Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues

Supplemental Data

  • combined supplementary figures - Figure S1-S5
  • Supplemenatry_figure_legends - Supplemenatry_figure_legends
  • Table_S1 - Table S1: Summary of transitions monitored by SRM for six HER2 and three KRT19 peptides as well as for their heavy internal standards.
  • Table_S2 - Table S2A: HER2 peptide identifications by untargeted mass spectrometry (EasyProt). Table S2B: HER2 peptide identifications by untargeted mass spectrometry (SEQUEST).
  • Table_S3 - Table S3 Comparison of the linear response in a P. furiosus and in a triple-negative breast cancer matrix. Average slopes, intercepts and r square values (r2) are given for the entire calibration domain as well as for the 8 upper calibrators in log10/log10 representation.
  • Table_S4 - Table S4 (A) Intra-day and (B) inter-day linearity data for the 6 HER2 peptides. Linearity was assessed in a bacterial protein digest of Pyroccoccus furiosus (load on column corresponding to approximately 200 ng of proteins). The calibration curves were plotted as the log10 of the peak area ratio (unlabeled peptide / heavy-labeled peptide) against the log10 of the spiked unlabeled peptide on column. The spiked unlabeled peptide ranged from 0.012 to 100 fmol on column, whereas the spiked heavy-labeled peptide was set at a fixed amount of 1 fmol on column.
  • Table_S5 - Table S5A Precision of analytical method: average peptide amounts and CV of 3 repeated injections of the same tissue extract. Table S5B Precision of sample preparation: average peptide amounts and CV of 3 single injections of extracts from adjacent tissue slices.
  • Table_S6 - Table S6: Quantification and normalization data for the 40 HER2 samples included in the cohort.
  • Table_S7 - Table S7: Classification of HER2 tumors by IHC, FISH, and by the SRM data for peptides ELVSSEFSR and GLQSLPTHDPDPLQR.
  • Table_S8 - Table S8: Prediction of IHC scores by peptide ELVSEFSR and FISH categories by peptide GLQSLPTHDPDPLQR. Prediction of HER2 amplification status (ASCO) by ELVSEFSR or GLQSLPTHDPDPLQR.
  • Table_S9 - Table S9: Batches and order used for sample collection, extraction and LC-MS analysis.
  • Supplementary table legends - Supplemenatry table legends
  • Supplementary materials and methods - Supplementary materials and methods