ArticleAngewandte Chemie (International ed. in English)2023
Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics.
Article in Angewandte Chemie (International ed. in English), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed.
- Optimization of trap column properties and loading conditions for proteome profiling of single-cell-level sample inputs.Analytical and bioanalytical chemistry · 2026Article
- What Are the Practical Applications of Single-Cell Proteomics?Proteomes · 2026Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- Deep Proteome Profiling of Rat Dorsal Striatal Synaptoneurosomes Following Methamphetamine Exposure.ACS chemical neuroscience · 2026Article
- Simultaneous single-cell proteomics and epigenetic analysis of histone deacetylase inhibition in human cells.Communications biology · 2025Article
- Review
- High-Throughput Label-free Single-Cell Proteomics Enabled by Multicolumn NanoLC with a 5-min Cycle Time.Research square · 2025Article
- Real-Time Eco-AI, Electrophoresis-Correlative Data-Dependent Acquisition with AI-Based Data Processing Broadens Access to Single-Cell Mass Spectrometry Proteomics.Angewandte Chemie (International ed. in English) · 2025Article
- The $10 proteome: low-cost, deep and quantitative proteome profiling of limited sample amounts using the Orbitrap Astral and timsTOF Ultra 2 mass spectrometers.bioRxiv : the preprint server for biology · 2025Article
- High-Performance Proteomics Using Nano-, Capillary-, and Microflow Chromatographic Separations.Journal of proteome research · 2025Article
- Single-cell proteomics using mass spectrometry.Cell genomics · 2025Review
- Improved Detection of Differentially Abundant Proteins through FDR-Control of Peptide-Identity-Propagation.Journal of proteome research · 2025Article
- scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.Genome biology · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search.Nature communications · 2025Article
- MSConnect: Open-Source, End-to-End Platform for Automated Mass Spectrometry Data Management, Analysis, and Visualization.Journal of proteome research · 2025Article
- Data-Independent Acquisition Shortens the Analytical Window of Single-Cell Proteomics to Fifteen Minutes in Capillary Electrophoresis Mass Spectrometry.Journal of proteome research · 2025Article
- Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses.Journal of proteome research · 2025Review
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
- Mapping Nanoscale-To-Single-Cell Phosphoproteomic Landscape by Chip-DIA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
We combined efficient sample preparation and ultra-low-flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in rapid label-free analyses. WWA employs large isolation windows to intentionally co-isolate and co-fragment adjacent precursors along with the selected precursor. Optimized WWA increased the number of MS2-identified proteins by ≈40 % relative to standard data-dependent acquisition. For a 40-min LC gradient operated at ≈15 nL/min, we identified an average of 3,524 proteins per single-cell-sized aliquot of protein digest. Reducing the active gradient to 20 min resulted in a modest 10 % decrease in proteome coverage. Using this platform, we compared protein expression between single HeLa cells having an essential autophagy gene, atg9a, knocked out, with their isogenic WT parental line. Similar proteome coverage was observed, and 268 proteins were significantly up- or downregulated. Protein upregulation primarily related to innate immunity, vesicle trafficking and protein degradation.
Indexed as
Identifiers
What OpenQuestion holds
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.