Digging deeper into bile proteome

Ciordia, Sergio; Álvarez‐Sola, Gloria; Rullán, María; Urmán, Jesús; Ávila, Matías A.; Corrales, Fernando J.

doi:10.1016/j.jprot.2020.103984

Cited by 21 publications

(18 citation statements)

References 10 publications

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“…The antibody used to immunoprecipitate human SLU7 and the pre-immune IgG are described in Table S1. Eluted samples were subjected to LC-ESI-MS/MS TRIPLE-TOF analysis as previously described (8). According to the analysis, proteins with at least 5 peptide sequences identified in SLU7 and none in the IgG immunoprecipitated were considered for crossmatching with two stress granule components databases: MSGP (https://msgp.pt/index/) (9) and RNA Granule Database (http://rnagranuledb.lunenfeld.ca/) (10).…”

Section: Mass Spectrometry Analysismentioning

confidence: 99%

Splicing Factor SLU7 Prevents Oxidative Stress‐Mediated Hepatocyte Nuclear Factor 4α Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage

et al. 2021

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Section: Mass Spectrometry Analysismentioning

confidence: 99%

Splicing Factor SLU7 Prevents Oxidative Stress‐Mediated Hepatocyte Nuclear Factor 4α Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage

et al. 2021

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“…Protein digestion using S-Trap filter (Protifi, Huntington, New York) was performed following the protocol described in. 14 Peptide quantification was done with Qubit™ Fluorometric Quantitation (Thermo Fisher Scientific) using spiked in PQ500™ Reference Peptide kit (Biognosys) as reference. Liquid chromatography-tandem mass spectrometry (LC-MS/ MS) analysis was done by reversed-phase chromatographic separations and SureQuant method as indicated in Supplementary methods S1.…”

Section: Surequant-targeted Quantitationmentioning

confidence: 99%

Mapping early serum proteome signatures of liver regeneration in living donor liver transplant cases

Carmona‐Rodríguez,

Gajadhar,

Blázquez‐García

et al. 2023

BioFactors

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The liver is the only solid organ capable of regenerating itself to regain 100% of its mass and function after liver injury and/or partial hepatectomy (PH). This exceptional property represents a therapeutic opportunity for severe liver disease patients. However, liver regeneration (LR) might fail due to poorly understood causes. Here, we have investigated the regulation of liver proteome and phosphoproteome at a short time after PH (9 h), to depict a detailed mechanistic background of the early LR phase. Furthermore, we analyzed the dynamic changes of the serum proteome and metabolome of healthy living donor liver transplant (LDLT) donors at different time points after surgery. The molecular profiles from both analyses were then correlated. Insulin and FXR‐FGF15/19 signaling were stimulated in mouse liver after PH, leading to the activation of the main intermediary kinases (AKT and ERK). Besides, inhibition of the hippo pathway led to an increased expression of its target genes and of one of its intermediary proteins (14‐3‐3 protein), contributing to cell proliferation. In association with these processes, metabolic reprogramming coupled to enhanced mitochondrial activity cope for the energy and biosynthetic requirements of LR. In human serum of LDLT donors, we identified 56 proteins and 13 metabolites statistically differential which recapitulate some of the main cellular processes orchestrating LR in its early phase. These results provide mechanisms and protein mediators of LR that might prove useful for the follow‐up of the regenerative process in the liver after PH as well as preventing the occurrence of complications associated with liver resection.

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“…The S‐Trap method yielded the highest number of peptides and proteins. In a recent study, ISD and S‐Trap methods were used to identify proteins in the bile of rats [53]. The S‐Trap method identified 3280 peptides and 553 proteins, higher than those obtained by the ISD method (1256 peptides and 235 proteins).…”

Section: Comparison Of Suspension Trapping and Other Sample Preparati...mentioning

confidence: 99%

A review of suspension trapping digestion method in bottom‐up proteomics

Duong

Park

Lee

2022

J of Separation Science

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The standard bottom‐up proteomic workflow is comprised of sample preparation, data acquisition, and data analysis. While the latter two parts have made considerable advances in the last decade, sample preparation has remained an important challenge within the workflow due to the multi‐step nature of complex biological samples, and still requires much development. Several sample preparation methods have been developed and used in the last two decades, including in‐gel, in‐solution, on‐bead, filter‐aided sample preparation, and suspension trapping, to improve reproducibility, efficiency, scalability, and reduce the handling time of this process. One of the most recent methods developed and applied in proteomics studies in recent years is suspension trapping, which combines rapid detergent removal, reactor‐type protein digestion, and peptide clean‐up in a tip or spin column. Suspension trapping is a simple, rapid, and reproducible digestion method that can effectively handle proteins in low microgram or sub‐microgram amounts. This review discusses the benefits of the suspension trapping digestion method in relation to its development and application in bottom‐up proteomics studies. We also discuss recent applications of suspension trapping digestion to different sample types and the features of the suspension trapping digestion method compared with other sample preparation methods.

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Digging deeper into bile proteome

Cited by 21 publications

References 10 publications

Splicing Factor SLU7 Prevents Oxidative Stress‐Mediated Hepatocyte Nuclear Factor 4α Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage

Splicing Factor SLU7 Prevents Oxidative Stress‐Mediated Hepatocyte Nuclear Factor 4α Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage

Mapping early serum proteome signatures of liver regeneration in living donor liver transplant cases

A review of suspension trapping digestion method in bottom‐up proteomics

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