Dataset Information

Role of EVs in inflammation propagation and oxidative stress during vascular calcification

ABSTRACT: Role of EVs in inflammation propagation and oxidative stress during vascular calcification

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Macrophage

SUBMITTER: Vincent Jung

LAB HEAD: Chiara Guerrera

PROVIDER: PXD029441 | Pride | 2022-05-19

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	210603_LiYA_nE_EV_n1-5_1-1_941.d.zip	Other
	210603_LiYA_nE_EV_n1-5_1-2_942.d.zip	Other
	210603_LiYA_nE_EV_n1-5_1-3_943.d.zip	Other
	210603_LiYA_nE_EV_n1-5_1-4_944.d.zip	Other
	210603_LiYA_nE_EV_n1-5_1-5_945.d.zip	Other

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Publications

Extracellular Vesicles From LPS-Treated Macrophages Aggravate Smooth Muscle Cell Calcification by Propagating Inflammation and Oxidative Stress.

Yaker Linda L Tebani Abdellah A Lesueur Céline C Dias Chloé C Jung Vincent V Bekri Soumeya S Guerrera Ida Chiara IC Kamel Saïd S Ausseil Jérôme J Boullier Agnès A

Frontiers in cell and developmental biology 20220309

<b>Background:</b> Vascular calcification (VC) is a cardiovascular complication associated with a high mortality rate among patients with diseases such as atherosclerosis and chronic kidney disease. During VC, vascular smooth muscle cells (VSMCs) undergo an osteogenic switch and secrete a heterogeneous population of extracellular vesicles (EVs). Recent studies have shown involvement of EVs in the inflammation and oxidative stress observed in VC. We aimed to decipher the role and mechanism of act ...[more]

PMID: 35356285

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Project description:Plasma proteomics holds immense potential for clinical research and biomarker discovery, serving as a non-invasive "liquid biopsy" for tissue sampling. Mass spectrometry (MS)-based proteomics, thanks to improvement in speed and robustness, emerges as an ideal technology for exploring the plasma proteome for its unbiased and highly specific protein identification and quantification. Despite its potential, plasma proteomics is still a challenge due to the vast dynamic range of protein abundance, hindering the detection of less abundant proteins. Different approaches can help overcome this challenge. Conventional depletion methods face limitations in cost, throughput, accuracy, and off-target depletion. Nanoparticle-based enrichment shows promise in compressing dynamic range, but cost remains a constraint. Enrichment strategies for extracellular vesicles (EVs) can enhance plasma proteome coverage dramatically, but current methods are still too laborious for large series. Neat plasma remains popular for its cost-effectiveness, time efficiency, and low volume requirement. We used a test set of 33 plasma samples for all evaluations. Samples were digested using Strap and analysed on Evosep and nanoElute coupled to a timsTOF Pro using different elution gradients and ion mobility ranges. Data were mainly analyzed using library-free searched using DIANN. This study explores ways to improve proteome coverage in neat plasma both in MS data acquisition and MS data analysis. We demonstrate the value of sampling smaller hydrophilic peptides, increasing chromatographic separation, and using library-free searches. Additionally, we introduce the EV boost approach, that leverages on the extracellular vesicle fraction to enhances protein identification in neat plasma samples. Globally, out optimized analysis workflow allows the quantification of over 1000 proteins in neat plasma with a 24SPD throughput. We believe that these considerations can be of help independently of the LC-MS platform used.