Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Temporal Insights into Molecular and cellular responses during rAAV production in HEK293T cells

ABSTRACT: To understand the dynamic role of HEK293T cells at different cellular states post-transfection we have performed a comprehensive comparative proteome profiling of the host cell system post-transfection at 24, 48, and 72 hpt. For this study, we developed an in-house label-free HEK293T-AAV spectral library

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture

SUBMITTER: Alok Tanala Patra

LAB HEAD: Dr. Bi Xuezhi

PROVIDER: PXD046574 | Pride | 2024-08-09

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20210906_Hek_4ug.mzML	Mzml
	20210909_DDA_HEK293_F1.mzML	Mzml
	20210913_HEK293_F10_4ug.mzML	Mzml
	20210913_HEK293_F11_4ug.mzML	Mzml
	20210913_HEK293_F1_4ug.mzML	Mzml

Items per page:

1 - 5 of 70

Publications

Temporal insights into molecular and cellular responses during rAAV production in HEK293T cells.

Patra Alok Tanala AT Tan Evan E Kok Yee Jiun YJ Ng Say Kong SK Bi Xuezhi X

Molecular therapy. Methods & clinical development 20240608 3

The gene therapy field seeks cost-effective, large-scale production of recombinant adeno-associated virus (rAAV) vectors for high-dosage therapeutic applications. Although strategies like suspension cell culture and transfection optimization have shown moderate success, challenges persist for large-scale applications. To unravel molecular and cellular mechanisms influencing rAAV production, we conducted an SWATH-MS proteomic analysis of HEK293T cells transfected using standard, sub-optimal, and ...[more]

PMID: 39022743

Similar Datasets

Phosphoproteomics of endothelin signalling

Project description:Time resolved phosphorylation changes were measured the melanoma cell lines A2058 and UACC257. An endothelin B receptor knockout of UACC257 was processed in parallel. Protein abundance was also compared at the latest time point of the study (90 min) using DIA-SWATH

2019-10-09 | PXD012316 | Pride

The DIALib-QC software tool for the systematic assessment of spectral library quality in data-independent acquisition proteomics

Project description:DIALib-QC (DIA library quality control) tool is used for the systematic evaluation of a spectral library’s characteristics, completeness and mass-accuracy ensuring correct identification and accurate quantitation of peptides and proteins from DIA/SWATH processing tools.

2020-10-16 | PXD020953 | Pride

Rapid, Deep and Precise Profiling of the Plasma Proteome with Multi-Nanoparticle Protein Corona

Project description:We report a highly parallel protein quantitation platform integrating nanoparticle (NP) protein coronas with liquid chromatography-mass spectrometry for large-scale, efficient proteomic profiling. A protein corona is a protein layer adsorbed onto NPs upon contact with biofluids. Varying the physicochemical properties of engineered NPs translates to distinct protein corona patterns enabling differential and reproducible interrogation of biological samples. Spike experiments confirmed a linear signal response. The median coefficient of variation was ~22%. The NP corona formation enables deep sampling of the plasma proteome. We screened 43 NPs and selected a panel of 5, which detected more than 2,000 proteins from 141 plasma samples using a 96-well automated workflow in a pilot cancer classification study. Our streamlined workflow combines depth of coverage and throughput with precise relative quantification based on unique interactions between proteins and a panel of engineered NPs for deep and scalable quantitative proteomic studies and biomarker discovery.

2020-08-12 | PXD017052 | Pride

Protein content of blood-derived extracellular vesicles. An approach to the pathophysiology of cerebral hemorrhage

Project description:Extracellular vesicles (EVs) participate in cell-to-cell paracrine signaling and can be biomarkers of the pathophysiological processes underlying disease. In intracerebral hemorrhage (ICH), the study of the number and molecular content of circulating EVs may help elucidate the biological mechanisms involved in damage and repair, contributing valuable information to the identification of new therapeutic targets. The objective of this study was to describe the number and protein content of blood-derived EVs following an ICH in an animal model in rats. The protein content in the EVs was analyzed by mass spectrometric data-dependent acquisition; protein quantification was obtained by sequential window acquisition of all theoretical mass spectra data and compared at pre-defined time points.

2023-01-17 | PXD037246 | Pride

Circulating extracellular vesicles promote recovery in a preclinical model of intracerebral haemorrhage.

Project description:Extracellular vesicles (EVs) participate in cell-to-cell paracrine signaling and can be biomarkers of the pathophysiological processes underlying disease. In intracerebral hemorrhage (ICH), the study of the number and molecular content of circulating EVs may help elucidate the biological mechanisms involved in damage and repair, contributing valuable information to the identification of new therapeutic targets. The objective of this study was to describe the number and protein content of blood-derived EVs following an ICH in an animal model in rats treated with allogenic or xenogenic (human) EVs. The protein content of the EVs from the treated animals and control group was analyzed by mass spectrometric data-dependent acquisition; protein quantification was obtained by sequential window acquisition of all theoretical mass spectra data and compared at pre-defined time points.

