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Related Experiment Video

Updated: Oct 4, 2025

Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog Xenopus laevis Embryos
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High-Throughput, Comprehensive Single-Cell Proteomic Analysis of Xenopus laevis Embryos at the 50-Cell Stage Using a

Zhenbin Zhang1, Kyle M Dubiak1, Evgenia Shishkova2

  • 1Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.

Analytical Chemistry
|February 10, 2022
PubMed
Summary

We developed MICROFASP, a high-throughput system for analyzing single cell proteomes. This method achieved the deepest proteome coverage to date for single Xenopus laevis blastomeres, identifying thousands of proteins per cell.

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Area of Science:

  • Developmental Biology
  • Proteomics
  • Single-cell analysis

Background:

  • Single-cell proteomic analysis is crucial for understanding cellular heterogeneity.
  • Previous methods lacked the throughput and depth for analyzing numerous single blastomeres.

Purpose of the Study:

  • To design and validate a high-throughput system for comprehensive proteomic analysis of single blastomeres.
  • To establish a new standard for proteome coverage in early embryonic cells.

Main Methods:

  • Development of the miniaturized filter aided sample preparation (MICROFASP) system.
  • Parallel processing of 146 single Xenopus laevis blastomeres.
  • Analysis using capillary LC-ESI-MS/MS coupled to an Orbitrap Fusion Lumos mass spectrometer.

Main Results:

  • Identification of 4189 protein groups and 40,998 unique peptides across 109 blastomeres.
  • Average identification of 3468 protein groups and 14,525 unique peptides per blastomere.
  • Comparison of Newport and CMFM dissociation buffers showed similar proteomic yields.

Conclusions:

  • The MICROFASP system enables unprecedented throughput and depth in single blastomere proteomic analysis.
  • This technology advances the study of early embryonic development at the proteome level.
  • Both tested dissociation buffers are suitable for proteomic analysis using MICROFASP.