ArticleMolecular systems biology2023
Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel.
Article in Molecular systems biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- N-Terminal protein sequencing by nicotinic acid derivatization and MS analysis.Analytical and bioanalytical chemistry · 2026Article
- Implementation of Nonisobaric TMT Analogs for Accurate Precursor-Level Quantification by plexDIA.Rapid communications in mass spectrometry : RCM · 2026Article
- High-throughput label-free single-cell proteomics enabled by multicolumn NanoLC.Nature communications · 2026Article
- Cell-type-specific surfaceome profiling of 100-500 isolated cells using a droplet-based Magnetic Affinity Purification System.Nature communications · 2026Article
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- Single-Cell Protein Assays in Context: From 2D to 3D and In Situ Analysis.Annual review of analytical chemistry (Palo Alto, Calif.) · 2026Review
- Duplexing metabolic deuterated water-labeled samples using dimethyl labeling to estimate protein turnover rates.Communications chemistry · 2025Article
- The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells.Communications biology · 2025Review
- High-Throughput Label-free Single-Cell Proteomics Enabled by Multicolumn NanoLC with a 5-min Cycle Time.Research square · 2025Article
- Interactome Profiling of a Lysine Deacetylase Trapping Probe Library Uncovers Crosstalk Between HDAC6 and NF-κB Signaling.Angewandte Chemie (International ed. in English) · 2025Article
- Single-cell proteomics using mass spectrometry.Cell genomics · 2025Review
- Proteomic landscape of Alzheimer's disease: emerging technologies, advances and insights (2021 - 2025).Molecular neurodegeneration · 2025Review
- Ontology-guided clustering enables proteomic analysis of rare pediatric disorders.EMBO molecular medicine · 2025Article
- An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF).Nature protocols · 2025Review
- A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy.Nature communications · 2025Article
- Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.Nature communications · 2025Article
- Increasing mass spectrometry throughput using time-encoded sample multiplexing.bioRxiv : the preprint server for biology · 2025Article
- Multiplexed phosphoproteomics of low cell numbers using SPARCE.Communications biology · 2025Article
- Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis.Journal of proteome research · 2025Article
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Authors and funding
17 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.
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