ArticleJournal of proteome research2017
Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags.
Article in Journal of proteome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 34 citations in OpenAlex.
- Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome.Journal of the American Society for Mass Spectrometry · 2024Pooled it
- Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications.Biomolecules · 2026Review
- Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions.Communications chemistry · 2025Article
- Acid Cleavable Biotin-Alkyne Improves Sensitivity for Direct Detection of Biotin Labeled Peptides in Biorthogonal Noncanonical Amino Acid Tagging Analysis.Journal of proteome research · 2024Article
- Acid cleavable biotin-alkyne improves sensitivity for direct detection of biotin labeled peptides in BONCAT analysis.bioRxiv : the preprint server for biology · 2024Article
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics.Nature biomedical engineering · 2024Article
- Common Post-translational Modifications (PTMs) of Proteins: Analysis by Up-to-Date Analytical Techniques with an Emphasis on Barley.Journal of agricultural and food chemistry · 2023Review
- Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides.Nature communications · 2023Article
- Optimization of Higher-Energy Collisional Dissociation Fragmentation Energy for Intact Protein-Level Tandem Mass Tag Labeling.Journal of proteome research · 2023Article
- MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics.Molecular & cellular proteomics : MCP · 2023Article
- Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics.Analytical chemistry · 2022Article
- The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry.Analytical chemistry · 2022Article
- Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging.Expert review of proteomics · 2021Review
- Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update.Analytical chemistry · 2019Review
- MS3-IDQ: Utilizing MS3 Spectra beyond Quantification Yields Increased Coverage of the Phosphoproteome in Isobaric Tag Experiments.Journal of proteome research · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
While developing a multiplexed phosphotyrosine peptide quantification assay, an unexpected observation was made: significant neutral loss from phosphotyrosine (pY) containing peptides. Using a 2000-member peptide library, we sought to systematically investigate this observation by comparing unlabeled peptides with the two highest-plex isobaric tags (iTRAQ8 and TMT10) across CID, HCD, and ETD fragmentation using high resolution high mass accuracy Orbitrap instrumentation. We found pY peptide neutral loss behavior was consistent with reduced proton mobility, and does not occur during ETD. The site of protonation at the peptide N-terminus changes from a primary to a tertiary amine as a result of TMT labeling which would increase the gas phase basicity and reduce proton mobility at this site. This change in fragmentation behavior has implications during instrument method development and interpretation of MS/MS spectra, and therefore ensuing follow-up studies. We show how sites not localized to tyrosine by search and site localization algorithms can be confidently reassigned to tyrosine using neutral loss and phosphotyrosine immonium ions. We believe these findings will be of general interest to those studying pY signal transduction using isobaric tags.
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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.