PXD017473

PXD017473 is an original dataset announced via ProteomeXchange.

Title	Quantative proteomic analysis of teh central amygdala in neuropathic pain model rats
Description	Neuropathic pain is a major clinic probelm as it is very difficult to treat and mechanism remain unknown. Here, we investigated the differential expression of proteins in the central nuecleus of amygdala (CeA) in neuropathic pain moldel spinal nerve transection (SNT)in rats. CeA was excised from naive, sham, SNTmodels at days 3, 7, 14 and 21 rats. The aim was to quatify the differential proteins in CeA including memebrane proteins. We used gel- and mass spectrometry- based proteomics. For gel-proteomics, total tissue lysate proteins were separated by 2D-PAGE. The 2D gels from different SNT time points against Sham and control rats were compared using Progenesis SameSpot software. The spots with fold change greater then 2 excised for the proteins IDs by LC-MS/MS. Protein spots were digested using trypsin. Extracted peptides were injected on the nano C18 column and measured by a LTQ Orbitrap XL or a LTQ Orbitrap Velos mass spectrometers. For the identification of membrane proteins in CeA, we used 1-SDS-PAGE and cut the gel region of MW 80 kDa and higher for nano-LC-MS/MS analysis. We also quantified membrane proteins by utilising triplex stabel isotope dimethyl labelling at the peptide level. Sham, control and day 3, 7 and 21 after SNT surgery rats CeA membrane proteins were purified and digested by trypsin and labelled with "light", "medium" and "heavy" dimethyl labelling reagents. The resulting peptides were analysed by a nano LC connected to the Q Exactive mass spectrometer. Quantification of peptide was processed using Proteome Discoverer 1.3.
HostingRepository	PRIDE
AnnounceDate	2020-02-21
AnnouncementXML	Submission_2020-02-21_07:07:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kersti Karu
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; LCQ Classic; 4700 Proteomics Analyzer; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-12 03:01:56	ID requested
⏵ 1	2020-02-21 07:07:09	announced

Karu K, Swanwick RS, Novejarque-Gadea A, Antunes-Martins A, Thomas B, Yoshimi E, Foster W, Fang M, McMahon SB, Bennett DLH, Rice ASC, Okuse K, Quantitative Proteomic Analysis of the Central Amygdala in Neuropathic Pain Model Rats. J Proteome Res, 19(4):1592-1619(2020) [pubmed]

submitter keyword: 2D-gel, LC-MS/MS, ncentral amygdala, spinal nerve transcection

Kersti Karu
contact affiliation	Mass Spectrometry Manager
contact email	kersti.karu@ucl.ac.uk
lab head
Kersti Karu
contact affiliation	PhD
contact email	karu.kersti@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017473
     1. Label: PRIDE project
     2. Name: Quantative proteomic analysis of teh central amygdala in neuropathic pain model rats