PXD001685

PXD001685 is an original dataset announced via ProteomeXchange.

Title	A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery
Description	Metastasizing breast cancer is an incurable disease. Thus, it is important to find proteins responsible for tumor dissemination, which may be used as biomarkers or treatment targets. In this study, we established the combination of a non-targeted LC-MS/MS discovery and a targeted LC-SRM verification workflow for improved discovery and validation of biomarkers. We collected 80 breast tumors, stratified for estrogen receptor status and development of distant recurrence (DR+/-). After enrichment of N-glycosylated proteins, label-free LC-MS/MS was performed on all of the individual tumors in triplicates. In total, 1515 glycopeptides from 778 proteins were identified, used to create a map of the breast cancer N-glycosylated proteome. Based on the breast cancer N-glycosylated proteome map we constructed a 92-plex targeted label-free LC-SRM panel, enriched for interesting proteins, and analyzed the samples for the selected proteins, resulting in 10 proteins differentially regulated between DR+/DR- tumors. We also compared the LC-SRM results to clinically reported HER2 status. 17 of 18 patients could be classified the same way, demonstrating the clinical accuracy of LC-SRM. In conclusion, we demonstrated the use of a combined non-targeted LC-MS/MS and targeted LC-SRM strategy, at large scale on clinical samples, and identified 10 proteins as potential biomarkers.
HostingRepository	PRIDE
AnnounceDate	2015-06-16
AnnouncementXML	Submission_2015-06-16_12:08:38.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Reto Ossola
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ FT

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-15 06:59:49	ID requested
⏵ 1	2015-06-16 12:08:40	announced

Sj, ö, str, ö, m M, Ossola R, Breslin T, Rinner O, Malmstr, ö, m L, Schmidt A, Aebersold R, Malmstr, ö, m J, Nim, é, us E, A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res, 14(7):2807-18(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: SRM, MRM, Shotgun, Breast cancer, distant recurrence

Emma Nimeus-Malmstroem
contact affiliation	Kirurgiska kliniken, SUS Institutionen för kliniska vetenskaper i Lund Lunds universitet
contact email	emma.nimeus@med.lu.se
lab head
Reto Ossola
contact affiliation	Genedata AG
contact email	retoossola@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/06/PXD001685

PRIDE project URI

• PRIDE
  1. PXD001685
     1. Label: PRIDE project
     2. Name: A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery