Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Insulin Resistance in a Type 1 Diabetes Rat Model

ABSTRACT: A automated 32-plex cPILOT chemical labeling strategy was utilized to identify proteome changes in type 1 diabetes in rats. We utilized an Orbitrap Fusion Lumos mass spectrometer to analyze 8 fractions in technical triplicates where proteins were quantified using Tandem Mass Tag pro reagents (16-plex reagents) and LC-SPS-MS3 acquisiton.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Liver

SUBMITTER: Bailey Bowser

LAB HEAD: Renã Robinson

PROVIDER: PXD033761 | Pride | 2025-05-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Fraction1_TR1_2ug_BLB_02132021.raw	Raw
	Fraction1_TR2_2ug_BLB_02132021.raw	Raw
	Fraction1_TR3_2ug_BLB_02132021.raw	Raw
	Fraction2_TR1_2ug_BLB_02132021.raw	Raw
	Fraction2_TR2_2ug_BLB_02132021.raw	Raw

Items per page:

1 - 5 of 49

Publications

Hyperinsulinemic male LEW.1WR1 rats show early signs of impaired liver metabolism.

Wimalarathne Madushika M Bowser Bailey L BL Arul Albert B AB Wilkerson-Vidal Quiana C QC David Moses A MA Hunt Emily C EC Gibson Helen H Robinson Renã A S RAS Love-Rutledge Sharifa T ST

Experimental and molecular pathology 20250211

Weanling LEW.1WR1 (1WR1) rats are susceptible to type 1 diabetes (T1D) and hyperinsulinemic. Similar to human patients with T1D, these animals are susceptible to developing fatty liver infiltrates. Insulin resistance-related steatosis can lead to the development of severe forms of nonalcoholic fatty liver disease (NAFLD). Previous work in 1WR1 rats suggests that in the absence of T1D, they have increased body mass that is not reconciled by measuring their abdominal fat pads; this suggests 1WR1 r ...[more]

PMID: 39938190

Similar Datasets

Human HeLa cells LC MS/MSLC-MSMS

Project description:We developed a reagent of 10-plex isobaric tags (IBT) with high stability and low cost. The labeled peptides were sensitively detected on Orbitrap Q Exactive MS with MS2 resolution of 35000 at 30% NCE, while the peptides were efficiently labelled over 97% by IBT at ratio of 20:1 of reagent/peptide (w/w) in 200mM TEAB buffer within 2h. The IBT labeling was demonstrated in a wide dynamic range of 50 folds but without obvious matrix effect on quantification. Importantly, there was little quantification bias found among the individual IBT tags, indicating that the peptides labeled by different tags were quantitatively comparable. The IBT 10-plex reagents were applied for dynamically monitoring the quantitative responses of phosphoproteome ignited by EGF treatment in Hela cells. Total 5361 unique phosphopeptides were identified, which reached a similar conclusion as other reported. The IBT reagents were therefore experimentally proven as a new type of isobaric labeling peptides and useful for a large quantity peptides of quantitative proteomics.

2022-03-04 | PXD008681 | Pride

Human Plasma from non-Hispanic White and African American Sepsis Survivors and Non-Survivors with Primary Urinary Tract Infection LC-MS/MS

Project description:This study examined global proteomic changes in blood plasma from non-Hispanic White and African American sepsis patients with primary urinary tract infection using LC-MS/MS on a Q-Exactive HF. Proteins were quantified in the LC-MS/MS experiments using Tandem Mass Tags 16-plex (TMTpro).

2023-07-26 | PXD039509 | Pride

Proteomic analysis of APC7 KO mouse Cerebella

Project description:A proteomic comparison of the cerebella of APC7 KO mice versus controls using TMT11-plex reagents

2023-03-10 | PXD016683 | Pride

Human Plasma from non-Hispanic White and African American Sepsis Survivors and Non-Survivors with Primary Intra-Abdominal Infection LC-MS/MS

Project description:This study examined global proteomic changes in blood plasma from non-Hispanic White and African American sepsis patients with primary intra-abdominal infection using LC-MS/MS on a Q-Exactive HF. Proteins were quantified in the LC-MS/MS experiments using Tandem Mass Tags 16-plex (TMTpro).

2022-09-13 | PXD030476 | Pride

Proteomics profiling of human brain cortex for JUMPlib manuscript

Project description:We generated a large TMT proteomics dataset to evaluate the performance of JUMPlib software (an integrative search tool combining fragment ion indexing with comprehensive TMT spectral libraries). This dataset consists of 40 LC-MS/MS fractions generated by the 16/18-plex TMT strategy from the human brain cortex, which were not utilized for the library generation.

