

• Developed a targeted approach for single-cell proteomics.
• Replaced the traditional carrier proteome with synthetic peptides from selected proteins.
• Utilized mass spectrometry with sample multiplexing and isobaric labeling.

Main Results:

• The targeted approach successfully replaced the carrier proteome.
• Achieved improved identification of selected proteins in single human cells.
• Demonstrated enhanced quantification accuracy for target proteins compared to carrier proteome methods.

Conclusions:

• The synthetic peptide-based targeted approach is a viable alternative to carrier proteomes in single-cell proteomics.
• This method offers improved performance for identifying and quantifying specific proteins in single human cells.
• The protocol advances the capabilities of mass spectrometry-based single-cell proteomic analysis.