ArticleAnalytical chemistry2023
Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics.
Article in Analytical chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 24 citations in OpenAlex.
- Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day.bioRxiv : the preprint server for biology · 2026Article
- Plasma-Derived Extracellular Vesicle Proteomics.Journal of proteome research · 2025Review
- Cell Population-resolved Multiomics Atlas of the Developing Lung.American journal of respiratory cell and molecular biology · 2025Article
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
- Data acquisition approaches for single cell proteomics.Proteomics · 2025Review
- Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows.bioRxiv : the preprint server for biology · 2024Article
- Solid-Phase Microextraction-Aided Capillary Zone Electrophoresis-Mass Spectrometry: Toward Bottom-Up Proteomics of Single Human Cells.Journal of the American Society for Mass Spectrometry · 2024Article
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics.Communications chemistry · 2024Article
- Proteomics Applications inPathogens (Basel, Switzerland) · 2023Review
- Challenges and Opportunities for Single-cell Computational Proteomics.Molecular & cellular proteomics : MCP · 2023Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Herein, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.