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Related Concept Videos

Proteomics01:33

Proteomics

8.9K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
8.9K

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Updated: Nov 26, 2025

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier
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Defining the carrier proteome limit for single-cell proteomics.

Tommy K Cheung1, Chien-Yun Lee2, Florian P Bayer2

  • 1Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA.

Nature Methods
|December 8, 2020
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Summary

Single-cell proteomics by mass spectrometry (SCoPE-MS) requires careful optimization. Increasing carrier proteome amounts necessitates more sampled ions to maintain accurate single-cell proteomic quantification.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Single-cell analysis

Background:

  • Single-cell proteomics by mass spectrometry (SCoPE-MS) enables multiplexed proteome quantification.
  • Isobaric labeling and mass spectrometry have limitations impacting data quality and biological interpretation.

Purpose of the Study:

  • Evaluate the impact of carrier proteome levels on SCoPE-MS quantitative accuracy.
  • Identify parameters affecting data quality in single-cell proteomics.
  • Introduce a software tool for data evaluation and parameter recommendation.

Main Methods:

  • Controlled experiments with varying carrier proteome amounts.
  • Assessment of quantitative accuracy relative to mass analyzer dynamic range, multiplexing, and ion sampling.
  • Development and application of the SCPCompanion software tool.

Main Results:

  • Quantitative accuracy in SCoPE-MS is sensitive to carrier proteome levels.
  • Increased carrier proteome requires a proportional increase in sampled ions for accurate quantification.
  • SCPCompanion facilitates rapid data evaluation and parameter optimization.

Conclusions:

  • Optimizing carrier proteome and ion sampling is crucial for reliable SCoPE-MS data.
  • SCPCompanion aids researchers in improving single-cell proteomic data quality and interpretation.
  • Addressing technical limitations enhances the utility of SCoPE-MS for biological discovery.