Eagle, Gina L, Herbert, John MJ, Zhuang, Jianguo 
ORCID: 0000-0003-3245-0789, Oates, Melanie, Khan, Umair T, Kitteringham, Neil R, Clarke, Kim, Park, B Kevin ORCID: 0000-0001-8384-824X, Pettitt, Andrew R, Jenkins, Rosalind E et al (show 1 more authors)
(2021)
Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells.
Scientific Reports, 11 (1).
p. 2932.
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Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells.pdf - Published version Download (1MB) | Preview |
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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Humans, Receptors, Antigen, B-Cell, Proteome, Gene Expression Profiling, Proteomics, Genetic Heterogeneity, Mutation, Aged, Middle Aged, Female, Male, Tandem Mass Spectrometry, Leukemia, Lymphocytic, Chronic, B-Cell, Datasets as Topic, Biological Variation, Population |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 12 Feb 2021 13:12 |
| Last Modified: | 18 Jan 2023 23:00 |
| DOI: | 10.1038/s41598-021-82609-2 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3115558 |
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