2023-03-31 | PXD038630 | Pride

Breaking the mucin barrier: a new affinity chromatography-mass spectrometry approach to unveil potential cell markers and pathways altered in Pseudomyxoma peritonei

Project description:Pseudomyxoma peritonei (PMP) is a rare, malignant tumour with unknown underlying molecular mechanisms characterised by a progressive accumulation of mucin and secreting tumour cells within the abdomen and pelvis. Cytoreductive surgery (CRS) combined with hyperthermic intraperitoneal chemotherapy (HIPEC) is the only therapeutic option currently available for its treatment and recurrence with a fatal outcome is common despite its use. The lack of information available about the molecular mechanisms underlying this condition is mainly due to the physicochemical characteristics of mucin, whose main purpose is to protect epithelial cells, which makes it inaccessible to a proteomic analysis. In this paper we describe the first protocol available to break this barrier and offer a chance to isolate proteins from soft and hard mucinous tumour tissues. This approach is based on the depletion of glycoproteins, immunoglobins, and albumins by affinity liquid chromatography, which makes the mucin available for label free quantification by mass spectrometry. As in the case of non mucinous tissues, our protocol yields a mix of total proteins and has allowed us to establish the first protein profile in mucinous tumours. In addition, our protein-protein interaction networks and pathway enrichment analyses revealed MUC13 and TFF1 as potential therapeutic targets in this disease.

2024-06-22 | PXD037364 | Pride

VPBrowse, genome-based representation of MS/MS spectra to quantify 10,000 bovine proteins

Project description:SWATH is a mass spectrometry data acquisition strategy that relies on peptide spectral libraries to perform quantitatively accurate and consistent measurement of proteins across multiple samples. Public libraries have been developed for humans and several laboratory species that have accelerated biomarker discovery, and similarly comprehensive resources would be useful for other species. The Veterinary Proteome Browser, VPBrowse (http://browser.proteo.cloud/), is an on-line platform developed for genome-based representation of the Bos taurus proteome and is equipped with an interactive database and tools for visualization and building quantitative mass spectrometry assays. VPBrowse contains high quality tandem mass spectrometry (MS/MS) spectra acquired on QToF instrument for over 36,000 proteotypic peptides corresponding to over 10,000 bovine proteins. Data can be downloaded in different formats to enable analysis using popular software packages for SWATH data processing whilst normalization to iRT scale ensures compatibility with diverse chromatography systems. When applied to 25 different tissues and body fluids, the resource supported label-free quantification of nearly 30% of the protein-coding genes annotated in bovine section of UniprotKB.

2024-03-07 | PXD044768 | Pride

Proteomics of Campylobacter glycosylation

Project description:N-linked glycosylation is an essential virulence determinant in Campylobacter jejuni, the major causative agent of gastroenteritis in the developed world. Glycosylation is encoded by the pgl gene cluster which encodes for the biosynthesis and attachment of a conserved heptasaccharide glycan to proteins in the C. jejuni periplasm. Over 80 membrane-associated proteins have been identified, however the functional role played by glycan attachment is almost completely unknown. We used quantitative proteomics by label-based and targeted strategies to examine glycosylation negative C. jejuni in comparison to wild-type. These technical approaches were considered as ‘discovery’ (label-based) and ‘validation’ data sets in our subsequent analysis. Inclusion of a glycosylation restored strain enabled us to further exploit the proteomics data to exclude non-specific protein abundance changes that could be considered as off-target effects. These data have provided a reference set of changes associated with protein N-glycosylation that could subsequently be tested by phenotypic analysis to determine the role of this modification in Campylobacter biology.

2019-01-11 | PXD011646 | Pride

Using SWATH-MS to Identify New Molecular Biomarkers in Gingival Crevicular Fluid for Detecting Periodontitis and its Response to Treatment

Project description:Over the last years, proteomic techniques have been demonstrated to be valuable tools for analysing the periodontal proteome in gingival crevicular fluid (GCF) samples contributing to identifying extensive and comprehensive protein profiles associated with periodontitis. However, the periodontal proteome has not yet been studied using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Consequently, the objective of the present longitudinal research was to investigate the periodontal proteome in GCF in three clinical conditions (periodontal health, untreated periodontitis, and treated periodontitis), applying SWATH-MS to 1) analyse the periodontal proteome structure in the three clinical groups, 2) compare the differential protein expression between the three clinical groups, and 3) evaluate the diagnostic accuracy of the proteins quantified to identify new biomarkers with a high capacity to discriminate the three clinical conditions. A total of 84 subjects, 44 periodontally healthy and 40 with generalised untreated periodontitis in stages III-IV, were included, and GCF samples were collected. The diagnosis of periodontal status was conducted by two experienced dentists using clinical and radiographic criteria. The definition of periodontal status was established following the Classification of Periodontal Diseases and Conditions published in 2018. In the untreated periodontitis group, 38 underwent conventional non-surgical treatment and were evaluated clinically after two months (treated periodontitis group). In the revaluation, 25 individuals showed significant clinical improvement in probing pocket depth (PPD) at the selected sites, and GCF samples were collected from them.

2024-10-17 | PXD043474 | Pride

Inhibitor of Differentiation 4 (ID4) represses myoepithelial differentiation of mammary stem cells through its interaction with HEB

Project description:Differentiation of stem cells embedded within the mammary epithelium is orchestrated by lineage-specifying transcription factors. Unlike the well-defined luminal hierarchy, dissection of the basal lineage has been hindered by a lack of specific markers. Inhibitor of Differentiation 4 (ID4) is a basally-restricted helix-loop-helix (HLH) transcription factor essential for mammary development. Here we show that ID4 is highly expressed in basal stem cells and decreases during myoepithelial differentiation. By integrating transcriptomic, proteomic and chromatin-association data we reveal that ID4 is required to suppress myoepithelial gene expression and cell fate.

2021-01-25 | PXD017517 | 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