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Updated: Oct 2, 2025
06:13
Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier
Published on: December 9, 2022
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A deeper look at carrier proteome effects for single-cell proteomics.
Zilu Ye1, Tanveer S Batth1, Patrick Rüther1
1Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Communications Biology
|February 23, 2022
Summary
Carrier proteomes in single-cell proteomics boost protein identification but can limit quantitative precision at high levels. Optimizing mass spectrometry acquisition and comparison methods is crucial for accurate analysis.
Area of Science:
- Proteomics
- Mass Spectrometry
- Cell Biology
Background:
- Single-cell proteomics by mass spectrometry (SCoPE-MS) utilizes multiplexing with carrier proteomes to enhance sensitivity.
- Carrier proteomes are essential for improving protein identification in low-input samples.
Purpose of the Study:
- To investigate the impact of carrier proteomes on protein identification and quantification in single-cell proteomics.
- To evaluate the effects of mixed-species tandem mass tag (TMTpro) labeling on carrier proteome performance.
Main Methods:
- Utilized mixed-species TMTpro-labeled samples for single-cell proteomics experiments.
- Analyzed the influence of varying carrier proteome levels on protein identification and quantitative accuracy.
- Optimized mass spectrometry acquisition parameters.
Main Results:
- Carrier proteomes significantly increase the number of identified proteins.
- High carrier proteome levels can limit quantitative precision and signal intensity.
- The choice of carrier proteome influences which specific proteins are identified.
Conclusions:
- Carrier proteomes are a double-edged sword in SCoPE-MS, enhancing identification but potentially compromising quantification.
- Guidelines for optimizing MS acquisition and data analysis strategies are provided to mitigate these effects.
- Careful consideration of carrier proteome composition and abundance is necessary for robust single-cell proteomic studies.
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