Dataset Information

Glucose-dependent phosphorylation in insulin secreting cells

ABSTRACT: Shotgun proteomics including TiO2 enrichment of phosphorylated peptides followed by reversed-phase liquid chromatography tandem mass spectrometry (RP-LC MS/MS) on lysates from glucose-stimulated INS-1E cells was used to identify glucose regulated phosphorylated proteins and signal transduction pathways.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Cell Culture

SUBMITTER: Loïc Dayon

LAB HEAD: Loïc Dayon

PROVIDER: PXD011329 | Pride | 2019-02-25

REPOSITORIES: Pride

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			Action	DRS
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	File Name_ MitoCells_Full_LongRun_2_02.raw (F006785).mzid_File_Name__MitoCells_Full_LongRun_2_02.raw_(F006785).pride.mgf.gz	Mzid

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Publications

Glucose-dependent phosphorylation signaling pathways and crosstalk to mitochondrial respiration in insulin secreting cells.

Santo-Domingo Jaime J Galindo Antonio Núñez AN Cominetti Ornella O De Marchi Umberto U Cutillas Pedro P Dayon Loïc L Wiederkehr Andreas A

Cell communication and signaling : CCS 20190220 1

<h4>Background</h4>Glucose is the main secretagogue of pancreatic beta-cells. Uptake and metabolism of the nutrient stimulates the beta-cell to release the blood glucose lowering hormone insulin. This metabolic activation is associated with a pronounced increase in mitochondrial respiration. Glucose stimulation also initiates a number of signal transduction pathways for the coordinated regulation of multiple biological processes required for insulin secretion.<h4>Methods</h4>Shotgun proteomics i ...[more]

PMID: 30786936

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Project description:Being inspired by metabolomic data processing, we have developed a bioinformatic pipeline that optimizes the processing of mass spectral data obtained from isobaric Tandem Mass Tag (TMT) experiments. Our method focuses on the tandem mass spectral level by first quantifying and then identifying (QtI), while preserving unidentified spectra for further investigations. The raw datasets were previously generated [1, 2]. Two-proteome model experiments were considered where identical pools of human CSF or plasma samples were mixed with E. coli samples at different concentrations. E. coli protein extract was spiked in 400 µL of CSF at amounts of 0, 2, 3, 5, 6.25, and 7.5 µg. Such sets of 6 spiked CSF samples were prepared in triplicate for comparison using sixplex isobaric tagging and analyzed in triplicates on two independent but identical LC MS/MS, for a total of 18 raw files [1]; this experiment is called “CSF-E.coli”. E. coli protein extract was spiked at 0, 2.5, 5, 6.25, 12.5, and 25 µg in 30 µL human plasma. Such sets of 6 spiked plasma samples were prepared in quadruplicate for comparison using sixplex isobaric tagging and analyzed in triplicates on one LC MS/MS, for a total of 12 raw files [2]; this experiment is referred as “Plasma-E.coli”.The so-called “96samples-CSF” experiment consists of 16 replicate TMT sixplex experiments measuring identical CSF samples from the pool described above [2], analyzed in triplicates on one LCMS/MS for a total of 48 raw files. The so-called “96samples-plasma” experiment consists of 16 replicate TMT sixplex experiments measuring identical plasma samples from the pool described before, analyzed in triplicates on one LC MS/MS for a total of 48 raw files [1]. References: [1] Dayon, L., Núñez Galindo, A., Corthésy, J., Cominetti, O. & Kussmann, M. Comprehensive and scalable highly automated MS-based proteomic workflow for clinical biomarker discovery in human plasma. J. Proteome Res. 13, 3837-3845 (2014). [2] Núñez Galindo, A., Kussmann, M. & Dayon, L. Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery. Anal. Chem. 87, 10755-10761 (2015).