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The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies

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 monitor...

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Autores principales: Sweet, Steve, Chain, David, Yu, Wen, Martin, Philip, Rebelatto, Marlon, Chambers, Andrew, Cecchi, Fabiola, Kim, Yeoun Jin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9381555/
https://www.ncbi.nlm.nih.gov/pubmed/35974054
http://dx.doi.org/10.1038/s41598-022-16358-1
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author Sweet, Steve
Chain, David
Yu, Wen
Martin, Philip
Rebelatto, Marlon
Chambers, Andrew
Cecchi, Fabiola
Kim, Yeoun Jin
author_facet Sweet, Steve
Chain, David
Yu, Wen
Martin, Philip
Rebelatto, Marlon
Chambers, Andrew
Cecchi, Fabiola
Kim, Yeoun Jin
author_sort Sweet, Steve
collection PubMed
description 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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spelling pubmed-93815552022-08-18 The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies Sweet, Steve Chain, David Yu, Wen Martin, Philip Rebelatto, Marlon Chambers, Andrew Cecchi, Fabiola Kim, Yeoun Jin Sci Rep Article 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. Nature Publishing Group UK 2022-08-16 /pmc/articles/PMC9381555/ /pubmed/35974054 http://dx.doi.org/10.1038/s41598-022-16358-1 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Sweet, Steve
Chain, David
Yu, Wen
Martin, Philip
Rebelatto, Marlon
Chambers, Andrew
Cecchi, Fabiola
Kim, Yeoun Jin
The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies
title The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies
title_full The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies
title_fullStr The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies
title_full_unstemmed The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies
title_short The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies
title_sort addition of faims increases targeted proteomics sensitivity from ffpe tumor biopsies
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9381555/
https://www.ncbi.nlm.nih.gov/pubmed/35974054
http://dx.doi.org/10.1038/s41598-022-16358-1
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