Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast

Noah Dephoure and Steven P. Gygi*

*To whom correspondence should be addressed. E-mail: sgygi{at}hms.harvard.edu

This PDF file includes:

• Fig. S1. Proteomic analysis of rapamycin-stimulated yeast by hyperplexing.
• Fig. S2. Quantitative reproducibility and accuracy of the hyperplexing method.
• Fig. S3. Protein quantification by SILAC.
• Fig. S4. "3 × 6" hyperplexed analysis of rapamycin-stimulated yeast.
• Fig. S5. Workflow for identification and quantification of a representative protein from the "3 × 6" experiment.
• Fig. S6. Delayed response of the yeast proteome to 200 nM rapamycin.

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Other Supplementary Material for this manuscript includes the following:

• Table S1 (Microsoft Excel format). Log₂ ratios of the proteins from the "2 × 6" experiment.
• Table S2 (Microsoft Excel format). Gene ontology analysis of the regulated proteins from the "2 × 6" and "3 × 6" experiments.
• Table S3 (Microsoft Excel format). Log₂ ratios of the proteins from the "3 × 6" experiment of rapamycin-treated yeast.

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© 2012 American Association for the Advancement of Science