Dataset Information

PBMC_A data-independent acquisition (DIA)-based quantification workflow for proteome analysis of 5000 cells

ABSTRACT: An optimized workflow for nanoscale proteomics is applied to the proteomics profiling of 5000 PBMCs in DIA mode on Orbitrap Lumos.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood

SUBMITTER: Na Jiang

LAB HEAD: Ruibing Chen

PROVIDER: PXD029721 | Pride | 2022-04-27

REPOSITORIES: Pride

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			Action	DRS
	PBMC_20201228_150um_30cm_120MIN_DIA_GPF_1025_1200mz.raw	Raw
	PBMC_20201228_150um_30cm_120MIN_DIA_GPF_350_425mz.raw	Raw
	PBMC_20201228_150um_30cm_120MIN_DIA_GPF_425_500mz.raw	Raw
	PBMC_20201228_150um_30cm_120MIN_DIA_GPF_500_575mz.raw	Raw
	PBMC_20201228_150um_30cm_120MIN_DIA_GPF_575_650mz.raw	Raw

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Project description:Evolution of multicellular life forms has involved adaptation of organs that consist of multiple cell types, each with unique functional properties that as a collection, achieve complex organ function. Since each cell type is adapted to deliver specific functionality within the context of an organ, knowledge on functional landscapes occupied by individual cell types could improve comprehension of organ function at the molecular level. In kidney, podocytes and tubules are two cell types that work together, each with vastly different functional roles. Podocytes envelop the blood vessels in the glomerulus and act as filters while tubules, located downstream of the glomerulus, are responsible for reabsorption of important nutrients. Mitochondria hold a critical and well-studied role in tubules due to the high energetic requirements required to fulfill their function. In podocytes however, questions remain regarding the relevance of mitochondrial function in both normal physiology and pathology . Quantitative cross-linking mass spectrometry and proteomics together with a transgenic mitochondrial tagging strategy were used to investigate kidney cell-type specificity of mitochondria. These efforts revealed that despite similarities of podocyte and tubule mitochondrial proteomes, each contain unique features corresponding to known distinct functional roles. These include increased demand for energy production through the TCA cycle in tubules and increased detoxification demand in podocytes. Moreover, tubule and podocyte mitochondrial interactome differences revealed additional cell-type specific functional insights with alterations in betaine metabolism, lysine degradation, and other pathways not regulated through proteome abundance levels. Most importantly, these efforts illustrate that cell specific mitochondrial interactome differences within an organ can now be visualized. Therefore, this approach can generally be used to map cell-specific mitochondrial changes in disease, aging or even with therapy to better understand the roles and contributions of each cell type in normal physiology and pathology within an organ in ways not previously possible .

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PBMC_A data-independent acquisition (DIA)-based quantification workflow for proteome analysis of 5000 cells

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