ArticleNature methods2025
Unifying the analysis of bottom-up proteomics data with CHIMERYS.
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 25 papers.
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Who cites it
25 citing papers in PubMed.
- Preprocessing Large-Scale Proteomics Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Mass spectrometry proteomics for studying mitostasis.Protein science : a publication of the Protein Society · 2026Review
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Quantitative Host Cell Protein Analysis of Antibody-Based Protein Therapeutics Using the Orbitrap Astral Mass Spectrometer.Journal of the American Society for Mass Spectrometry · 2026Article
- A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Review
- Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery.Journal of proteome research · 2026Article
- Article
- Carafe2 enables high qualitybioRxiv : the preprint server for biology · 2026Article
- MiProChip: A Scalable Microfluidic Platform for Multiplexed Single-Cell Proteomics via Isobaric Labeling.Analytical chemistry · 2026Article
- Subcellular proteomics reveals a blueprint for endosymbiont integration in trypanosomatid Angomonas deanei.Nature communications · 2026Article
- Proteoforms as the true units of physiological function.European journal of applied physiology · 2026Review
- EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery.bioRxiv : the preprint server for biology · 2026Article
- Artificial Intelligence Drives Advances in Multi-Omics Analysis and Precision Medicine for Sepsis.Biomedicines · 2026Review
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- 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
- ATM promotes reversed fork processing during DNA interstrand cross-link repair.bioRxiv : the preprint server for biology · 2025Article
- Mass Spectrometry-Based Proteomics for Seafood Allergen Detection and Quantification: Current Trends and Technological Frontiers.International journal of molecular sciences · 2025Review
- Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics.Nature communications · 2025Article
- Rapid assay development for low input targeted proteomics using a versatile linear ion trap.Nature communications · 2025Article
- MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search.Nature communications · 2025Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography-tandem mass spectrometry, creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such as data-dependent, data-independent or parallel reaction monitoring, separate software packages employing different analysis concepts are used for peptide identification and quantification, even though the underlying information is principally the same. Here, we introduce CHIMERYS, a spectrum-centric search algorithm designed for the deconvolution of chimeric spectra that unifies proteomic data analysis. Using accurate predictions of peptide retention time, fragment ion intensities and applying regularized linear regression, it explains as much fragment ion intensity as possible with as few peptides as possible. Together with rigorous false discovery rate control, CHIMERYS accurately identifies and quantifies multiple peptides per tandem mass spectrum in data-dependent, data-independent or parallel reaction monitoring experiments.
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