ArticleJournal of proteome research2017
Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling.
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 20 papers.
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Who cites it
20 citing papers in PubMed.
- Proteomics in Antitumor Drug Target Discovery, Toxicity, Resistance, and Precision Oncology.Drug design, development and therapy · 2026Review
- A Roadmap for the Future of Systems Biology in Cancer Research.Cancer research · 2025Review
- Transitions in the proteome and phospho-proteome during Xenopus laevis development.Developmental biology · 2025Article
- Enriching Cysteine-Containing Peptides Using a Sulfhydryl-Reactive Alkylating Reagent with a Phosphonic Acid Group and Immobilized Metal Affinity Chromatography.Journal of proteome research · 2023Article
- Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation.Nature communications · 2022Article
- Review
- A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment.Nature communications · 2022Article
- Challenges and Opportunities for Bayesian Statistics in Proteomics.Journal of proteome research · 2022Review
- Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging.Expert review of proteomics · 2021Review
- Categorization of Phosphorylation Site Behavior during the Diauxic Shift inJournal of proteome research · 2021Article
- Advances in quantitative high-throughput phosphoproteomics with sample multiplexing.Proteomics · 2021Review
- Stoichiometric Thiol Redox Proteomics for Quantifying Cellular Responses to Perturbations.Antioxidants (Basel, Switzerland) · 2021Review
- In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.EMBO reports · 2021Article
- Article
- Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation.Science signaling · 2020Article
- Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model.Journal of proteome research · 2019Article
- Sample Multiplexing Strategies in Quantitative Proteomics.Analytical chemistry · 2019Review
- Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools.International journal of molecular sciences · 2018Review
- Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3.Journal of proteome research · 2018Article
- Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential.The Journal of biological chemistryArticle
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Authors and funding
4 authors.
Funding
Abstract
Phosphorylation stoichiometry, or occupancy, is one element of phosphoproteomics that can add useful biological context (Gerber et al. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 6940-5). We previously developed a method to assess phosphorylation stoichiometry on a proteome-wide scale (Wu et al. Nat. Methods 2011, 8, 677-83). The stoichiometry calculation relies on identifying and measuring the levels of each nonphosphorylated counterpart peptide with and without phosphatase treatment. The method, however, is problematic in that low stoichiometry phosphopeptides can return negative stoichiometry values if measurement error is larger than the percent stoichiometry. Here, we have improved the stoichiometry method through the use of isobaric labeling with 10-plex TMT reagents. In this way, five phosphatase treated and five untreated samples are compared simultaneously so that each stoichiometry is represented by five ratio measurements with no missing values. We applied the method to determine basal stoichiometries of HCT116 cells growing in culture. With this method, we analyzed five biological replicates simultaneously with no need for phosphopeptide enrichment. Additionally, we developed a Bayesian model to estimate phosphorylation stoichiometry as a parameter confined to an interval between 0 and 1 implemented as an R/Stan script. Consequently, both point and interval estimates are consistent with the plausible range of values for stoichiometry. Finally, we report absolute stoichiometry measurements with credible intervals for 6772 phosphopeptides containing at least a single phosphorylation site.
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