ArticleNature methods2025
Uncovering hidden protein modifications with native top-down mass spectrometry.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Post‑translational modifications in atherosclerosis: Roles, mechanisms and therapeutic potential (Review).International journal of molecular medicine · 2026Review
- Differential lipid selectivity of StARD phospholipid transporters revealed by native MS.Nature communications · 2026Article
- Structure of NHE6 and its lipid-mediated interactions regulating endosomal pH.Nature communications · 2026Article
- Native Multidimensional Protein Complex Identification and Topology Characterization (Native MudPIT).Analytical chemistry · 2026Article
- A Unified Mass Spectrometry Workflow Integrating Bottom-Up and Native Top-Down Proteomics via Nanodroplet Enzymatic Digestion.Analytical chemistry · 2026Article
- Isotope Decluttering Reduces Spectral Complexity while Maintaining Protein Structure.Analytical chemistry · 2026Article
- Native Top-Down Mass Spectrometry Combined with High-Resolution Charge Variant Analysis of Trastuzumab Originator and Biosimilars.Journal of the American Society for Mass Spectrometry · 2026Article
- Quantitative Mapping of NHS Ester-Protein Reactivity Using Native Top-Down Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2026Article
- Ribosome heterogeneity and specialization in musculoskeletal physiology and pathology.JBMR plus · 2026Article
- Organoid research: new concepts and new technologies.Burns & trauma · 2026Review
- Imaging of Protein Assemblies up to 231 kDa in Tissues with Nano-DESI Mass Spectrometry.Analytical chemistry · 2025Article
- Uncovering hidden protein modifications with native top-down mass spectrometry.Nature methods · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Protein modifications drive dynamic cellular processes by modulating biomolecular interactions, yet capturing these modifications within their native structural context remains a significant challenge. Native top-down mass spectrometry promises to preserve the critical link between modifications and interactions. However, current methods often fail to detect uncharacterized or low-abundance modifications, limiting insights into proteoform diversity. To address this gap, we introduce precise and accurate Identification Of Native proteoforms (precisION), an interactive end-to-end software package that leverages a robust, data-driven fragment-level open search to detect, localize and quantify 'hidden' modifications within intact protein complexes. Applying precisION to four therapeutically relevant targets-PDE6, ACE2, osteopontin (SPP1) and a GABA transporter (GAT1)-we discover undocumented phosphorylation, glycosylation and lipidation, and resolve previously uninterpretable density in an electron cryo-microscopy map of GAT1. As an open-source software package, precisION offers an intuitive means for interpreting complex protein fragmentation data. This tool will empower the community to unlock the potential of native top-down mass spectrometry, advancing integrative structural biology, molecular pathology and drug development.
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