PXD021893

PXD021893 is an original dataset announced via ProteomeXchange.

Title	Quantification of HER2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) and Frozen Breast Cancer Tissues
Description	Background: Conventional HER2-targeting therapies improve outcomes for patients with HER2-positive breast cancer (BC), defined as tumors showing HER2 protein overexpression by an immunohistochemistry (IHC) assay and/or ERBB2 gene amplification determined by in situ hybridization (ISH). Emerging HER2-targeting compounds show benefit in some patients with neither HER2 protein overexpression nor ERBB2 gene amplification, creating a need for new assays to select HER2-low tumors for treatment with these compounds. Here, we report the analytical performance of a targeted mass spectrometry-based assay for quantifying HER2 protein in formalin fixed paraffin-embedded (FFPE) and frozen BC biopsies. Methods: We used immuno-enrichment coupled to multiple reaction monitoring-mass spectrometry (immuno-MRM-MS) to quantify HER2 protein (as peptide GLQSLPTHDPSPLQR) in 96 frozen and 119 FFPE BC biopsies. We characterized linearity, lower limit of quantification (LLOQ), and intra- and inter-day variation of the assay in frozen and FFPE tissue matrices. We determined concordance between HER2 immuno-MRM and predicate IHC and ISH assays and examined the benefit of multiplexing the assay to include proteins expressed in tumor sub-compartments (e.g. stroma, adipose, lymphocytes, epithelium) to account for tissue heterogeneity. Results: HER2 immuno-MRM assay linearity was ≥103, assay coefficient of variation (CV) was 7.8% (FFPE) and 5.9% (frozen), and endogenous measurement CV was 7.7% (FFPE) and 7.9% (frozen). Immuno-MRM-based HER2 measurements strongly correlated with predicate assay HER2 determinations, and concordance was improved by normalizing to GAPDH. HER2 was quantified above LLOQ in all HER2-low and -negative tumors. Conclusions: Immuno-MRM-MS can be used to quantify HER2 in FFPE and frozen BC biopsies, even at low HER2 expression levels.
HostingRepository	PanoramaPublic
AnnounceDate	2021-07-07
AnnouncementXML	Submission_2021-07-07_09:32:54.742.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jacob Kennedy
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Label:13C(6); Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	QTRAP 6500

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-08 06:09:45	ID requested
⏵ 1	2021-07-07 09:32:55	announced

submitter keyword: HER2, breast cancer, multiple reaction monitoring, Formalin-Fixed Paraffin-Embedded, FFPE, targeted mass spectrometry, immuno-MRM, immunopeptide enrichment, microheterogeneity

Amanda G. Paulovich
contact affiliation	Fred Hutchinson Cancer Research Center
contact email	apaulovi@fredhutch.org
lab head
Jacob Kennedy
contact affiliation	Fred Hutchinson Cancer Research Center
contact email	jkennedy@fhcrc.org
dataset submitter

Panorama Public dataset URI