Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sexual dimorphism in zebrafish liver proteins

ABSTRACT: The aim of the present study was to carry out a high-throughput screening of proteins using proteomics tool to identify and quantify proteins and related biochemical pathways that orchestrate the sexual dimorphism in the liver of zebrafish. In addition, we tried to discover potential connections between the sex-biased levels of proteins in liver and hepatic diseases and regeneration via review of related literature.

INSTRUMENT(S):

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Liver

SUBMITTER: Hamid Niksirat

LAB HEAD: Fredrik Levander

PROVIDER: PXD061886 | Pride | 2025-09-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	220323_Hamid_10FL.raw	Raw
	220323_Hamid_11FL.raw	Raw
	220323_Hamid_12FL.raw	Raw
	220323_Hamid_13FL.raw	Raw
	220323_Hamid_14FL.raw	Raw

Items per page:

1 - 5 of 14

Similar Datasets

Proteomic effects of budesonide and imiquimod on human bronchial epithelial cells

Project description:We carry out a comparative proteomic analysis of human bronchial epithelial cells from patients clinically treated or not with inhaled budesonide and stimulated or not with the viral mimic Poly(I:C).We also wanted to investigate the potential anti-viral effects of imiquimod, a TLR7 agonist, on the bronchial epithelial cells proteome in vitro.

2021-11-22 | PXD029135 | Pride

Effects of SLIRP knockout in mouse mitochondria

Project description:Effects of SLIRP knockout in mouse mitochondria and mitoribosomes was studied using label-free quantitative proteomics

2024-07-26 | PXD046268 | Pride

Linking acetyl-CoA labelling and histone acetylation dynamics for accurate determination of acetylation rates via ordinary differential equations

Project description:To study complex biological systems, multi-omics methods have become an important tool. They integrate data from multiple biological layers, such as the metabolome and the proteome, to gain better insights of the processes happening. However, challenges remain both in sample preparation for measurements of different types of analytes as well as in the integration of different data types. Post-translational modifications such as acetylation of proteins are an example of a highly dynamic, reversible process that combines core metabolism with protein function. Histones are small proteins binding DNA that are highly acetylated in their N-terminal region. In this study, we utilise a simultaneous extraction method for acetyl-CoA and histones in combination with combined metabolic and chemical acetylation (CoMetChem) to track metabolic label incorporation into both acetyl-CoA and histones. Acetyl-CoA formation rates as well as histone acetylation- and deacetyation rates are modelled by ordinary differential equation, allowing the combination of data from acetyl-CoA and histone acetylation measurements into a unified model. We find that correcting for acetyl-CoA formation is necessary to accurately determine histone acetylation rates, particularly in systems with changes in upstream metabolism.

2025-05-06 | PXD051487 | Pride

Urine-HILIC – An automated sample preparation for bottom-up urinary proteome profiling in clinical proteomics

Project description:Urine provides a diverse source of information related to health status and is ideal for clinical proteomics because of its ease of collection. To date, there is no standard operating procedure for reproducible and robust urine sample processing for mass spectrometry-based clinical proteomics. To address this need, a novel workflow was developed based on an on-bead protein capture, clean up, and digestion without the requirement from pre-processing steps such as precipitation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample were subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using a novel urine-HILIC (uHLC) approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analysed by LCMS in DIA mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. Data was searched in Spectronaut™ 17. Following statistical analysis, candidate protein markers were filtered at ≥ 2-fold change in abundance, ≥ 2 uniques peptides and ≤ 1% false discovery rate. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method. With fewer manuel processiing steps, a lower peptide and protein CV was observed in the uHLC technical replicates. Analysis of clinical samples revealed many significant, differentially abundant kidney injury-associated urinary proteins. The pilot data derived using this novel workflow provides information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.

2024-01-26 | PXD043925 | Pride

Proteomic dataset of two contrasting sorghum genotypes to drought, heat and combined drought and heat stress

Project description:The present study used Label-Free LC-MS/MS quantification approach to investigate changes in the proteomic profiles of two contrasting sorghum genotypes subjected to drought, heat and combined drought and heat stress. The interpretation of the data generated through this study could improve our understanding of sorghum molecular adaptations to these stresses.

