Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells

Abstract Chronic lymphocytic leukaemia (CLL) exhibits variable clinical course and response to therapy, but the molecular basis of this variability remains incompletely understood. Data independent acquisition (DIA)-MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical f...

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Autores principales:	Gina L. Eagle, John M. J. Herbert, Jianguo Zhuang, Melanie Oates, Umair T. Khan, Neil R. Kitteringham, Kim Clarke, B. Kevin Park, Andrew R. Pettitt, Rosalind E. Jenkins, Francesco Falciani
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b0b4a251ceac451c8bcb635f0d6ce38e
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spelling	oai:doaj.org-article:b0b4a251ceac451c8bcb635f0d6ce38e2021-12-02T14:06:25ZAssessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells10.1038/s41598-021-82609-22045-2322https://doaj.org/article/b0b4a251ceac451c8bcb635f0d6ce38e2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82609-2https://doaj.org/toc/2045-2322Abstract Chronic lymphocytic leukaemia (CLL) exhibits variable clinical course and response to therapy, but the molecular basis of this variability remains incompletely understood. Data independent acquisition (DIA)-MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. Here, a CLL-specific spectral library (7736 proteins) is described alongside an analysis of sample replication and data handling requirements for quantitative SWATH-MS analysis of clinical samples. The analysis was performed on 6 CLL samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins across 54 SWATH-MS acquisitions: the sources of variation and different computational approaches for batch correction were assessed. Functional enrichment analysis of proteins associated with IGHV mutational status showed significant overlap with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was implemented. This study provides a valuable resource for researchers working on the proteomics of CLL. It also establishes a sound framework for the design of sufficiently powered clinical proteomics studies. Indeed, this study shows that it is possible to derive biologically plausible hypotheses from a relatively small dataset.Gina L. EagleJohn M. J. HerbertJianguo ZhuangMelanie OatesUmair T. KhanNeil R. KitteringhamKim ClarkeB. Kevin ParkAndrew R. PettittRosalind E. JenkinsFrancesco FalcianiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gina L. Eagle John M. J. Herbert Jianguo Zhuang Melanie Oates Umair T. Khan Neil R. Kitteringham Kim Clarke B. Kevin Park Andrew R. Pettitt Rosalind E. Jenkins Francesco Falciani Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
description	Abstract Chronic lymphocytic leukaemia (CLL) exhibits variable clinical course and response to therapy, but the molecular basis of this variability remains incompletely understood. Data independent acquisition (DIA)-MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. Here, a CLL-specific spectral library (7736 proteins) is described alongside an analysis of sample replication and data handling requirements for quantitative SWATH-MS analysis of clinical samples. The analysis was performed on 6 CLL samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins across 54 SWATH-MS acquisitions: the sources of variation and different computational approaches for batch correction were assessed. Functional enrichment analysis of proteins associated with IGHV mutational status showed significant overlap with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was implemented. This study provides a valuable resource for researchers working on the proteomics of CLL. It also establishes a sound framework for the design of sufficiently powered clinical proteomics studies. Indeed, this study shows that it is possible to derive biologically plausible hypotheses from a relatively small dataset.
format	article
author	Gina L. Eagle John M. J. Herbert Jianguo Zhuang Melanie Oates Umair T. Khan Neil R. Kitteringham Kim Clarke B. Kevin Park Andrew R. Pettitt Rosalind E. Jenkins Francesco Falciani
author_facet	Gina L. Eagle John M. J. Herbert Jianguo Zhuang Melanie Oates Umair T. Khan Neil R. Kitteringham Kim Clarke B. Kevin Park Andrew R. Pettitt Rosalind E. Jenkins Francesco Falciani
author_sort	Gina L. Eagle
title	Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
title_short	Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
title_full	Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
title_fullStr	Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
title_full_unstemmed	Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
title_sort	assessing technical and biological variation in swath-ms-based proteomic analysis of chronic lymphocytic leukaemia cells
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/b0b4a251ceac451c8bcb635f0d6ce38e
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Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells

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