A deeper look at carrier proteome effects for single-cell proteomics
Open accessPublished version of a preprint
Abstract
Multiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. Guidelines for optimized mass spectrometry acquisition parameters and best practices for fold-change or protein copy number-based comparisons are provided.
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References 18 · Cited by 55
- Authors
- Ye, Z., Batth, T. S., Rüther, P., & Olsen, J. V.
- Affiliations
- University of Copenhagen (DK)
- Corresponding author
- Olsen, Jesper V.
- Venue
- Communications Biology
- Published
- 2022-02-22
- Volume
- 5
- Issue
- 1
- Pages
- 150-150
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC8863851
- OpenAlex
- W4220774682
- Cited by
- 55
- References
- 18
- Citations by year
- 2026: 4 · 2025: 9 · 2024: 19 · 2023: 13 · 2022: 10
- FWCI
- 4.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Novo Nordisk Fonden (NNF14CC0001, NNF17SA0027704)
- EC | Horizon 2020 Framework Programme (EPIC-XS-823839)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- single-cell proteomics, tandem mass tags, protein identification, signal intensity, fold change, protein copy number, acquisition parameter optimization
- MeSH terms
- Proteome, Proteomics, Tandem Mass Spectrometry
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