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Journal: Nature Biotechnology
Article Title: / A targeted proteomics-based biomarker pipeline meets analytical requirements for human studies
Author: / Whiteaker, J.R., Lin, C., Kennedy, J., Hou, L., Trute, M., Sokal, I., Yan, P., Schoenherr, R. M., Zhao, L., Voytovich, U.J., Kelly-Spratt, K.S., Krasnoselsky, A., Gafken, P.R., Hogan, J.M., Jones, L.A., Wang, P., Amon, L., Chodosh, L.A., Nelson, P.S., McIntosh, M.W., Kemp, C.J., and Paulovich, A. G.

Supplementary item and number (e.g., Supplementary Fig. 1)

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Titleor caption(this should match what is in the PDF)

Supplementary section 1 text / Identification (discovery) of candidate biomarkers
Supplementary Table S1.1 / Proteomic and Genomic datasets compiled using the Her2/Neu mouse model of breast cancer.
Supplementary Figure S1.1 / Integration of 13 biomarker candidate discovery datasets.
Supplementary Table S1.2 / Sources of candidate biomarkers.
Supplementary section 2 text / Triaging Candidates using Accurate Inclusion Mass Screening (AIMS)
Supplementary Table S2.1 / Tranche hash codes for AIMS datasets.
Supplementary Figure S2.1 / Distribution of peptides identified for each gene in the AIMS and shotgun LC-MS/MS analyses.
Supplementary Table S2.2 / Targeted AIMS and shotgun MS/MS analysis of plasma identified 572 candidates representing all classes of discovery data.
Supplementary Table S2.3 / Method of identification for candidates identified in AIMS and shotgun (SG) MS/MS.
Supplementary section 3 text / Prioritizing Candidates using Semi-Quantitative Selected Reaction Monitoring (SQ-SRM)
Supplementary Figure S3.1 / Workflow for semi-quantitative (SQ) SRM analysis.
Supplementary Figure S3.2 / Summary of the results from the SQ-SRM data.
Supplementary Figure S3.3 / Receiver operating characteristic (ROC) curves generated from SQ-SRM data.
Supplementary Table S3.1 / Summary of the source of discovery for the selected candidate biomarkers for quantitative SRM or immune-SRM assay development.
Supplementary section 4 text / Quantitative SRM (Q-SRM) Assay Development and Characterization
Supplementary Figure S4.1 / Actual cycle time measured in the multiplexed Q-SRM assay.
Supplementary Figure S4.2 / Characterizing individual Q-SRM assays by generating response curves in a plasma matrix.
Supplementary section 5 text / Quantitative Immuno-SRM Assay Development and Characterization
Supplementary Figure S5.1 / Actual cycle time measured in the multiplexed Immuno-SRM assay.
Supplementary Figure S5.2 / Characterizing individual Immuno-SRM assays by generating response curves in a plasma matrix.
Supplementary section 6 text / Verification Studies in the Mouse
Supplementary Figure S6.1 / Verification of candidate biomarkers in individual mice.
Supplementary Figure S6.2 / Measured concentrations for candidates showing elevation in cancer plasma vs. controls.
Supplementary Figure S6.3 / Measured peak area ratios for housekeeping targets.
Supplementary Figure S6.4 / Measurement of candidates by conventional Western blots and ELISA.
Supplementary Figure S6.5 / Correlation of protein concentrations determined by immune-SRM and ELISA.
Supplementary Table S6.1 / Summary of the source of discovery for verified candidate biomarkers in quantitative SRM and immune-SRM assays.
References for Supplementary Sections 1-6
Supplementary Appendix A / Response curves from Q-SRM assay characterization
Supplementary Appendix B / Response curves from immuno-SRM assay characterization
Supplementary Appendix C / Receiver operating characteristic curves
Supplementary Excel file / File name: “Supplemental Data Tables v19 final.xls” (17 worksheets)
Supplementary Data file / Skyline data file name: “mouseQSRM_targets.sky”
Supplementary Data file / Skyline data file name: “mouseImmunoSRM_targets.sky”