LC-MSE, Multiplex MS/MS, Ion Mobility, and Label-Free Quantitation in Clinical Proteomics

Souza, Gustavo H.M.F.; Guest, Paul C.; Martins-de-Souza, Daniel

doi:10.1007/978-1-4939-6730-8_4

Cited by 38 publications

(29 citation statements)

References 49 publications

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“…Synapt G2-Si was calibrated with [Glu1]-fibrinopeptide, [M+2H] 2+ = 785.84261 at � 1 ppm. The results generated from Progenesis Software were exported to � .xlsx files to verify two levels of data quality control for label-free experiments (peptide and protein level) according to the figures of merit (FOM) described by Souza et al [31]. All proteins considered with differential interaction with Akt presented at least a ratio ±1.2 (expressed as a base 2 logarithm); it means that these proteins had at least ± 2.29-absolute fold change interaction (diminished or increased) with Akt in cardiomyocytes of MetS vs control rats.…”

Section: Label-free Mass Spectrometrymentioning

confidence: 99%

Metabolic syndrome diminishes insulin-induced Akt activation and causes a redistribution of Akt-interacting proteins in cardiomyocytes

et al. 2020

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Metabolic syndrome (MetS) is a cluster of cardiometabolic risk factors, with insulin resistance as a critical component for its development. Insulin signaling in the heart leads to Akt (also known as PKB) activation, a serine/threonine protein kinase, which regulates cardiac glucose metabolism and growth. Cardiac metabolic inflexibility, characterized by impaired insulin-induced glucose uptake and oxidation, has been reported as an early and consistent change in the heart of different models of MetS and diabetes; however, the evaluation of Akt activation has yielded variable results. Here we report in cardiomyocytes of MetS rats, diminished insulin-induced glucose uptake and Akt activation, evaluated by its impaired mobilization towards the plasma membrane and phosphorylation, and reflected in a redistribution of its interacting proteins, assessed by label-free mass spectrometry (data are available via ProteomeXchange with identifier PXD013260). We report 45 proteins with diminished abundance in Akt complex of MetS cardiomyocytes, mainly represented by energy metabolism-related proteins, and also, 31 Akt-interacting proteins with increased abundance, which were mainly related to contraction, endoplasmic reticulum stress, and Akt negative regulation. These results emphasize the relevance of Akt in the regulation of energy metabolism in the heart and highlight Akt-interacting proteins that could be involved in the detrimental effects of MetS in the heart.

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Section: Label-free Mass Spectrometrymentioning

confidence: 99%

Metabolic syndrome diminishes insulin-induced Akt activation and causes a redistribution of Akt-interacting proteins in cardiomyocytes

et al. 2020

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“…MS acquisition. Prior to injection, each sample was acquired as "scouting runs" to access the total ion counts, and a stoichiometric normalization between conditions was conducted (75). Peptides were injected into a 2D-RP/RP ACQUITY UPLC M-Class System (Waters, Milford, MA), tandem to a Synapt G2-Si mass spectrometer (Waters, Manchester, U.K.).…”

Section: Protein Quantitative Analyses By Msmentioning

confidence: 99%

“…The used proteomic approach revealed a broad dynamic range of detected proteins with more than seven orders of magnitude as expected for this biological matrix and considering the instrument technology. More detailed information can be found in Supplemental Table II and references (75,81,88).…”

Section: Label-free Quantitative Ms: Quality Of Proteome Datamentioning

confidence: 99%

Immune Response Resetting in Ongoing Sepsis

Nowill

Fornazin

Spago

et al. 2019

The Journal of Immunology

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Cure of severe infections, sepsis, and septic shock with antimicrobial drugs is a challenge because morbidity and mortality in these conditions are essentially caused by improper immune response. We have tested the hypothesis that repeated reactivation of established memory to pathogens may reset unfavorable immune responses. We have chosen for this purpose a highly stringent mouse model of polymicrobial sepsis by cecum ligation and puncture. Five weeks after priming with a diverse Ag pool, high-grade sepsis was induced in C57BL/6j mice that was lethal in 24 h if left untreated. Antimicrobial drug (imipenem) alone rescued 9.7% of the animals from death, but >5-fold higher cure rate could be achieved by combining imipenem and two rechallenges with the Ag pool (p < 0.0001). Antigenic stimulation fine-tuned the immune response in sepsis by contracting the total CD3 + T cell compartment in the spleen and disengaging the hyperactivation state in the memory T subsets, most notably CD8 + T cells, while preserving the recovery of naive subsets. Quantitative proteomics/lipidomics analyses revealed that the combined treatment reverted the molecular signature of sepsis for cytokine storm, and deregulated inflammatory reaction and proapoptotic environment, as well as the lysophosphatidylcholine/phosphatidylcholine ratio. Our results showed the feasibility of resetting uncontrolled hyperinflammatory reactions into ordered hypoinflammatory responses by memory reactivation, thereby reducing morbidity and mortality in antibiotic-treated sepsis. This beneficial effect was not dependent on the generation of a pathogen-driven immune response itself but rather on the reactivation of memory to a diverse Ag pool that modulates the ongoing response.

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“…Qualitative and quantitative proteomic analysis were performed on a 2D-LC-MS/MS system with ion-mobility-enhanced data-independent acquisitions (Souza et al 2017). Peptides were injected into a two-dimensional reverse phase liquid chromatography using an Acquity UPLC M-Class System (Waters Corporation, Milford, MA) coupled to a Synapt G2-Si mass spectrometer (Waters Corporation, Milford, MA).…”

Section: Liquid Chromatography-mass Spectrometrymentioning

confidence: 99%

“…Qualitative and quantitative proteomic analysis were performed on a 2D-LC-MS/MS system with ion-mobility-enhanced data-independent acquisitions (Souza et al, 2017 Samples were all run in technical and biological triplicates.…”

Section: Liquid Chromatography-mass Spectrometrymentioning

confidence: 99%

Short term changes in the proteome of human cerebral organoids induced by 5-methoxy-N,N-dimethyltryptamine

Dakic

Nascimento

Sartore

et al. 2017

Preprint

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LC-MSE, Multiplex MS/MS, Ion Mobility, and Label-Free Quantitation in Clinical Proteomics

Cited by 38 publications

References 49 publications

Metabolic syndrome diminishes insulin-induced Akt activation and causes a redistribution of Akt-interacting proteins in cardiomyocytes

Metabolic syndrome diminishes insulin-induced Akt activation and causes a redistribution of Akt-interacting proteins in cardiomyocytes

Immune Response Resetting in Ongoing Sepsis

Short term changes in the proteome of human cerebral organoids induced by 5-methoxy-N,N-dimethyltryptamine

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