ArticleMolecular & cellular proteomics : MCP2018
ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides.
Article in Molecular & cellular proteomics : MCP, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 133 citations in OpenAlex.
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- InstaNovo-P: a de novo peptide sequencing model for phosphoproteomics.Nature communications · 2026Article
- Both L-Lactyl and D-Lactyl Enantiomers Modify Histones in Mouse Testis.Molecular & cellular proteomics : MCP · 2026Article
- iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.Analytical chemistry · 2026Article
- Zero-shot de novo peptide sequencing with open posttranslational modification discovery.Nature biotechnology · 2026Article
- Novel insights into the assembly of the yeast translation initiation multifactor complex: The critical role of eIF5.Protein science : a publication of the Protein Society · 2026Article
- High-throughput chemical proteomics workflow for profiling protein citrullination dynamics.Nature communications · 2026Article
- Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups.Nature communications · 2026Article
- Modanovo: A Unified Model for Post-translational Modification-Aware De Novo Sequencing Using Experimental Spectra From In Vivo and Synthetic Peptides.Molecular & cellular proteomics : MCP · 2026Article
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome.Journal of cardiovascular development and disease · 2026Review
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Simultaneous single-cell proteomics and epigenetic analysis of histone deacetylase inhibition in human cells.Communications biology · 2025Article
- Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions.Communications chemistry · 2025Article
- Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models.Proteomics · 2025Review
- Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes.Molecular & cellular proteomics : MCP · 2025Article
- Cracking Lysine Crotonylation (Kcr): Enlightening a Promising Post-Translational Modification.Chembiochem : a European journal of chemical biology · 2025Review
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing.Nature communications · 2025Article
- Ethylene Signaling in Plant Development and Stress Adaptation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Lysine Phoshoglycerylation Is Widespread in Bacteria and Overlaps with Acylation.Microorganisms · 2024Article
- A learned score function improves the power of mass spectrometry database search.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of the post-translational modification (PTM) state of proteins using mass spectrometry-based bottom-up proteomic workflows has evolved into a powerful tool for the study of cellular regulatory events that are not directly encoded at the genome level. Besides frequently detected modifications such as phosphorylation, acetylation and ubiquitination, many low abundant or less frequently detected PTMs are known or postulated to serve important regulatory functions. To more broadly understand the LC-MS/MS characteristics of PTMs, we synthesized and analyzed ∼5,000 peptides representing 21 different naturally occurring modifications of lysine, arginine, proline and tyrosine side chains and their unmodified counterparts. The analysis identified changes in retention times, shifts of precursor charge states and differences in search engine scores between modifications. PTM-dependent changes in the fragmentation behavior were evaluated using eleven different fragmentation modes or collision energies. We also systematically investigated the formation of diagnostic ions or neutral losses for all PTMs, confirming 10 known and identifying 5 novel diagnostic ions for lysine modifications. To demonstrate the value of including diagnostic ions in database searching, we reprocessed a public data set of lysine crotonylation and showed that considering the diagnostic ions increases confidence in the identification of the modified peptides. To our knowledge, this constitutes the first broad and systematic analysis of the LC-MS/MS properties of common and rare PTMs using synthetic peptides, leading to direct applicable utility for bottom-up proteomic experiments.
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