The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
A large-scale method to measure absolute protein phosphorylation stoichiometries
Open accessAbstract
The functional role of protein phosphorylation is impacted by its fractional stoichiometry. Thus, a comprehensive strategy to study phosphorylation dynamics should include an assessment of site stoichiometry. Here we report an integrated method that relies on phosphatase treatment and stable-isotope labeling to determine absolute stoichiometries of protein phosphorylation on a large scale. This approach requires the measurement of only a single ratio relating phosphatase-treated and mock-treated samples. Using this strategy we determined stoichiometries for 5,033 phosphorylation sites in triplicate analyses from Saccharomyces cerevisiae growing through mid-log phase. We validated stoichiometries at ten sites that represented the full range of values obtained using synthetic phosphopeptides and found excellent agreement. Using bioinformatics, we characterized the biological properties associated with phosphorylation sites with vastly differing absolute stoichiometries.
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
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
Self-citationA tissue-specific atlas of mouse protein phosphorylation and expression
Huttlin, E. L., Jedrychowski, M. P., Elias, J. E., Goswami, T., Rad, R., Beausoleil, S. A., Villén, J., Haas, W., Sowa, M. E., & Gygi, S. P. (2010) · Cell · doi:10.1016/j.cell.2010.12.001 · Cited by 1,778
Self-citationAbsolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0832254100 · Cited by 1,733
Self-citationQuantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
Olsen, J. V., Vermeulen, M., Santamaria, A., Kumar, C., Miller, M. L., Jensen, L. J., Gnad, F., Cox, J., Jensen, T. S., Nigg, E. A., et al. (2010) · Science Signaling · doi:10.1126/scisignal.2000475 · Cited by 1,479
Length-dependent prediction of protein intrinsic disorder
Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K., & Obradovic, Z. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-208 · Cited by 928
Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution
Holt, L. J., Tuch, B. B., Villén, J., Johnson, A. D., Gygi, S. P., & Morgan, D. O. (2009) · Science · doi:10.1126/science.1172867 · Cited by 869
Self-citationMapping protein post-translational modifications with mass spectrometry
Witze, E. S., Old, W. M., Resing, K. A., & Ahn, N. G. (2007) · Nature Methods · doi:10.1038/nmeth1100 · Cited by 792
The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry
Villén, J., & Gygi, S. P. (2008) · Nature Protocols · doi:10.1038/nprot.2008.150 · Cited by 629
Self-citation
Cited by
Multi-omics approaches to disease
Hasin, Y., Seldin, M., & Lusis, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1215-1 · Cited by 2,953
The growing landscape of lysine acetylation links metabolism and cell signalling
Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E., & Mann, M. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3841 · Cited by 1,324
The world of protein acetylation
Drazic, A., Myklebust, L. M., Ree, R., & Arnesen, T. (2016) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2016.06.007 · Cited by 804
Applications of multi‐omics analysis in human diseases
Chen, C., Wang, J., Pan, D., Wang, X., Xu, Y., Yan, J., Wang, L., Yang, X., Yang, M., & Liu, G. (2023) · MedComm · doi:10.1002/mco2.315 · Cited by 545
Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)
Theillet, F.-X., Binolfi, A., Frembgen-Kesner, T., Hingorani, K., Sarkar, M., Kyne, C., Li, C., Crowley, P. B., Gierasch, L., Pielak, G. J., et al. (2014) · Chemical Reviews · doi:10.1021/cr400695p · Cited by 503
Metadata
- Authors
- Wu, R., Haas, W., Dephoure, N., Huttlin, E. L., Zhai, B., Sowa, M. E., & Gygi, S. P.
- Venue
- Nature Methods
- Published
- 2011-07-03
- Volume
- 8
- Issue
- 8
- Pages
- 677-683
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1977637361
- Cited by
- 276
- References
- 38
- FWCI
- 11.08
- Type
- journal article
- Language
- en
- Open access
- green
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: A large-scale method to measure absolute protein phosphorylation stoichiometries. https://app.cochat.ai/papers/10.1038/nmeth.1636
- The paper
- Wu, R., Haas, W., Dephoure, N., Huttlin, E. L., Zhai, B., Sowa, M. E., & Gygi, S. P. (2011). A large-scale method to measure absolute protein phosphorylation stoichiometries. Nature Methods. https://doi.org/10.1038/nmeth.1636
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.
