Proteomics,Multiomics

Dataset Information

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Assessing Technical and Biological Variation in SWATH-MS -based Proteomics: A case study in Chronic Lymphocytic Leukaemia


ABSTRACT: Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in 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. This report describes the sample replication and data handling requirements for SWATH-MS analysis of clinical samples. A CLL-specific spectral library compromising over 1,500,000 spectra with digital information for over 150,000 peptides has been generated to enable the quantification of up to 7736 proteins. To assess the reproducibility of the assay, SWATH-MS analysis was performed on 6 cryopreserved CLL patient samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins (<1% FDR) across 54 SWATH-MS acquisitions. These analyses showed that SWATH-MS is a highly reproducible technique. However, replicate sample preparations on different days was identified as the main source of variation. To overcome the effect of variation between sample preparation batches, different computational approaches for batch correction were tested. All approaches successfully removed technical variability whilst retaining proteomic differences between clinical subgroups. Functional enrichment analysis of proteins associated to IGHV mutational status highlighted the importance of metabolic remodelling in the biology of CLL and overlapped significantly with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was developed. This approach could be used to drive the design of future CLL SWATH-MS studies. These fundamental requirements for DIA approaches should be widely applicable to other clinical proteomics studies.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Peripheral Blood Mononuclear Cell

DISEASE(S): Chronic Lymphocytic Leukemia

SUBMITTER: Gina Eagle  

LAB HEAD: Dr Rosalind Jenkins

PROVIDER: PXD011330 | Pride | 2021-02-08

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
GECLLDB25MSMSCEX283uL301015.wiff Wiff
GECLLDB25MSMSCEX283uL301015.wiff.scan Wiff
GECLLDB25MSMSCEX293uL301015.wiff Wiff
GECLLDB25MSMSCEX293uL301015.wiff.scan Wiff
GECLLDB25MSMSCEX303uL301015.wiff Wiff
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Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells.

Eagle Gina L GL   Herbert John M J JMJ   Zhuang Jianguo J   Oates Melanie M   Khan Umair T UT   Kitteringham Neil R NR   Clarke Kim K   Park B Kevin BK   Pettitt Andrew R AR   Jenkins Rosalind E RE   Falciani Francesco F  

Scientific reports 20210203 1


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 d  ...[more]

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