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A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery.

Type Information
Nr 50 (Research article)
Authors Sjöström, Martin; Ossola, Reto; Breslin, Thomas; Rinner, Oliver; Malmström, Lars; Schmidt, Alexander; Aebersold, Ruedi; Malmström, Johan; Niméus, Emma
Title A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery.
Journal J Proteome Res (2015) 14(7) 2807-18
DOI 10.1021/acs.jproteome.5b00315
Citations 32 citations (journal impact: 5.0)
Abstract It is of highest importance to find proteins responsible for breast cancer dissemination for use as biomarkers or treatment targets. We established and performed a combined non-targeted LC-MSMS and a targeted LC-SRM workflow for discovery and validation of protein biomarkers. 80 breast tumors stratified for estrogen receptor status and development of distant recurrence DR- were collected. After enrichment of N-glycosylated peptides label-free LC-MSMS was performed on each individual tumor in triplicate. In total 1515 glycopeptides from 778 proteins were identified and used to create a map of the breast cancer N-glycosylated proteome. Based on this specific proteome map we constructed a 92-plex targeted label-free LC-SRM panel. These proteins were quantified across samples by LC-SRM resulting in 10 proteins consistently differentially regulated between DRDR- tumors. Five proteins were further validated in a separate cohort as prognostic biomarkers at the gene expression level. We also compared the LC-SRM results to clinically reported HER2 status demonstrating its clinical accuracy. In conclusion we demonstrate a combined mass spectrometry strategy at large scale on clinical samples leading to the identification and validation of five proteins as potential biomarkers for breast cancer recurrence. All MS data are available via ProteomeXchange and PASSEL with identifiers PXD001685 and PASS00643.