ArticleNature communications2021
A data-independent acquisition-based global phosphoproteomics system enables deep profiling.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- A phosphoproteome atlas of human cell lines reveals the landscape of kinase activity.Nature structural & molecular biology · 2026Article
- PhosSight: A Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Phosphoproteomics in Vascular Biology and Disease: Illuminating Signaling in the Vessel.Arteriosclerosis, thrombosis, and vascular biology · 2026Review
- Deciphering O‑GlcNAc-Dependent Signaling Via Integrated Proteomics and Phosphoproteomics.ACS omega · 2026Article
- Evaluation of Data-Independent Acquisition-Based Phosphoproteomics Analysis in Mammalian and Bacterial Systems.Journal of proteome research · 2026Article
- Spectronaut and DIA-NN: A Comparison of their Performance in the Analysis of Lung Adenocarcinoma Biopsies.ACS omega · 2026Article
- Recent advances in phosphoproteomics based on mass spectrometry and its clinical application prospects.Frontiers in pharmacology · 2026Review
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells.Communications biology · 2025Review
- Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures.Molecular systems biology · 2025Article
- Metal Ion-Enhanced ZIC-cHILIC StageTip for N-Glycoproteomic and Phosphoproteomic Profiling in EGFR-Mutated Lung Cancer Cells.Molecular & cellular proteomics : MCP · 2025Article
- Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.Nature communications · 2025Article
- The SIK3-N783Y mutation is associated with the human natural short sleep trait.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Protecting centrosomes from fracturing enables efficient cell navigation.Science advances · 2025Article
- Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.Microbiome · 2025Article
- Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets.Frontiers in immunology · 2025Review
- Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.Proteomics · 2025Review
- Mapping Nanoscale-To-Single-Cell Phosphoproteomic Landscape by Chip-DIA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Targeting ErbB and tankyrase1/2 prevent the emergence of drug-tolerant persister cells in ALK-positive lung cancer.NPJ precision oncology · 2024Article
- STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within two hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values.
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Registered trials
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