PXD048773

PXD048773 is an original dataset announced via ProteomeXchange.

Title	Phosphoproteomic Analysis of PCB126 Impact on the Mouse Chronic-Binge Alcohol Feeding Model
Description	Environmental pollutants, including polychlorinated biphenyls (PCBs) have been implicated in the pathogenesis of liver disease. To better understand how PCB126 promoted alcohol-associated liver disease (ALD) in our previous model, the current study utilized a phosphoproteomic approach for hypothesis generation regarding mechanisms of action. Briefly, male C57B/6J mice were exposed to 0.2 mg/kg polychlorinated biphenyl PCB126 or corn oil vehicle prior to ethanol (EtOH) or control diet feeding in the chronic-binge alcohol feeding model. Liver tissues were harvested during euthanasia and tissue collection, snap frozen in liquid nitrogen, and then were archived in a -80C freezer. For phosphoproteome analysis, six random liver tissues from four groups (N=24) were homogenized in 2% sodium dodecyl sulfate (SDS) radioimmunoprecipitation (RIPA) buffer with 1X HALT protease and phosphatase inhibitors. Lysates were trypsinized at a 1:20 (enzyme:sample) ratio and prepared following ProtiFi S-Trap mini spin column digestion protocol. Phospho-peptides were enriched with MagReSyn titanium ion - immobilized metal affinity chromatography (Ti-IMAC) microparticles following ReSyn Biosciences MagReSyn Ti-IMAC protocol. Samples were then purified using C18 PROTO 300 A Ultra MicroSpin columns, dried under a SpeedVac, and stored at -80C prior to peptide concentration assessment. Digests were fractionated by UPLC nanoflow liquid chromatography using PepMap RSLC C18 EASY-spray separating column at 40C with a 90-minute linear gradient. Eluates were introduced into an Exploris480 using an EASY-spray source (320C and 1.8kV). Full MS-ddMS2 method with a 3 second cycle time was generated in Xcalibur (v4.5.445.18) operating in positive polarity. RAW data files were separately searched in PeaksXpro (Bioinformatics Solutions Inc.; Waterloo, ON, Canada) using Denovo, PeaksDB, and PeaksPTM algorithms against the UniprotKB Mus musculus canonical protein sequences (proteomics ID: UP000000589) downloaded March 17, 2023. Label Free Quantification algorithm was then used with PeaksPTM results utilizing a mass error tolerance of 10 ppm and retention time shift tolerance of 6-minutes. Peptides were accepted at a 1% FDR threshold for consideration by the Label Free Quantification algorithm.
HostingRepository	MassIVE
AnnounceDate	2024-03-28
AnnouncementXML	Submission_2024-03-28_07:36:29.292.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Michael Merchant
SpeciesList	scientific name: Mus ; NCBI TaxID: 10088;
ModificationList	O4'-phospho-L-tyrosine; O-phospho-L-threonine; O-phospho-L-serine; S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-22 12:28:14	ID requested
⏵ 1	2024-03-28 07:36:29	announced

no publication

submitter keyword: liver, PCB, binge ethanol, chronic ethanol

Timothy D. Cummins, PhD
contact affiliation	University of Louisville
contact email	timothy.cummins@louisville.edu
lab head
Michael Merchant
contact affiliation	University of Louisville
contact email	mlmerc02@louisville.edu
dataset submitter

MassIVE dataset URI

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v06/MSV000093903/