Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm
Open accessAbstract
Mass-tag cell barcoding (MCB) labels individual cell samples with unique combinatorial barcodes, after which they are pooled for processing and measurement as a single multiplexed sample. The MCB method eliminates variability between samples in antibody staining and instrument sensitivity, reduces antibody consumption and shortens instrument measurement time. Here we present an optimized MCB protocol. The use of palladium-based labeling reagents expands the number of measurement channels available for mass cytometry and reduces interference with lanthanide-based antibody measurement. An error-detecting combinatorial barcoding scheme allows cell doublets to be identified and removed from the analysis. A debarcoding algorithm that is single cell-based rather than population-based improves the accuracy and efficiency of sample deconvolution. This debarcoding algorithm has been packaged into software that allows rapid and unbiased sample deconvolution. The MCB procedure takes 3-4 h, not including sample acquisition time of ∼1 h per million cells.
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CyTOF data were first debarcoded with Single Cell Debarcoder using post-assignment stringency filtering and outlier trimming.
“CyTOF data was first debarcoded using Single Cell Debarcoder (Zunder et al., 2015) using post-assignment debarcode stringency filter and outlier trimming.”
From Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens (2018) · cites this paper as Zunder et al., 2015
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References 14 · Cited by 596
- Authors
- Zunder, E. R., Finck, R., Behbehani, G. K., Amir, E.-A. D., Krishnaswamy, S., Gonzalez, V. D., Lorang, C. G., Bjornson, Z., Spitzer, M. H., Bodenmiller, B., Fantl, W. J., Pe'er, D., & Nolan, G. P.
- Affiliations
- Stanford Medicine (US)
- Columbia University (US)
- Corresponding author
- Nolan, Garry P
- ORCID
- Venue
- Nature Protocols
- Published
- 2015-01-22
- Volume
- 10
- Issue
- 2
- Pages
- 316-333
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- PMC
- PMC4347881
- OpenAlex
- W1970170720
- Cited by
- 596
- References
- 14
- Citations by year
- 2026: 39 · 2025: 58 · 2024: 68 · 2023: 65 · 2022: 61 · 2021: 66 · 2020: 70 · 2019: 56 · 2018: 43 · 2017: 42 · 2016: 17 · 2015: 11
- FWCI
- 16.36
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (N01-HV 00242, HHSN268201000034C)
- National Cancer Institute (R33CA183654, U54CA149145, R01CA184968)
- National Institute of General Medical Sciences (T32GM007276)
- National Institute of Allergy and Infectious Diseases (U19AI100627, 5R01AI07372405, R01AI073724, U19AI057229, T32AI007328)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- mass cytometry
- MeSH terms
- Algorithms, Flow Cytometry, Palladium, Software, Staining and Labeling, Single-Cell Analysis
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