<<< Full experiment listing


PXD027134 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleThe addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies
DescriptionMass spectrometry-based targeted proteomics allows objective protein quantitation of clinical biomarkers from a single section of formalin-fixed, paraffin-embedded (FFPE) tumor tissue biopsies. We combined high-field asymmetric waveform ion mobility spectrometry (FAIMS) and parallel reaction monitoring (PRM) to increase assay sensitivity. The modular nature of the FAIMS source allowed direct comparison of the performance of FAIMS-PRM to PRM. Limits of quantitation were determined by spiking synthetic peptides into a human spleen matrix. In addition, 20 clinical samples were analyzed using FAIMS-PRM and the quantitation of HER2 was compared with that obtained with the Ventana immunohistochemistry assay. FAIMS-PRM improved the overall signal-to-noise ratio over that from PRM and increased assay sensitivity in FFPE tissue analysis for four (HER2, EGFR, cMET, and KRAS) of five proteins of clinical interest. FAIMS-PRM enabled sensitive quantitation of basal HER2 expression in breast cancer samples classified as HER2 negative by immunohistochemistry. Furthermore, we determined the degree of FAIMS-dependent background reduction and showed that this correlated with an improved lower limit of quantitation with FAIMS. FAIMS-PRM is anticipated to benefit clinical trials in which multiple biomarker questions must be addressed and the availability of tumor biopsy samples is limited.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterSteve Sweet
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListCarbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-07-06 21:50:23ID requested
12022-03-24 20:09:10announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: FAIMS PRM HER2
Contact List
Yeoun Jin Kim
contact affiliationTranslational Medicine, Oncology R&D, AstraZeneca
contact emailyeounjin.kim@astrazeneca.com
lab head
Steve Sweet
contact affiliationTranslational Medicine, Oncology R&D, AstraZeneca
contact emailsteve.sweet@astrazeneca.com
dataset submitter
Full Dataset Link List
Panorama Public dataset URI