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A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies

[Image: see text] Mass spectrometry (MS)-based proteomic measurements are uniquely poised to impact the development of cell and gene therapies. With the adoption of rigorous instrumental performance qualifications (PQs), large-scale proteomics can move from a research to a manufacturing control tool...

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Autores principales: Lombard-Banek, Camille, Pohl, Kerstin I., Kwee, Edward J., Elliott, John T., Schiel, John E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2022
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9087334/
https://www.ncbi.nlm.nih.gov/pubmed/35404046
http://dx.doi.org/10.1021/acs.jproteome.1c00887
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author Lombard-Banek, Camille
Pohl, Kerstin I.
Kwee, Edward J.
Elliott, John T.
Schiel, John E.
author_facet Lombard-Banek, Camille
Pohl, Kerstin I.
Kwee, Edward J.
Elliott, John T.
Schiel, John E.
author_sort Lombard-Banek, Camille
collection PubMed
description [Image: see text] Mass spectrometry (MS)-based proteomic measurements are uniquely poised to impact the development of cell and gene therapies. With the adoption of rigorous instrumental performance qualifications (PQs), large-scale proteomics can move from a research to a manufacturing control tool. Especially suited, data-independent acquisition (DIA) approaches have distinctive qualities to extend multiattribute method (MAM) principles to characterize the proteome of cell therapies. Here, we describe the development of a DIA method for the sensitive identification and quantification of proteins on a Q-TOF instrument. Using the improved acquisition parameters, we defined a control strategy and highlighted some metrics to improve the reproducibility of SWATH acquisition-based proteomic measurements. Finally, we applied the method to analyze the proteome of Jurkat cells that here serves as a model for human T-cells. Raw and processed data were deposited in PRIDE (PXD029780).
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spelling pubmed-90873342022-05-11 A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies Lombard-Banek, Camille Pohl, Kerstin I. Kwee, Edward J. Elliott, John T. Schiel, John E. J Proteome Res [Image: see text] Mass spectrometry (MS)-based proteomic measurements are uniquely poised to impact the development of cell and gene therapies. With the adoption of rigorous instrumental performance qualifications (PQs), large-scale proteomics can move from a research to a manufacturing control tool. Especially suited, data-independent acquisition (DIA) approaches have distinctive qualities to extend multiattribute method (MAM) principles to characterize the proteome of cell therapies. Here, we describe the development of a DIA method for the sensitive identification and quantification of proteins on a Q-TOF instrument. Using the improved acquisition parameters, we defined a control strategy and highlighted some metrics to improve the reproducibility of SWATH acquisition-based proteomic measurements. Finally, we applied the method to analyze the proteome of Jurkat cells that here serves as a model for human T-cells. Raw and processed data were deposited in PRIDE (PXD029780). American Chemical Society 2022-04-11 2022-05-06 /pmc/articles/PMC9087334/ /pubmed/35404046 http://dx.doi.org/10.1021/acs.jproteome.1c00887 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Lombard-Banek, Camille
Pohl, Kerstin I.
Kwee, Edward J.
Elliott, John T.
Schiel, John E.
A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
title A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
title_full A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
title_fullStr A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
title_full_unstemmed A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
title_short A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
title_sort sensitive and controlled data-independent acquisition method for proteomic analysis of cell therapies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9087334/
https://www.ncbi.nlm.nih.gov/pubmed/35404046
http://dx.doi.org/10.1021/acs.jproteome.1c00887
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