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Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

Lundby, Alicia, Secher, Anna, Lage, Kasper, Nordsborg, Nikolai B., Dmytriyev, Anatoliy, Lundby, Carsten, Olsen, Jesper V.·2012·Nature Communications
DOI 10.1038/ncomms1871PMC PMC3621391
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  • Phosphorylation at corresponding sites in SNX1, SNX3, SNX12, and SNX17 has been reported in various cancer types.

    “phosphorylation at corresponding sites in SNX1, SNX3, SNX12, and SNX17 has been reported in various cancer types (47, 48, 49, 50, 51, 52)”

    From Phosphorylation of SNX17 impedes activation of Retriever-mediated sorting (2025) · cites this paper as [49]

    The Results section reports phosphorylation sites across rat tissues, and the Discussion mentions cancer only in general terms; neither identifies the corresponding sites in SNX1, SNX3, SNX12, or SNX17 in cancer types. Searches for those SNX proteins and for sorting-neXin phosphorylation in cancer found no passage addressing the claim. (LLM, conf=0.75)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 48

  1. Schmelzle, K. et al. Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes 55, 2171 (2006). · DOI
  2. Rhodes, C. J. Type 2 diabetes-a matter of beta-cell life and death? Science 307, 380 (2005). · DOI
  3. Vivanco, I. & Sawyers, C. L. The phosphatidylinositol 3-Kinase AKT pathway in human cancer. Nat. Rev. Cancer 2, 489 (2002). · DOI
  4. Jope, R. S. Anti-bipolar therapy: mechanism of action of lithium. Mol. Psychiatry 4, 117 (1999). · DOI
  5. Perez, J. et al. Abnormalities of cAMP signaling in affective disorders: implication for pathophysiology and treatment. Bipolar Disord 2, 27 (2000). · DOI
  6. Huang, P. H., Xu, A. M. & White, F. M. Oncogenic EGFR signaling networks in glioma. Sci. Signal. 2, re6 (2009).
  7. Yamamoto, Y. et al. Activating mutation of D835 within the activation loop of FLT3 in human hematologic malignancies. Blood 97, 2434 (2001). · DOI
  8. Macek, B., Mann, M. & Olsen, J. V. Global and site-specific quantitative phosphoproteomics: principles and applications. Annu. Rev. Pharmacol. Toxicol. 49, 199 (2009). · DOI
  9. Posewitz, M. C. & Tempst, P. Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal. Chem. 71, 2883 (1999). · DOI
  10. Pinkse, M. W. et al. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem. 76, 3935 (2004). · DOI
  11. Sugiyama, N. et al. Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol. Cell. Proteomics 6, 1103 (2007). · DOI
  12. Ong, S. E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376 (2002). · DOI · Paper page
  13. Ross, P. L. et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154 (2004). · DOI · Paper page
  14. Makarov, A. et al. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78, 2113 (2006). · DOI
  15. Olsen, J. V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635 (2006). · DOI
  16. Matsuoka, S. et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160 (2007). · DOI · Paper page
  17. Choudhary, C. et al. Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes. Mol. Cell 36, 326 (2009). · DOI
  18. Olsen, J. V. et al. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci. Signal. 3, ra3 (2010). · DOI
  19. Huttlin, E. L. et al. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174 (2010). · DOI · Paper page
  20. Monetti, M. et al. Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat. Methods 8, 655 (2011). · DOI
  21. Wisniewski, J. R. et al. Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology. J. Proteome Res. 9, 3280 (2010). · DOI
  22. Jedrychowski, M. P. et al. Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol. Cell. Proteomics 10, M111.009910 (2011). · DOI
  23. Abbott, A. Laboratory animals: the renaissance rat. Nature 428, 464 (2004). · DOI
  24. Lindblad-Toh, K. Genome sequencing: three's company. Nature 428, 475 (2004). · DOI
  25. Olsen, J. V. et al. Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4, 709 (2007). · DOI
  26. Olsen, J. V. et al. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol. Cell. Proteomics 8, 2759 (2009). · DOI · Paper page
  27. Nagaraj, N. et al. Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J. Proteome Res. 9, 6786 (2010). · DOI
  28. Svensson, M. et al. Heat stabilization of the tissue proteome: a new technology for improved proteomics. J. Proteome Res. 8, 974 (2009). · DOI
  29. Lage, K. et al. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc. Natl Acad. Sci. USA 105, 20870 (2008). · DOI · Paper page
  30. Lage, K. et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat. Biotechnol. 25, 309 (2007). · DOI
  31. Lage, K. et al. Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol. Syst. Biol. 6, 381 (2010). · DOI
  32. Bergholdt, R. et al. Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol. 8, R253 (2007). · DOI
  33. Pasini, E. M. et al. Deep coverage mouse red blood cell proteome: a first comparison with the human red blood cell. Mol. Cell. Proteomics 7, 1317 (2008). · DOI
  34. Lundberg, E. et al. Defining the transcriptome and proteome in three functionally different human cell lines. Mol. Syst. Biol. 6, 450 (2010). · DOI · Paper page
  35. Bondar, V. M. et al. Inhibition of the phosphatidylinositol 3′-kinase-AKT pathway induces apoptosis in pancreatic carcinoma cells in vitro and in vivo. Mol. Cancer Ther. 1, 989 (2002).
  36. Meng, R., Gotz, C. & Montenarh, M. The role of protein kinase CK2 in the regulation of the insulin production of pancreatic islets. Biochem. Biophys. Res. Commun. 401, 203 (2010). · DOI
  37. Lemmon, M. A. & Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 141, 1117 (2010). · DOI · Paper page
  38. Fan, J. et al. Tyrosine phosphorylation of lactate dehydrogenase A is important for NADH/NAD(+) redox homeostasis in cancer cells. Mol. Cell. Biol. 31, 4938 (2011). · DOI
  39. Hitosugi, T. et al. Tyrosine phosphorylation of mitochondrial pyruvate dehydrogenase kinase 1 is important for cancer metabolism. Mol. Cell 44, 864 (2011). · DOI
  40. Rigbolt, K. T. et al. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci. Signal. 4, rs3 (2011). · DOI · Paper page
  41. Treisman, R. Regulation of transcription by MAP kinase cascades. Curr. Opin. Cell Biol. 8, 205 (1996). · DOI · Paper page
  42. Bergstrom, J. Muscle electrolytes in man - determined by neutron activation analysis on needle biopsy specimens - study on normal subjects, kidney patients, and patients with chronic diarrhoea. Scand. J. Clin. Lab. Inv. 14, 1 (1962). · DOI
  43. Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896 (2007). · DOI · Paper page
  44. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367 (2008). · DOI · Paper page
  45. Cox, J. et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat. Protoc. 4, 698 (2009). · DOI
  46. Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794 (2011). · DOI
  47. Geiger, T., Cox, J. & Mann, M. Proteomic changes resulting from gene copy number variations in cancer cells. PLoS Genet. 6, e1001090 (2010). · DOI
  48. Colaert, N. et al. Improved visualization of protein consensus sequences by iceLogo. Nat. Methods 6, 786 (2009). · DOI

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Metadata

Authors
Lundby, A., Secher, A., Lage, K., Nordsborg, N. B., Dmytriyev, A., Lundby, C., & Olsen, J. V.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2012-06-06
Volume
3
Issue
1
ISSN
2041-1723
DOI
10.1038/ncomms1871
PMC
PMC3621391
Cited by
343
References
6
Language
en
Licence

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