WITHDRAWN: Quantitative mass spectrometry analysis of PD-L1 protein expression, N-glycosylation and expression stoichiometry with PD-1 and PD-L2 in human melanoma

Morales-Betanzos, Carlos A.; Lee, Hyoung-joo; González-Ericsson, Paula I.; Balko, Justin M.; Johnson, Douglas B.; Zimmerman, Lisa J.; Liebler, D.C.

doi:10.1074/mcp.m117.067942

Cited by 1 publication

(2 citation statements)

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“…In the PRM method, fragment ion selection is carried out after acquisition from the complete MS/MS data set, and more stringent separation of signal from non-specific background is possible when relying on the high-resolution data. To further increase sensitivity, and if sufficient sample is available (typically at least 10× more than for direct analysis), front-end fractionation or immunoprecipitation can be added into the workflow 17,18 . For clinical samples with limited material, incorporation of a gas-phase ion mobility precursor selection step is an alternative approach to enhance sensitivity.…”

Section: Discussionmentioning

confidence: 99%

“…Although sample fractionation or enrichment strategies can be applied to reduce complexity and non-specific background signals 17,18 , they also decrease the overall throughput and, more importantly, are not feasible when there is limited availability of clinical samples. Ion mobility spectrometry (IMS) can reduce complexity in the gas phase without having to fractionate samples in advance and has been applied to peptide quantitation by SRM [19][20][21][22] .…”

Section: Introductionmentioning

confidence: 99%

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The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies

Sweet

Chain

Yao

et al. 2022

Preprint

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Mass 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.

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Section: Discussionmentioning

confidence: 99%