ArticleNature communications2023
Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 51 citations in OpenAlex.
- Self-buoyant cell-spheroid culture programming multi-spheroid assembly.Science advances · 2026Article
- A phosphoproteome atlas of human cell lines reveals the landscape of kinase activity.Nature structural & molecular biology · 2026Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- IsoPS-DIA: Dual Functionality of Absolute Targeted Quantification and Global Proteome Profiling.Analytical chemistry · 2026Article
- Challenges and Opportunities in State-of-the-Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles.Proteomics · 2026Review
- Multiomic profiling of ER-positive HER2-negative breast cancer reveals markers associated with metastatic spread.Breast cancer research : BCR · 2026Observational
- Recent advances in phosphoproteomics based on mass spectrometry and its clinical application prospects.Frontiers in pharmacology · 2026Review
- Data-independent acquisition-based quantitative proteomics in plants.Frontiers in plant science · 2026Review
- Endogenous Phosphopeptidomics Analysis by Using Mesoporous IMAC Materials.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells.Communications biology · 2025Review
- Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface.Journal of proteome research · 2025Article
- Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.Nature communications · 2025Article
- Multiplexed phosphoproteomics of low cell numbers using SPARCE.Communications biology · 2025Article
- Single-Cell Multi-omics Assessment of Spinal Cord Injury Blocking via Cerium-doped Upconversion Antioxidant Nanoenzymes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Mapping Nanoscale-To-Single-Cell Phosphoproteomic Landscape by Chip-DIA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Review
- Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.Proteomics · 2025Review
- Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics.International journal of molecular sciences · 2024Article
- Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition.Nature biotechnology · 2024Article
- Advancements in mass spectrometry-based proteomics: a new era in pathology research and diagnostics.Pathologie (Heidelberg, Germany) · 2024Review
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.
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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 Socratic graph.