Dataset Information

Macrophage proteome in response to Mycobacterium tuberculosis infection

ABSTRACT: This study investigates the proteomic alterations in human monocytic cell line (THP1) subsequent to infection with different strains of mycobacterium tuberculosis (H37Ra, H37Rv, BND433 and JAL2287) using the SWATH-MS strategy. THP1 proteome was analysed after 6, 18, 30 and 42 hours of infection with each strains and compared to that of uninfected cells. Our findings reveal temporal regulation of host response subsequent to Mtb infection.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human) Mycobacterium Tuberculosis

TISSUE(S): Cell Culture, Macrophage

SUBMITTER: Ajay Kumar

LAB HEAD: Ajay Kumar

PROVIDER: PXD009046 | Pride | 2020-09-23

REPOSITORIES: Pride

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Source:

			Action	DRS
	AJAYTHP1_WHOLECELLLIBRARY_UNINFECTED_80mM_F3.wiff	Wiff
	AJAYTHP1_WHOLECELLLIBRARY_UNINFECTED_80mM_F3.wiff.scan	Wiff
	AJAY_THP1_LIBRARY_Long_Column_whole_cell_ALL.group	Other
	AJAY_THP1_LIBRARY_Long_Column_whole_cell_species_none_1.group	Other
	AJAY_THP1_LIBRARY_Long_Column_whole_cell_species_none_2.group	Other

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Project description: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.

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Macrophage proteome in response to Mycobacterium tuberculosis infection

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