ArticleNature communications2024
Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics.Scientific reports · 2026Article
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- 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
- Single-cell proteomics using mass spectrometry.Cell genomics · 2025Review
- Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics.Nature communications · 2025Article
- The impact of exercise on skeletal muscle proteome of prediabetic subjects analyzed with data independent mass spectrometry.Scientific reports · 2025Article
- Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.Journal of proteome research · 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
- Micropillars in Cell Mechanobiology: Design, Fabrication, Characterization, and Biosensing Applications.Small science · 2025Review
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
- A Pilot Study of Exosome Proteomic Profiling Reveals Dysregulated Metabolic Pathways in Endometrial Cancer.Biomedicines · 2025Article
- Review
- MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search.bioRxiv : the preprint server for biology · 2024Article
- Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples.Analytical chemistry · 2024Article
- The Deep Proteomics Approach Identified Extracellular Vesicular Proteins Correlated to Extracellular Matrix in Type One and Two Endometrial Cancer.International journal of molecular sciences · 2024Article
- Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics.Angewandte Chemie (International ed. in English) · 2023Article
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Authors and funding
8 authors.
Funding
Abstract
Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.
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