2024-11-04 | PXD057366 | Pride

Identification of polyA sites in Drosophila melanogaster

Project description:The 3' ends of most Drosophila melanogaster genes are poorly annotated or are determined by only a single EST or cDNA clone. To enhance the annotation of poly(A) site use in Drosophila, we performed deep sequencing on RNA isolated from 29 dissected tissues using an approach designed to enrich for poly(A) spanning reads. From these experiments, we identified 1.4 million poly(A) spanning reads leading to the identification of many new poly(A) sites and the identification of many tissue-specific poly(A) sites. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf RNA from 29 dissected Drosophila melanogaster tissues (in duplicate) were used to prepare polyA enriched RNA-Seq libraries. Briefly, total RNA was poly(A) selected, fragmented, and ligated to 5' and 3' RNA linkers. These libraries were amplified using Illumina paired-end primers, and subsequently reamplified using a 3' primer complementary to the 3' adapter but containing 6 Ts at the 3' end. The libraries were also multiplexed and up to 12 samples mixed per lane and sequenced on an Illumina GAIIx using paired-end 76 bp reads, or an illumina HiSeq 2000 using paired-end 100 bp reads. All reads were mapped to the Drosophila melanogaster genome to identify unmapped reads. Unmapped reads containing at least 10 A residues at the 3' end were identified, the terminal A residues trimmed, realigned to the genome to identify uniquely mapped reads. Such reads were identified as polyA spanning reads

2011-11-23 | E-GEOD-33905 | biostudies-arrayexpress

NHS-Ester Tandem Labeling in One Pot for 48-Plex Proteomics

Project description:Stable-isotope labeling strategies are extensively used for multiplex quantitative proteomics. Hybrid isotope labeling strate-gies that combine the use of isotopic mass difference labeling and isobaric tags can greatly increase sample multiplexity. In this work, we present a novel hybrid isotope labeling approach that we termed NHS-ester tandem labeling in one pot (NETLOP). We first optimized 16-plex isobaric TMTpro labeling of lysine residues followed by 2-plex or 3-plex isotopic mTRAQ labeling of peptide N-termini, both of which with commercially available NHS-ester reactive reagents. We then demonstrated the utility of the NETLOP approach by labeling HeLa cell samples and performing proof-of-principle quanti-tative 32-plex and 48-plex proteomic analyses, each in a single LC-MS/MS experiment. Compared to current hybrid isotope labeling methods, our NETLOP approach requires no sample cleanup between different labeling steps to minimize sample losses, induces no retention time shifts that compromise quantification accuracy, can be adapted to other NHS-ester isotop-ic labeling reagents to further increase multiplexity, and is compatible with samples from any origin in a wide array of bio-logical and clinical proteomics applications.

2022-02-17 | PXD024780 | Pride

Biomarkers discovery for progressive supranuclear palsy from the human cerebrospinal fluid using mass spectrometry-based proteomics

Project description:Progressive supranuclear palsy (PSP) is a neurodegenerative parkinsonian disorder. This study using CSF samples of PSP patients is a follow-up study to discover biomarkers related to the previous PSP brain results. This study is the first-ever attempt at an in-depth global proteomic study using more than 100 CSF samples for PSP study. In this study, we used the 11-plex isobaric tandem-mass-tag (TMT) technology for more accurate and sensitive quantification of CSF proteins and analyzed them using Orbitrap Fusion Lumos mass spectrometry on 40 PSP and 40 PD patients as well as 40 HC individuals CSF samples for the discovery experiment. These candidate biomarkers discovered in this study will pave the way for the development of reliable PSP biomarkers.

2025-05-06 | PXD041417 | Pride

Global quantitative analysis of the human brain proteome in Alzheimer’s and Parkinson’s Disease

Project description:Patients with Alzheimer’s disease (AD) and Parkinson disease (PD) often have overlap in brain neuropathology and clinical presentation suggesting that these two diseases share common underlying mechanisms. Currently, the molecular events linking AD and PD are incompletely understood. Utilizing 10-plex Tandem Mass Tag (TMT) assays and MultiNotch MS3 mass spectrometry, we performed an unbiased quantitative proteomic analysis of post-mortem human brain tissues (n=80) from four different groups defined as healthy controls, AD, PD, and co-morbid AD/PD cases across two brain regions (frontal cortex and anterior cingulate gyrus). In total, we identified 11,840 protein groups representing 10,230 gene symbols, which map to ~65% of the protein coding genes in brain. The utility of including two reference standards in each TMT 10-plex assay to assess intra-batch and inter-batch variance is also described. Ultimately, this comprehensive human brain proteomic dataset serves as a valuable resource for various research endeavors including, but not limited to, the identification of protein signatures and neuro-centric signaling pathways that are common or distinct in AD and PD.

2018-02-07 | PXD007160 | Pride

YTHDF1 links hypoxia adaptation and non-small cell lung cancer progression

Project description:10plex TMT labelling quantification expriments were performed to access the knockdown effect of YTHDF1 in cells.3 shGFPs control samples, 3 YTHDF1 shRNA-2 knockdown samples , 3 YTHDF1 shRNA-3 knockdown samples and 1 mixture sample were labelled by TMT 10-plex reagents.

2019-09-27 | PXD015182 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data