Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling Reveals System-Wide Modulation of Protein-Protein Interactions

Viveka Mayya, Deborah H. Lundgren, Sun-Il Hwang, Karim Rezaul, Linfeng Wu, Jimmy K. Eng, Vladimir Rodionov, David K. Han*

*To whom correspondence should be addressed. E-mail: han{at}nso.uchc.edu

This PDF file includes:

• Materials and Methods (incorporating figs. S1 to S4)
• Fig. S5. Accumulation of unique phosphopeptides in the Jurkat phosphoproteome.
• Fig. S6. Distribution of the number of sites in phosphopeptides and the certainty in their localization.
• Fig. S7. Summary of TCR-responsive fold changes in the abundance of phosphopeptides as determined by SILAC experiments.
• Fig. S8. Illustration of the quantification of fold change by targeted MS/MS.
• Fig. S9. Comparison of phosphopeptide spectral count data with SILAC data.
• Fig. S10. Global trends in the phosphorylation data set.
• Fig. S11. Abundance and subcellular localization of phosphoproteins based on protein spectral count data.
• Fig. S12. Putative substrates of ERK during TCR signaling.
• Fig. S13. Validation of Thr²⁶⁰ of BCL11B as a target of ERK.
• Fig. S14. Predicted substrates of Zap70.
• Fig. S15. Primary sequence representation of transcriptional regulators with TCR-responsive phosphorylation sites.
• Fig. S16. Interactions among proteins involved in alternative splicing of mRNA that have TCR-responsive phosphorylation sites.
• Fig. S17. TCR-responsive phosphorylation events in nuclear pore components.
• Fig. S18. Network analysis to assess the influence of inducible phosphorylation of Ser or Thr residues on PPIs.
• Fig. S19. Typical product ion chromatogram showing the lack of phosphorylation in polymerized microtubules.
• Fig. S20. Network representation of nuclear proteins involved in hematopoiesis, lymphoma, and leukemia for which phosphorylation sites were identified in the current study.
• Fig. S21. Schematic of the experimental work flow used to identify TCR-responsive phosphorylation sites by SILAC.
• Fig. S22. Phosphorylated forms of tubulins are excluded from polymerized microtubules.
• Descriptions of supplementary tables
• References

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Other Supplementary Material for this manuscript includes the following:

Tables S1 to S14

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Citation: V. Mayya, D. H. Lundgren, S.-I. Hwang, K. Rezaul, L. Wu, J. K. Eng, V. Rodionov, D. K. Han, Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci. Signal. 2, ra46 (2009).

© 2009 American Association for the Advancement of Science