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

Sjöström, Martin LU ; Ossola, Reto; Breslin, Thomas LU ; Rinner, Oliver; Malmstroem, Lars; Schmidt, Alexander; Aebersold, Ruedi; Malmström, Johan LU and Niméus, Emma LU (2015) In Journal of Proteome Research 14(7). p.2807-2818
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 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... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
breast cancer, biomarker, shotgun proteomics, targeted proteomics, LC-MS/MS, SRM, MRM, N-glycosylation, estrogen receptor, HER2
in
Journal of Proteome Research
volume
14
issue
7
pages
2807 - 2818
publisher
The American Chemical Society
external identifiers
  • wos:000357624400007
  • scopus:84939840284
ISSN
1535-3893
DOI
10.1021/acs.jproteome.5b00315
language
English
LU publication?
yes
id
ee5dbecc-6268-435a-960b-96e2830d6d58 (old id 7789434)
date added to LUP
2015-09-01 16:07:06
date last changed
2017-07-30 03:23:05
@article{ee5dbecc-6268-435a-960b-96e2830d6d58,
  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 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.},
  author       = {Sjöström, Martin and Ossola, Reto and Breslin, Thomas and Rinner, Oliver and Malmstroem, Lars and Schmidt, Alexander and Aebersold, Ruedi and Malmström, Johan and Niméus, Emma},
  issn         = {1535-3893},
  keyword      = {breast cancer,biomarker,shotgun proteomics,targeted proteomics,LC-MS/MS,SRM,MRM,N-glycosylation,estrogen receptor,HER2},
  language     = {eng},
  number       = {7},
  pages        = {2807--2818},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.5b00315},
  volume       = {14},
  year         = {2015},
}