The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Global analysis of protein localization in budding yeast
Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248 · cited 1×
“…(19), due to its small, well-annotated proteome and its extensive resources detailing protein expression levels (20) and protein localizations (21), Saccharomyces cerevisiae is well matched to current technical capabilities and is an ideal model to evaluate the feasibility and importance of…”
BackgroundElias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
Self-citationGlobal analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Self-citationSemi-supervised learning for peptide identification from shotgun proteomics datasets
Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods · doi:10.1038/nmeth1113 · Cited by 2,424
Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577
Self-citationComprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., & Mann, M. (2008) · Nature · doi:10.1038/nature07341 · Cited by 873
Large-scale phosphorylation analysis of mouse liver
Villén, J., Beausoleil, S. A., Gerber, S. A., & Gygi, S. P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609836104 · Cited by 730
Self-citationA dual pressure linear ion trap orbitrap instrument with very high sequencing speed
Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., et al. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900375-mcp200 · Cited by 464
Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases
Smolka, M. B., Albuquerque, C. P., Chen, S.-H., & Zhou, H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701622104 · Cited by 404
Quantitative Analysis of Synaptic Phosphorylation and Protein Expression
Trinidad, J. C., Thalhammer, A., Specht, C. G., Lynn, A. J., Baker, P. R., Schoepfer, R., & Burlingame, A. L. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700170-mcp200 · Cited by 194
Cited by
Next-generation proteomics: towards an integrative view of proteome dynamics
Altelaar, A. F. M., Munoz, J., & Heck, A. J. R. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3356 · Cited by 782
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
Vlastaridis, P., Kyriakidou, P., Chaliotis, A., Van de Peer, Y., Oliver, S. G., & Amoutzias, G. D. (2017) · GigaScience · doi:10.1093/gigascience/giw015 · Cited by 733
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome
Hebert, A. S., Dittenhafer-Reed, K. E., Yu, W., Bailey, D. J., Selen, E. S., Boersma, M. D., Carson, J. J., Tonelli, M., Balloon, A. J., Higbee, A. J., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.10.024 · Cited by 636
Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., & Coon, J. J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.034769 · Cited by 528
Tan, H., Yang, K., Li, Y., Shaw, T. I., Wang, Y., Blanco, D. B., Wang, X., Cho, J.-H., Wang, H., Rankin, S., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.02.010 · Cited by 372
Metadata
- Authors
- Wu, R., Dephoure, N., Haas, W., Huttlin, E. L., Zhai, B., Sowa, M. E., & Gygi, S. P.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2011-08
- Volume
- 10
- Issue
- 8
- Pages
- M111.009654
- ISSN
- 1535-9476 (ISSN-L)
- OpenAlex
- W2038801176
- Cited by
- 176
- References
- 10
- FWCI
- 7.11
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes. https://app.cochat.ai/papers/10.1074/mcp.m111.009654
- The paper
- Wu, R., Dephoure, N., Haas, W., Huttlin, E. L., Zhai, B., Sowa, M. E., & Gygi, S. P. (2011). Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes. Molecular & Cellular Proteomics. https://doi.org/10.1074/mcp.m111.009654
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
