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

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A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. / Sjöström, Martin; Ossola, Reto; Breslin, Thomas; Rinner, Oliver; Malmstroem, Lars; Schmidt, Alexander; Aebersold, Ruedi; Malmström, Johan; Niméus, Emma.

In: Journal of Proteome Research, Vol. 14, No. 7, 2015, p. 2807-2818.

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Sjöström, Martin ; Ossola, Reto ; Breslin, Thomas ; Rinner, Oliver ; Malmstroem, Lars ; Schmidt, Alexander ; Aebersold, Ruedi ; Malmström, Johan ; Niméus, Emma. / A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. In: Journal of Proteome Research. 2015 ; Vol. 14, No. 7. pp. 2807-2818.

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TY - JOUR

T1 - A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery

AU - Sjöström, Martin

AU - Ossola, Reto

AU - Breslin, Thomas

AU - Rinner, Oliver

AU - Malmstroem, Lars

AU - Schmidt, Alexander

AU - Aebersold, Ruedi

AU - Malmström, Johan

AU - Niméus, Emma

PY - 2015

Y1 - 2015

N2 - 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 nontargeted LC MS/MS and a targeted LC SRM workflow for discovery and validation of protein biomarkers. Eighty breast tumors, stratified for estrogen receptor status and development of distant recurrence (DR +/-), were collected. After enrichment of N-glycosylated peptides, label-free LC-MS/MS 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 DR+/DR- 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.

AB - 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 nontargeted LC MS/MS and a targeted LC SRM workflow for discovery and validation of protein biomarkers. Eighty breast tumors, stratified for estrogen receptor status and development of distant recurrence (DR +/-), were collected. After enrichment of N-glycosylated peptides, label-free LC-MS/MS 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 DR+/DR- 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.

KW - breast cancer

KW - biomarker

KW - shotgun proteomics

KW - targeted proteomics

KW - LC-MS/MS

KW - SRM

KW - MRM

KW - N-glycosylation

KW - estrogen receptor

KW - HER2

U2 - 10.1021/acs.jproteome.5b00315

DO - 10.1021/acs.jproteome.5b00315

M3 - Article

VL - 14

SP - 2807

EP - 2818

JO - Journal of Proteome Research

T2 - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 7

ER -