ArticleMolecular & cellular proteomics : MCP2011
Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes.
Article in Molecular & cellular proteomics : MCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers, 1 of them a synthesis that pooled it.
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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
101 citing papers in PubMed, 1 synthesis or guideline pooled it, 190 citations in OpenAlex.
- Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes.GigaScience · 2017Pooled it
- A comprehensive proteome and the first phosphoproteome reveal extensive phosphorylation of carbohydrate metabolism in Cryptosporidium parvum sporozoites.Parasites & vectors · 2026Article
- SPOTTER: Automated Tissue-Barcoding Platform for Spatial Proteomics and Phosphoproteomics.bioRxiv : the preprint server for biology · 2026Article
- Systems Biology of Recombinant 2G12 and 353/11 mAb Production in CHO-K1 Cell Lines at Phosphoproteome Level.Proteomes · 2025Article
- Phosphoproteomics for studying signaling pathways evoked by hormones of the renin-angiotensin system: A source of untapped potential.Acta physiologica (Oxford, England) · 2025Review
- Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.Proteomics · 2025Review
- In-Depth Analysis of Tissue Phosphoproteomics with TiOMethods in molecular biology (Clifton, N.J.) · 2025Article
- Shape-Shifting Mechanisms: Integrative Multi-Omics Insights IntoMycobiology · 2025Review
- Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.Nature communications · 2024Article
- Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity.iScience · 2024Article
- A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics.Molecular & cellular proteomics : MCP · 2024Article
- Signatures of Cysteine Oxidation on Muscle Structural and Contractile Proteins Are Associated with Physical Performance and Muscle Function in Older Adults: Study of Muscle, Mobility and Aging (SOMMA).medRxiv : the preprint server for health sciences · 2023Article
- Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival.Molecular systems biology · 2023Article
- Systematic characterization of extracellular glycoproteins using mass spectrometry.Mass spectrometry reviews · 2023Review
- Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways.Molecules (Basel, Switzerland) · 2023Review
- MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics.Molecular & cellular proteomics : MCP · 2023Article
- Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment.eLife · 2022Article
- IQGAP1 and RNA Splicing in the Context of Head and Neck via Phosphoproteomics.Journal of proteome research · 2022Article
- Selective modulation of cell surface proteins during vaccinia infection: A resource for identifying viral immune evasion strategies.PLoS pathogens · 2022Article
- Quantifying phosphorylation dynamics in primary neuronal cultures using LC-MS/MS.STAR protocols · 2022Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The interpretation of quantitative phosphoproteomics studies is complicated because each differential phosphorylation event integrates both changes in protein expression and phosphorylation. Here we investigated this phenomenon by performing parallel comparisons of protein expression and phosphorylation in S. cerevisiae. In each of two experiments comparing yeast mutants bearing deletions in FUS3 or STE7 with their wild-type counterparts, we quantified over 4100 proteins, including all members of the yeast mating pathway. We also identified 12,499 unique phosphorylation sites in this work. We demonstrate the critical importance of controlling the protein-level false-discovery rate and provide a novel method to assess the accuracy of protein false-discovery rate estimates. For the first time, 96% of nonredundant phosphopeptide ratios could be calibrated by protein levels, allowing truly differential phosphorylation to be distinguished from altered protein expression. This revealed a starkly different view, with 25% of seemingly differential phosphopeptides now attributed to changes in protein expression. Combined protein expression and phosphorylation surveys uncovered both independent and concerted changes in protein expression and phosphorylation, while highlighting the partially redundant role of a second MAPK (Kss1) in the mating pathway.
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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.