ArticleJournal of proteome research2015
Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 62 citations in OpenAlex.
- Proteome-Wide Multipoint Internal Calibration Curves for Evaluating Peptide-Level Linearity in Relative Quantitative Proteomics.Journal of proteome research · 2026Article
- SUMO-targeted Ubiquitin Ligases as crucial mediators of protein homeostasis in Candida glabrata.PLoS pathogens · 2024Article
- The deubiquitinase Ubp3/Usp10 constrains glucose-mediated mitochondrial repression via phosphate budgeting.eLife · 2024Article
- Driver Mutations Dictate the Immunologic Landscape and Response to Checkpoint Immunotherapy of Glioblastoma.Cancer immunology research · 2023Article
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- Identification of Deubiquitinase Substrates in Saccharomyces cerevisiae by Systematic Overexpression.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Transcriptome innovations in primates revealed by single-molecule long-read sequencing.Genome research · 2022Article
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- Blistering1 ModulatesMolecular & cellular proteomics : MCP · 2020Article
- Multibatch TMT Reveals False Positives, Batch Effects and Missing Values.Molecular & cellular proteomics : MCP · 2019Article
- Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides.Analytical chemistry · 2019Article
- Quantitative Proteomics Reveals a Role for SERINE/ARGININE-Rich 45 in Regulating RNA Metabolism and Modulating Transcriptional SuppressionFrontiers in plant science · 2019Article
- A balance of deubiquitinating enzymes controls cell cycle entry.Molecular biology of the cell · 2018Article
- Activity-based ubiquitin-protein probes reveal target protein specificity of deubiquitinating enzymes.Chemical science · 2018Article
- A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine.Nature communications · 2018Article
- Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma.Life science alliance · 2018Article
- Proteome-Wide Evaluation of Two Common Protein Quantification Methods.Journal of proteome research · 2018Article
- Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.Genetics · 2018Article
- Phosphate Acquisition and Virulence in Human Fungal Pathogens.Microorganisms · 2017Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Characterizing a protein's function often requires a description of the cellular state in its absence. Multiplexing in mass spectrometry-based proteomics has now achieved the ability to globally measure protein expression levels in yeast from 10 cell states simultaneously. We applied this approach to quantify expression differences in wild type and nine deubiquitylating enzyme (DUB) knockout strains with the goal of creating "information networks" that might provide deeper, mechanistic insights into a protein's biological role. In total, more than 3700 proteins were quantified with high reproducibility across three biological replicates (30 samples in all). DUB mutants demonstrated different proteomics profiles, consistent with distinct roles for each family member. These included differences in total ubiquitin levels and specific chain linkages. Moreover, specific expression changes suggested novel functions for several DUB family members. For instance, the ubp3Δ mutant showed large expression changes for members of the cytochrome C oxidase complex, consistent with a role for Ubp3 in mitochondrial regulation. Several DUBs also showed broad expression changes for phosphate transporters as well as other components of the inorganic phosphate signaling pathway, suggesting a role for these DUBs in regulating phosphate metabolism. These data highlight the potential of multiplexed proteome-wide analyses for biological investigation and provide a framework for further study of the DUB family. Our methods are readily applicable to the entire collection of yeast deletion mutants and may help facilitate systematic analysis of yeast and other organisms.
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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.