PXD002281-1

PXD002281 is an original dataset announced via ProteomeXchange.

Title	Identification of HER2 peptides for quantification in formalin-fixed paraffin-embedded breast cancer tissues
Description	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.
HostingRepository	PRIDE
AnnounceDate	2015-07-16
AnnouncementXML	Submission_2015-07-16_02:54:44.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Carine Steiner
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-01 08:08:43	ID requested
⏵ 1	2015-07-16 02:54:46	announced

Steiner C, Tille JC, Lamerz J, Kux van Geijtenbeek S, McKee TA, Venturi M, Rubbia-Brandt L, Hochstrasser D, Cutler P, Lescuyer P, Ducret A, Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues. Mol Cell Proteomics, 14(10):2786-99(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: human receptor tyrosine-protein kinase erbB-2 (HER2), formalin-fixed parrafin-embedded tissues (FFPE), breast cancer, human, LTQ Orbitrap Velos

Ducret Axel
contact affiliation	Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
contact email	axel.ducret@roche.com
lab head
Carine Steiner
contact affiliation	F. Hoffmann-La Roche
contact email	carine.steiner@roche.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/2015/07/PXD002281

PRIDE project URI

• PRIDE
  1. PXD002281
     1. Label: PRIDE project
     2. Name: Identification of HER2 peptides for quantification in formalin-fixed paraffin-embedded breast cancer tissues