1. 1 Quantitative Proteomic Sample Set Amounts displayed as fmols per µg of digested yeast lysate Each sample theoretically contains 15 µg of digested yeast lysate

2. 2 Quantitative Proteomic Sample Set Green bars represent the Tier 1 protein CAH1 Red bars represent the Tier 2 protein PPIA Blue bars represent the Tier 3 protein CATA Gray bars represent PRDX1

3. 3 Numbers displayed are theoretical fold change calculated as: Theoretical amount for sample 5/theoretical amount for sample x where x = A, B,C, or D) Quantitative Proteomic Sample Set – Fold Change

4. 4 Mixture of 10 Digested Target Human Proteins Digested Yeast Lysate Mixture of 20 IS Peptides Individual Stocks of Target Human Proteins Yeast Lysate Five samples containing digested yeast lysate and digested target human proteins Five samples containing digested yeast lysate, digested target human proteins, and IS peptides Individual Stocks of IS Peptides AAA LC-MS/MS LC-MS e LC-MRM Quantitative Proteomic Sample Prep Workflow AAA Trypsin DigestTrypsin Digests

5. 5 Quantitative Proteomic Sample Set: Measured Fold Change Accuracy by MRM