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Reply to "Phosphorylation sites of higher stoichiometry are more conserved"

Nature Methods volume 9, page 318 (2012)Cite this article

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Gygi et al. reply:

We are pleased that our large-scale method for measuring phosphorylation stoichiometries1 has inspired additional analysis2. We had reported stoichiometries for ∼5,000 yeast protein phosphorylation sites, only a small fraction of which were highly conserved across 25 fungal species. We noted as a minor point that lowest-occupancy sites appeared more highly conserved than the highest-stoichiometry sites. Tan & Bader2 propose an explanation for this second observation: the lowest-stoichiometry phosphorylation sites disproportionately occur on high-abundance proteins, which tend to be more highly conserved. Once background protein conservation rates are taken into account, high-stoichiometry sites may be somewhat more conserved than lower-occupancy ones2.

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Figure 1: Phosphorylation versus protein abundance.

References

  1. Wu, R. et al. Nat. Methods 8, 677–683 (2011).

    Article  CAS  Google Scholar 

  2. Tan, C.S.H. & Bader, G.D. Nat. Methods 9, 317 (2012).

    Article  CAS  Google Scholar 

  3. Wu, R. et al. Mol. Cell. Proteomics 10, M111.009654 (2011).

    Article  Google Scholar 

  4. Ghaemmaghami, S. et al. Nature 425, 737–741 (2003).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA

    Steven P Gygi, Edward L Huttlin, Ronghu Wu, Wilhelm Haas, Noah Dephoure, Mathew Sowa & Bo Zhai

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  1. Steven P Gygi
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  2. Edward L Huttlin
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  3. Ronghu Wu
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  4. Wilhelm Haas
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  5. Noah Dephoure
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  6. Mathew Sowa
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  7. Bo Zhai
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Correspondence to Steven P Gygi.

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The authors declare no competing financial interests.

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Gygi, S., Huttlin, E., Wu, R. et al. Reply to "Phosphorylation sites of higher stoichiometry are more conserved". Nat Methods 9, 318 (2012). https://doi.org/10.1038/nmeth.1942

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