Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1784769105193074688 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9381555 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT sweetsteve theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT chaindavid theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT yuwen theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT martinphilip theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT rebelattomarlon theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT chambersandrew theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT cecchifabiola theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT kimyeounjin theadditionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT sweetsteve additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT chaindavid additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT yuwen additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT martinphilip additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT rebelattomarlon additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT chambersandrew additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT cecchifabiola additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies AT kimyeounjin additionoffaimsincreasestargetedproteomicssensitivityfromffpetumorbiopsies |