ArticleNature communications2023
Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides.
Article in Nature communications, 2023. 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.
- Cellular Consequences, Citrullination Substrates, and Antigenicity of Targeting PAD4 to Cell Surfaces.ACS central science · 2026Article
- Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics.Nature chemistry · 2026Article
- Review
- Expanding the repertoire of chemically induced covalent neoantigens.Nature chemical biology · 2026Article
- Review
- Improved Peptide Search for Identification of SUMO and Sequence-Based Modifiers, in MaxSBM.Molecular & cellular proteomics : MCP · 2026Article
- Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications.Biomolecules · 2026Review
- Cellular consequences, citrullination substrates, and antigenicity resulting from wild-type and targeted PAD4 on cell surfaces.bioRxiv : the preprint server for biology · 2026Article
- Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.BMC bioinformatics · 2026Article
- Review
- Untargeted Proteomics Identifies Plant Substrates of the Bacterial-Derived ADP-Ribosyltransferase AvrRpm1.Plant direct · 2025Article
- Review
- Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer.Cell reports. Medicine · 2025Article
- A transcriptomic, proteomic, and functional genetic atlas dissects neurofibromin function in the peripheral nervous system.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Mechanisms of metabolism-coupled protein modifications.Nature chemical biology · 2025Review
- Metabolic and Proteomic Divergence is Present in Spleens and Livers from Berkeley Sickle Cell Anemia and β-Thalassemia Mice.Journal of proteome research · 2025Article
- Navigating the maze of mass spectra: a machine-learning guide to identifying diagnostic ions in O-glycan analysis.Analytical and bioanalytical chemistry · 2025Article
- Article
- Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.Molecular & cellular proteomics : MCP · 2024Review
- Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics.Communications chemistry · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Post-translational modifications are an area of great interest in mass spectrometry-based proteomics, with a surge in methods to detect them in recent years. However, post-translational modifications can introduce complexity into proteomics searches by fragmenting in unexpected ways, ultimately hindering the detection of modified peptides. To address these deficiencies, we present a fully automated method to find diagnostic spectral features for any modification. The features can be incorporated into proteomics search engines to improve modified peptide recovery and localization. We show the utility of this approach by interrogating fragmentation patterns for a cysteine-reactive chemoproteomic probe, RNA-crosslinked peptides, sialic acid-containing glycopeptides, and ADP-ribosylated peptides. We also analyze the interactions between a diagnostic ion's intensity and its statistical properties. This method has been incorporated into the open-search annotation tool PTM-Shepherd and the FragPipe computational platform.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.