PXD025135

PXD025135 is an original dataset announced via ProteomeXchange.

Title	Biomarker Discovery in FFPE tissues by SRM
Description	The identification of clinically relevant biomarkers represents an important challenge in oncology. This can be addressed with biomarker discovery studies in formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring large sets of proteins in FFPE tissues remains challenging. Here we demonstrate the use of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) as a promising technique for such applications. An LC-MS/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples. 200 proteins were measured in 48 triple-negative (TNBC), 19 HER2-overexpressing, and 20 luminal A breast tumors. Quantitative information was obtained for 185 proteins, including known markers such as HER2, hormone receptors, ki-67, or inflammation-related proteins. MS results for these proteins matched IHC or CISH data. In addition, several proteins representing potential biomarkers were identified as differentially expressed in TNBC samples. Comparison of our results with data from the literature showed that MS assays can reliably and simultaneously measure many proteins in FFPE tissues using the analysis of surrogate peptides. Therefore LC-MS/MS is a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.
HostingRepository	PanoramaPublic
AnnounceDate	2022-09-25
AnnouncementXML	Submission_2022-09-25_21:45:21.469.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Carine Steiner
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Label:13C(6)15N(2); Label:13C(6)15N(4); Carbamidomethyl
Instrument	TSQ Vantage

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-31 11:23:54	ID requested
⏵ 1	2022-09-25 21:45:22	announced

Steiner C, Lescuyer P, Cutler P, Tille JC, Ducret A, Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays. Mol Cell Proteomics, 21(11):100416(2022) [pubmed]

submitter keyword: SRM, triple-negative breast cancer, luminal A breast cancer, HER2 breast cancer, formalin-fixed paraffin-embedded (FFPE), biomarker discovery, targeted mass spectrometry

Axel Ducret
contact affiliation	F. Hoffmann-La Roche
contact email	axel.ducret@roche.com
lab head
Carine Steiner
contact affiliation	F. Hoffmann-La Roche
contact email	carine.steiner@roche.com
dataset submitter

Panorama Public dataset URI