Supplementary Materials

Supplementary Materials for:

Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-β

Rochelle C. J. D'Souza, Anna M. Knittle, Nagarjuna Nagaraj, Maarten van Dinther, Chunaram Choudhary, Peter ten Dijke, Matthias Mann, Kirti Sharma*

*Corresponding author. E-mail: kisharma@biochem.mpg.de

This PDF file includes:

  • Fig. S1. Schematic illustration of the MS experimental design.
  • Fig. S2. Evaluation of the reproducibility of MS replicates.
  • Fig. S3. Functional assessment of PRSS23 in TGF-β–induced EMT.
  • Fig. S4. Heatmap of CDK-specific phosphorylation sites regulated by TGF-β.
  • Fig. S5. Protein interaction network of proteins with TGF-β–induced changes in abundance or phosphorylation.

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Technical Details

Format: Adobe Acrobat PDF

Size: 2.33 MB

Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Protein groups identified in proteome MS analysis.
  • Table S2 (Microsoft Excel format). Protein groups quantified from proteome MS analysis.
  • Table S3 (Microsoft Excel format). Functional annotation enrichment analysis of proteins with TGF-β–regulated abundance.
  • Table S4 (Microsoft Excel format). Cluster-specific functional annotation enrichment analysis of proteins with TGF-β–regulated abundance.
  • Table S5 (Microsoft Excel format). 1D annotation enrichment analysis for KEGG pathways and time point–specific quantification of corresponding pathway proteins.
  • Table S6 (Microsoft Excel format). Upstream regulator analysis of proteins with TGF-β–regulated abundance.
  • Table S7 (Microsoft Excel format). Phosphosites quantified from MS analysis.
  • Table S8 (Microsoft Excel format). Functional annotation enrichment analysis of proteins with TGF-β–regulated phosphorylation.
  • Table S9 (Microsoft Excel format). Functional annotation enrichment analysis of proteins with TGF-β–regulated abundance or phosphorylation or both.
  • Table S10 (Microsoft Excel format). Explanation for proteins and phosphopeptides tables from MaxQuant.

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Citation: R. C. J. D'Souza, A. M. Knittle, N. Nagaraj, M. van Dinther, C. Choudhary, P. ten Dijke, M. Mann, K. Sharma, Time-resolved dissection of early phosphoproteomeand ensuing proteome changes in response to TGF-β. Sci. Signal. 7, rs5 (2014).

© 2014 American Association for the Advancement of Science