ArticleNature protocols2024
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.
Article in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Article
- Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics.bioRxiv : the preprint server for biology · 2026Article
- Differential protein network and biological functions atlas from multi-tissue proteomics in patients with depression.Molecular psychiatry · 2026Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- Navigating the Landscape of Cytometry-Based Single-Cell Proteomics: Quantification, Annotation, and Resources.International journal of molecular sciences · 2026Review
- Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day.bioRxiv : the preprint server for biology · 2026Article
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Alternate RNA decoding results in stable and abundant proteins in mammals.bioRxiv : the preprint server for biology · 2025Article
- Blood proteomics for quantitative biomarkers of cellular therapies.Biomarker research · 2025Review
- Single-cell proteomics using mass spectrometry.Cell genomics · 2025Review
- Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics.bioRxiv : the preprint server for biology · 2025Article
- Integration of multi-omics approaches in exploring intra-tumoral heterogeneity.Cancer cell international · 2025Review
- Increasing mass spectrometry throughput using time-encoded sample multiplexing.bioRxiv : the preprint server for biology · 2025Article
- Limiting the impact of protein leakage in single-cell proteomics.Nature communications · 2025Article
- Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective.Journal of proteome research · 2025Review
- Dynamics of Single-Cell Protein Covariation during Epithelial-Mesenchymal Transition.Journal of proteome research · 2025Article
- Precision cardiovascular medicine: shifting the innovation paradigm.Frontiers in science · 2025Article
- Spatial Proteomics towards cellular Resolution.Expert review of proteomics · 2024Article
- Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.Nature protocols · 2024Article
- Inferring post-transcriptional regulation within and across cell types in human testis.bioRxiv : the preprint server for biology · 2024Article
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Abstract
Single-cell proteomics by mass spectrometry (MS) allows the quantification of proteins with high specificity and sensitivity. To increase its throughput, we developed nano-proteomic sample preparation (nPOP), a method for parallel preparation of thousands of single cells in nanoliter-volume droplets deposited on glass slides. Here, we describe its protocol with emphasis on its flexibility to prepare samples for different multiplexed MS methods. An implementation using the plexDIA MS multiplexing method, which uses non-isobaric mass tags to barcode peptides from different samples for data-independent acquisition, demonstrates accurate quantification of ~3,000-3,700 proteins per human cell. A separate implementation with isobaric mass tags and prioritized data acquisition demonstrates analysis of 1,827 single cells at a rate of >1,000 single cells per day at a depth of 800-1,200 proteins per human cell. The protocol is implemented by using a cell-dispensing and liquid-handling robot-the CellenONE instrument-and uses readily available consumables, which should facilitate broad adoption. nPOP can be applied to all samples that can be processed to a single-cell suspension. It takes 1 or 2 d to prepare >3,000 single cells. We provide metrics and software (the QuantQC R package) for quality control and data exploration. QuantQC supports the robust scaling of nPOP to higher plex reagents for achieving reliable and scalable single-cell proteomics.
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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.