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Normalizing and denoising protein expression data from droplet-based single cell profiling.
Matthew P Mulè1,2, Andrew J Martins1, John S Tsang3,4
1Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
Nature Communications
|April 20, 2022
Summary
A new method called denoised and scaled by background (dsb) effectively removes technical noise in single-cell protein expression data. This approach enhances the identification of true biological variations, improving cellular heterogeneity analysis.
Area of Science:
- Single-cell biology
- Immunology
- Computational biology
Background:
- Multimodal single-cell profiling measures protein expression using oligo-conjugated antibodies.
- Technical noise in protein counts can obscure true biological variations in cellular heterogeneity.
Purpose of the Study:
- To identify major sources of technical noise in droplet-based protein expression data.
- To develop a computational method for normalizing and denoising this data.
- To improve the accuracy of downstream single-cell analyses.
Main Methods:
- Developed the "denoised and scaled by background" (dsb) method.
- Estimated and corrected protein-specific noise using unbound antibodies in empty droplets.
- Corrected cell-to-cell technical noise using correlations between isotype controls and background protein levels.
Main Results:
- Identified unbound antibodies and cell-specific background correlations as key noise sources.
- dsb accurately corrects technical noise in droplet-based protein expression data.
- Validated dsb across eight independent datasets and multiple technologies (CITE-seq, ASAP-seq, TEA-seq).
Conclusions:
- dsb significantly improves the unmasking of biologically meaningful cell populations compared to existing methods.
- The dsb method enhances the reliability of multimodal single-cell profiling.
- dsb is an open-source R package compatible with major single-cell analysis platforms.
