Supplementary Materials

Supplementary Materials for:

Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis

Ana Paula Oliveira,* Christina Ludwig, Mattia Zampieri, Hendrik Weisser, Ruedi Aebersold, Uwe Sauer

*Corresponding author. E-mail: oliveira{at}imsb.biol.ethz.ch (A.P.O.); sauer{at}ethz.ch (U.S.)

This PDF file includes:

  • Text S1. Details of the experimental setup: Strain, growth conditions, and dynamic perturbations.
  • Fig. S1. Assessment of the quality of the quantified phosphopeptide intensities obtained with OpenMS based on Spearman correlation coefficients.
  • Fig. S2. Comparative assessment of data quality before and after phosphopeptide lumping.
  • Fig. S3. Comparison of the rapamycin-responsive phosphoproteome across the present and previous studies.
  • Fig. S4. Dynamic phosphopeptide profiles of TOR-related proteins reliably quantified with FC > 2 in at least two experimental perturbations.
  • Fig. S5. Distribution of timeFC2 for the reliably quantified TOR-related proteins.
  • Fig. S6. All overrepresented docking motifs identified with MotifX.
  • Fig. S7. Heatmap of dynamic responses for the early bin phosphopeptides with the motif RRxS*.
  • Fig. S8. Clustering results of phosphopeptides quantified in all three experimental perturbations.
  • Fig. S9. Clustering results of phosphopeptides reliably quantified with FC > 2 after nitrogen downshift and rapamycin treatment.
  • Fig. S10. Clustering results of phosphopeptides reliably quantified with FC > 2 after nitrogen upshift and rapamycin treatment.
  • Fig. S11. Clustering results of phosphopeptides reliably quantified with FC > 2 after nitrogen upshift and downshift.
  • Fig. S12. Number of identified phosphosites per peptide and phosphoserines, phosphothreonines, and phosphotyrosines.
  • Fig. S13. Automated label-free data analysis pipeline using OpenMS.

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Technical Details

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Phosphosite localization scores determined using the LuciPHOr algorithm.
  • Table S2 (Microsoft Excel format). Intensities of phosphopeptides identified and quantified with OpenMS.
  • Table S3 (Microsoft Excel format). Intensities of lumped phosphopeptides and correspondence between original (unlumped) and lumped phosphopeptides.
  • Table S4 (.txt format). Phosphosite positions associated with the lumped phosphopeptides.
  • Table S5 (Microsoft Excel format). Reliably quantified phosphopeptides with more than twofold change (fold changes, P values, and temporal bin assignments).
  • Table S6 (Microsoft Excel format). Known TOR-related proteins collected from the literature.
  • Table S7 (Microsoft Excel format). Pre-aligned peptide sequences used for the docking motif search, centered at the regulated phosphosite and comprising ±7 residues.
  • Table S8 (Microsoft Excel format). Clustering results associated with figs. S8 to S11.
  • Table S9 (Microsoft Word format). Early bin phosphopeptides regulated in at least two perturbations.
  • Table S10 (Microsoft Excel format). Significantly correlated phosphopeptide/metabolite pairs used to infer the functional role of enzyme phosphorylation.
  • Table S11 (Microsoft Word format). Average number of phosphorylation sites in yeast protein kinases relative to other protein types.
  • Table S12 (Microsoft Excel format). Results (z scores) from the reporter kinase analysis.
  • Table S13 (Microsoft Word format). Parameter settings used in the automated labelfree analysis pipeline in OpenMS.

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Citation: A. P. Oliveira, C. Ludwig, M. Zampieri, H. Weisser, R. Aebersold, U. Sauer, Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Sci. Signal. 8, rs4 (2015).

© 2015 American Association for the Advancement of Science