ArticleNature communications2025
Limiting the impact of protein leakage in single-cell proteomics.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Democratized single-cell proteomics resolves cell state heterogeneity in skin tumors.Life science alliance · 2026Article
- Off‑the‑shelf, engineered non-living stem cell strategy for advancing cellular therapies.Nature biomedical engineering · 2026Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- The good, the bad, and the ugly: opportunities, challenges, and pitfalls in spatial proteomics modeling.Briefings in bioinformatics · 2026Review
- Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day.bioRxiv : the preprint server for biology · 2026Article
- Mitochondrial Unfolded Protein Responsive Imaging and Surgical Navigation in Ovarian Cancer.Chemical & biomedical imaging · 2025Article
- High-Throughput Label-free Single-Cell Proteomics Enabled by Multicolumn NanoLC with a 5-min Cycle Time.Research square · 2025Article
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Increasing mass spectrometry throughput using time-encoded sample multiplexing.bioRxiv : the preprint server for biology · 2025Article
- Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis.Journal of proteome research · 2025Article
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
- Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.Nature protocols · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
Limiting artifacts during sample preparation can significantly increase data quality in single-cell proteomics experiments. Towards this goal, we characterize the impact of protein leakage by analyzing thousands of primary single cells from mouse trachea. The cells were prepared either fresh immediately after dissociation or first cryopreserved and prepared at a later date. We directly identify permeabilized cells by imaging a cell permeable dye and use the data to define a signature for protein leakage. This signature is similar across diverse cell types and reflects increased leakage propensities for cytosolic and nuclear proteins compared to membrane and mitochondrial proteins. A classifier based on the signature allowed for the accurate identification of permeabilized cells across cell types and species. The classifier is integrated into QuantQC ( scp.slavovlab.net/QuantQC ) to support its application to diverse samples and workflows.
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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.