Identification of HER2 peptides for quantification in formalin-fixed paraffin-embedded breast cancer tissues

ABSTRACT: The ability to accurately quantify proteins in formalin-fixed paraffin-embedded (FFPE) tissues using targeted mass spectrometry opens exciting perspectives for biomarker discovery. We have developed and evaluated a selected reaction monitoring (SRM) assay for the human receptor tyrosine-protein kinase erbB-2 (HER2) in FFPE breast tumors. Peptide candidates were identified using an untargeted mass spectrometry approach in relevant cell lines. A selected reaction monitoring (SRM) assay was developed for the six best candidate peptides and evaluated for linearity, precision and lower limit of quantification. The six HER2 peptides of interest were then quantified by SRM in a cohort of 40 archival formalin-fixed paraffin-embedded tumor tissues from women with invasive breast carcinomas, showing different levels of HER2 gene amplification. Finally, the agreement was tested between data generated by SRM and data generated using standard clinical pathology methods, namely immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). The high agreement observed indicates that SRM is a suitable method to quantify peptides from FFPE material, and therefore represents a powerful approach for biomarker discovery studies.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Carine Steiner  

LAB HEAD: Ducret Axel

PROVIDER: PXD002281 | Pride | 2015-07-16

REPOSITORIES: Pride