Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the rat hippocamus proteome

ABSTRACT: Rat brain tissue lysed, then analyzed by 2D-LC-MSE, processed with Elucidator and PLGS

INSTRUMENT(S): instrument model

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Hippocampus

SUBMITTER: Yishai Levin

PROVIDER: PRD000298 | Pride | 2011-02-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_13661.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_13661.xml.gz	Xml

Items per page:

1 - 2 of 2

Similar Datasets

Analysis of the rat hypothalamus proteome by data independent label-free liquid chromatography tandem mass spectrometry

Project description:Studies of neuronal, endocrine and metabolic disorders would be facilitated by characterization of the hypothalamus proteome. Protein extracts prepared from 16 whole rat hypothalami were measured by data independent label-free nanoflow liquid chromatography mass spectrometry (nLC-MSE). Peptide features were detected, aligned and searched against a rat SwissProt database using ProteinLynx Global Server v.2.5. The final combined dataset comprised 21,455 peptides, corresponding to 622 unique proteins, each identified by a minimum of two distinct peptides. The majority of the proteins (69%) were cytosolic, and 16% were membrane proteins. Important proteins involved in neurological and synaptic function were identified including several members of RAB family and proteins involved in glutamate biosynthesis.

2012-08-22 | PXD000017 | Pride

Triton X-100 reference proteome of brain capillary endothelial cells

Project description:Bovine brain capillary endothelial cells (BBCEC) are cocultured in presence of rat astrocytes to reinduce blood brain barrier properties. After checking of BBB propereties reinduction, BBCEC are harvested by collagenase treatment, lysed with Triton X-100 based lysis buffer. Triton X-100 soluble proteins are subjected to organic fractionation step and the 5 generated fractions were submitted to 1D-LC-MS/MS analysisi on MALDI-TOF-TOF-MS.

2010-12-03 | PRD000250 | Pride

Global mapping of rat plasma proteins with a native proteomic approach using nondenaturing micro 2DE and label-free quantitative LC-MS/MS

Project description:Plasma samples from adult male rats were separated by nondenaturing micro 2DE and a representative gel was selected, on which a total of 136 CBB-stained spots were numbered and subjected to in-gel digestion and label-free quantitative LC-MSE (MS/MS in data-independent acquisition mode). The analysis provided the assignment of 1-25 (average eight) nonredundant proteins in each spot and totally 199 proteins were assigned in the 136 spots. The quantity data from the LC-MSE analysis were further analyzed to reconstruct the quantity distribution on the 2D gel for each of the assigned proteins (a native protein map). This work provides not only a reference library containing 199 native protein maps for rat plasma proteome, but also useful information for subsequent analysis for protein-protein interactions.

2016-10-14 | PXD004395 | Pride

Proteomics characterization of the ram and rat testicular fluid

Project description:Proteomics characterization of the ram and rat testicular fluid

2014-08-29 | PRD000847 | Pride

Rat LAD IR study

Project description:Rats underwent surgery for LAD ligation for 30 min followed by reperfusion. Heart ventricles were collected 2d or 7d after reperfusion. Keywords: rat heart ventricles, LAD - left anterior descending coronary artery, IR - ischemia-reperfusion

2006-03-24 | GSE4105 | GEO

Murine Rat Brain Injury

Project description:Murine Rat Brain Injury

| PRJNA91203 | ENA

Transcription profiling of rat subfornical organ

Project description:In these studies we have for the first time described the transcriptome of the rat SFO, and have in addition identified genes the expression of which is significantly modified by either water or food deprivation. Experiment Overall Design: For each condition (food deprivation, water deprivation, untreated), 25 animals were denied food for 48 hours prior to sacrifice. The Subfornical organ was removed under a dissecting microscope from a 1mm slice of brain removed from an ice cold brain matrix. SFO's from 5 animals were pooled for each sample prior to RNA extraction to give n=5.

2008-10-26 | E-GEOD-12978 | biostudies-arrayexpress

MSE vs IM-MSE comparison - The experiment was conducted to compare the MSE and IM-MSE acquisiton modes

Project description:The experiment was conducted to compare the MSE and IM-MSE acquisiton modes as well as to find the optimal on column loading. This was done using 1DLC and cytosolic e coli digest.Raw data were processed and searched using Proteinlynx Global Server version 3.0. The following parameters were used to generate peak lists: minimum intensity for precursors was set to 140, minimum intensity for fragment ions 30 and total bin-count was set to minimum of 400. Processed data was searched against the UniprotKB, Escherichia coli K12 strain, concatenated with 125 common laboratory contaminates. Fixed modification was set to carbamidomethylation of C and variable modification was set to oxidation of M. Searches were conducted against a froward and reverse sequence database. Minimum identification criteria included 3 fragment ions per peptide, 5 fragment ions per protein, minimum peptide identification score of 5.9 and minimum of 2 peptides per protein. Search results and spectra were imported into Scaffold and the global false discovery rate was less than 1%.

2013-02-18 | PXD000150 | Pride

Evaluation of drift time specific collision energies

Project description:Comparison among the following data independent acquisition modes provided on the Waters Synapt G2-S instrument: MSE, MSE with Ion Mobility (HDMSE), and MSE with Ion Mobility and drift time specific collision energies (UDMSE). The following on-column loads and LC gradient lengths have been used for the DDA data (1-20130710-63647): * 200 ng, 90 minutes gradient * 300 ng, 180 minutes gradient * 1000 ng, 180 minutes gradient. DDA data has been processed by using MaxQuant (v.1.3.0.5) software, searching against a organism specific (Homo Sapiens) Uniprot/Swissprot database. FDR has been controlled by using a pseudo-reverse (KR positions kept) database at both protein and peptide levels to 1%. Proteins with less than two peptides (minimum of 6 amino acids length, up to 2 missed cleavages and 3 variable modifications allowed. Variable identifications were : methionine oxidation, fixed modifications were : cysteine carbamidomethylation ) identified have been discarded. A match between runs of a 2 minutes windows among the three technical replicates has been performed.

2013-12-05 | PXD000303 | Pride

Immortalized cardiac cell line characterization and comparison (rat/rat-derived)

Project description:Immortalized cardiac cell line characterization and comparison (rat/rat-derived)

| PRJEB47457 | ENA