Supplementary Materials

Supplementary Materials for:

Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics

Ruth Hüttenhain,* Martin Soste, Nathalie Selevsek, Hannes Röst, Atul Sethi, Christine Carapito, Terry Farrah, Eric W. Deutsch, Ulrike Kusebauch, Robert L. Moritz, Emma Niméus-Malmström, Oliver Rinner, Ruedi Aebersold*

*To whom correspondence should be addressed. E-mail: aebersold{at}imsb.biol.ethz.ch (R.A.); huettenhain{at}imsb.biol.ethz.ch (R.H.)

Published 11 July 2012, Sci. Transl. Med. 4, 142ra94 (2012)
DOI: 10.1126/scitranslmed.3003989

This PDF file includes:

  • Materials and Methods
  • Results
  • Fig. S1. Success rate of the assay generation and detectability depending on the peptide selection source.
  • Fig. S2. mProphet results for the detectability test for cancer-associated proteins in depleted plasma and urine.
  • Fig. S3. Distribution of estimated concentrations extracted from Human Plasma and Urine PA of detected proteins in crude plasma, depleted plasma, and urine.
  • Fig. S4. Transition specificity of detected peptides in the background of the Human PA.
  • Fig. S5. Functional protein interaction network for ovarian clear cell carcinoma.
  • Fig. S6. Functional protein interaction network for pancreatic cancer.
  • Fig. S7. Functional protein interaction network for pancreatic neuroendocrine cancer.
  • Fig. S8. Functional protein interaction network for childhood medulloblastoma.
  • Fig. S9. Functional protein interaction network for glioblastoma.
  • Fig. S10. Functional protein interaction network for breast cancer.
  • Fig. S11. Functional protein interaction network for colorectal cancer.
  • Fig. S12. mProphet results for the first round of the detectability test for cancerassociated proteins in depleted plasma and urine.
  • Fig. S13. Transition specificity of detected peptides in the background of the complete human proteome.
  • Captions for Tables S1 to S6

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Cancer-associated proteins.
  • Table S2 (Microsoft Excel format). Proteotypic peptides for SRM assay generation.
  • Table S3 (Microsoft Excel format). SRM assays for cancer-associated proteins.
  • Table S4 (Microsoft Excel format). Detected peptides and proteins of the cancerassociated proteins in depleted plasma.
  • Table S5 (Microsoft Excel format). Detected peptides and proteins of the cancerassociated proteins in plasma.
  • Table S6 (Microsoft Excel format). Detected peptides and proteins of the cancerassociated proteins in urine.

[Download Tables S1-S6]

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