Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Sci. Signal., 12 January 2010
[DOI: 10.1126/scisignal.2000475]

Supplementary Materials for:

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

[Download PDF]

Technical Details

Format: Adobe Acrobat PDF

Size: 15.8 MB

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).
[Download Supplementary Tables (Compressed)]

Technical Details

Format: Microsoft Excel

Size: 17.6 MB (compressed); 72.0 MB (decompressed)


For files packaged as a compressed archive, in *.zip format; users should download the compressed file to their machine and decompress the file on their local hard drive, using the following instructions.

Instructions for downloading and decompressing files:

1. Create a temporary folder on your machine's hard drive.

2. Save the compressed archive to the temporary folder you created, using the links above.

3. Decompress the compressed file in the temporary folder using decompression software, such as WinZip (Windows; www.winzip.com) or StuffIt Expander (Windows and Mac; www.stuffit.com).

Excel files can be opened and viewed using Microsoft Excel, the spreadsheet module of the freely downloadable Open Office suite, or the freely downloadable Excel Viewer available from Microsoft.


Citation: J. V. Olsen, M. Vermeulen, A. Santamaria, C. Kumar, M. L. Miller, L. J. Jensen, F. Gnad, J. Cox, T. S. Jensen, E. A. Nigg, S. Brunak, M. Mann, Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis. Sci. Signal. 3, ra3 (2010).

© 2010 American Association for the Advancement of Science


To Advertise     Find Products


Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882