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PXD021893 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleQuantification of HER2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) and Frozen Breast Cancer Tissues
DescriptionBackground: 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterJacob Kennedy
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListCarbamidomethyl; Label:13C(6); Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentQTRAP 6500
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-10-08 06:09:45ID requested
12021-07-07 09:32:55announced
Publication List
Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG, Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Clin Chem, 67(7):1008-1018(2021) [pubmed]
Keyword List
submitter keyword: HER2, breast cancer, multiple reaction monitoring, Formalin-Fixed Paraffin-Embedded, FFPE, targeted mass spectrometry, immuno-MRM, immunopeptide enrichment, microheterogeneity
Contact List
Amanda G. Paulovich
contact affiliationFred Hutchinson Cancer Research Center
contact emailapaulovi@fredhutch.org
lab head
Jacob Kennedy
contact affiliationFred Hutchinson Cancer Research Center
contact emailjkennedy@fhcrc.org
dataset submitter
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