ArticleJournal of proteome research2018
CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Instrument-Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring Methods.Journal of proteome research · 2026Article
- iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.Analytical chemistry · 2026Article
- Proteomic datasets of threeData in brief · 2026Article
- The Peptonizer2000: Bringing Confidence to Metaproteomics.Journal of proteome research · 2026Article
- Article
- End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data.Scientific reports · 2026Article
- Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups.Nature communications · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Proteoform Identification Using Multiplexed Top-Down Mass Spectra.Proteomics · 2025Article
- Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep.Analytical chemistry · 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
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search.bioRxiv : the preprint server for biology · 2024Article
- Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.Molecular & cellular proteomics : MCP · 2024Review
- Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification.Molecular & cellular proteomics : MCP · 2024Article
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing.Nature communications · 2024Article
- Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis.Analytical chemistry · 2023Article
- Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics.Journal of pharmaceutical analysis · 2023Article
- Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics.Journal of proteome research · 2023Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coeluting peptides are still a major challenge for the identification and validation of MS/MS spectra, but carry great potential. To tackle these problems, we have developed the here presented CharmeRT workflow, combining a chimeric spectra identification strategy implemented as part of the MS Amanda algorithm with the validation system Elutator, which incorporates a highly accurate retention time prediction algorithm. For high-resolution data sets this workflow identifies 38-64% chimeric spectra, which results in up to 63% more unique peptides compared to a conventional single search strategy.
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