Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

Jesper V. Olsen, Michiel Vermeulen, Anna Santamaria, Chanchal Kumar, Martin L. Miller, Lars J. Jensen, Florian Gnad, Jürgen Cox, Thomas S. Jensen, Erich A. Nigg, Søren Brunak, Matthias Mann*

*To whom correspondence should be addressed. E-mail: mmann{at}biochem.mpg.de

This PDF file includes:

• Fig. S1. GO analysis of protein and phosphoproteins subcellular localization.
• Fig. S2. Comparison of steady state HeLa transcriptome with quantified proteome.
• Fig. S3. Peptide and protein ratio reproducibility.
• Fig. S4. Benchmark curves for periodically regulated proteins.
• Fig. S5. Benchmark curves for periodically phosphorylated proteins.
• Fig. S6. Proteomic phenotyping of biological processes (BP).
• Fig. S7. Proteomic phenotyping of cellular components (CC).
• Fig. S8. Proteomic phenotyping of KEGG pathways.
• Fig. S9. WB profiles and MS data of key cell cycle regulated phosphorylation sites.
• Fig. S10. MS identification of S-phase induced MCM phosphopeptides.
• Fig. S11. NetworKIN analysis to identify potential substrates of the DDR kinases.
• Fig. S12. SILAC based absolute phosphorylation site stoichiometry equations.
• Fig. S13. 1D-SDS PAGE loading control of lysates.
• Fig. S14. Data analysis workflow to cluster and circularize proteome and phosphoproteome changes.
• Fig. S15. Coordinate system for circularization.
• Table S4. Enrichment of degradation signals for cell cycle-regulated proteins.
• Table S5. Protein regulated at multiple levels during the cell cycle.
• References

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Format: Adobe Acrobat PDF

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Other Supplementary Material for this manuscript includes the following:

• Table S1. List of all identified proteins (Excel file).
• Table S2. List of all identified phosphopeptides (Excel file).
• Table S3. List of identified protein kinases (Excel file).
• Table S6. List of DNA damage response kinase substrates identified according to the kinase motif pS/pT-Q (Excel file).
• Table S7. List of regulated mitotic phosphorylation sites with high occupancy (Excel file).
• Table S8. Quantification of Western blots using ImageJ software (Excel file).
• Table S9. Overlap of quantified HeLa proteome with known cycle protein complexes (Excel file).

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© 2010 American Association for the Advancement of Science