PXD002281 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-06-01 08:08:43 | ID requested | |
⏵ 1 | 2015-07-16 02:54:46 | announced | |
Publication List
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] |
Keyword List
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 |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002281
- Label: PRIDE project
- Name: Identification of HER2 peptides for quantification in formalin-fixed paraffin-embedded breast cancer tissues