2024-12-06 | PXD052255 | Pride

Evaluation of protein purification techniques and effects of storage duration on LC-MS/MS analysis of archived FFPE human CRC tissues

Project description:To elucidate cancer pathogenesis and its mechanisms at the molecular level, the collecting and characterisation of large individual patient tissue cohorts are required. Since most pathology institutes routinely preserve biopsy tissues by standardised methods of formalin fixation and paraffin embedment, these archived FFPE tissues are important collections of pathology material that include patient’s metadata (medical history/treatments). FFPE blocks can be stored under ambient conditions for decades, while retaining cellular morphology, due to modifications induced by formalin. However, the effect of long-term storage, at resource-limited institutions in developing countries, on extractable protein quantity/quality has not yet been investigated. In addition, the optimal sample preparation techniques required for accurate, reproducible results from label-free LC-MS/MS analysis across block ages remains unclear. This study investigated protein extraction efficiency of 1, 5 and 10-year old human colorectal carcinoma resection tissue and assessed three different gel-free sample preparation methods for label-free LC-MS/MS analysis. The results indicate that the amount of protein extracted (mg/ml) is significantly dependent on block age, with older blocks yielding less protein than newer blocks. This may be due to the effect of formalin-fixation, which is an ongoing process, over long periods of storage. Detergent removal plates were the most efficient and overall reproducible sample preparation method with regard to number of peptide and protein identifications, followed by the SP3/HILIC method, and lastly the APFAR method. Therefore, block age mainly affects initial protein extraction and does not show significant differences/biases with regard to subsequent label-free LC-MS/MS analysis results.

2021-04-06 | PXD017198 | Pride

Integrated Single-Tip IMAC-HILIC Enrichment Enables Simultaneous and Efficient Analysis of Plant Phosphoproteomics and N-glycoproteomics

Project description:Protein phosphorylation and N-glycosylation are key post-translational modifications (PTMs) in plants that regulate critical signaling processes. However, analyzing both PTMs simultaneously remains challenging due to low abundance and divergent enrichment requirements. Here, we present a single-tip IMAC-HILIC approach that integrates immobilized metal affinity chromatography (IMAC) and hydrophilic interaction chromatography (HILIC) materials within one pipette tip, enabling concurrent enrichment and sequential elution of phosphopeptides and N-glycopeptides. This workflow effectively reduces coelution of phosphopeptides during N-glycopeptide elution and significantly streamlines sample processing. Benchmarking against the tandem-tip TIMAHAC method demonstrates comparable identification depth and superior quantitative accuracy for N-glycopeptides. We further apply IMAC-HILIC to examine calcium deprivation in Arabidopsis, revealing distinct global changes in both phosphoproteome and N-glycoproteome. Our optimized protocol offers a practical, high-throughput solution for dual PTM profiling in complex plant samples, paving the way for broader investigations for PTM crosstalk in diverse physiological and stress responses.

2025-05-14 | PXD061247 | Pride

Methylation profiling in colorectal cancer

Project description:Methylation profiling in colorectal cancer : adjacent normal tissue vs colon tumor tissue indirect comparison experiment : CRD(common reference DNA) vs tumor-adjacent normal, CRD vs Colon tumor

2012-03-10 | E-GEOD-36380 | biostudies-arrayexpress

Human brain glycoproteomic network alterations in Alzheimer’s disease

Project description:We performed a large-scale, site-specific N-glycoproteome profiling study of human Alzheimer’s disease (AD) and control brains using mass spectrometry–based quantitative N-glycoproteomics. The study provided a system-level view of human brain N-glycoproteins and in vivo N-glycosylation sites and identified disease signatures of altered N-glycopeptides, N-glycoproteins, and N-glycosylation site occupancy in AD. Glycoproteomic data-driven network analysis showed 13 modules of co-regulated N-glycopeptides/glycoproteins, 6 of which are associated with AD phenotypes.

2022-11-02 | PXD037229 | Pride

SARS-CoV-2 spike protein glycosylation enriched by HILIC and Ti-IMAC

Project description:In this work, we performed a fully descriptive analysis N- and O- linked glycosylation of SARS-COV-2 S glycoprotein. We investigated that dual-functionalized Ti-IMAC material enable the simultaneous enrichment and separation of neutral and sialyl glycopeptides of a recombinant SARS-CoV-2 S glycoprotein from HEK293, which will eliminate the signal suppression of neutral glycopeptides to sialyl glycopeptides and improve the glycoform coverage of S protein. We have profiled 19 of its 22 potential N-glycosylated sites with 398 unique glycoforms in dual-functional Ti-IMIAC approach that is 1.6-fold of that in conventional HILIC method. We also identified O-linked glycosylation site that was not found in dual-functional Ti-IMIAC approach. In addition, we have also identified mannose-6-phosphate (M6P) glycosylation, which substantially expands the current knowledge of the spike protein’s glycosylation and enables the investigation of the influence of mannose-6-Phosphate on its cell entry.

2022-01-11 | PXD026450 | 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