Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of human naive pluripotent and trophoblastic stem cells

ABSTRACT: This project aims at identifying missing proteins in naive pluripotent and trophoblastic stem cells in the framework of the human proteome project (HPP). To date, as much as 1343 missing proteins remain to be credibly identified essentially, but not entirely, by mass spectrometry. The present results also constitute a first step towards the identification of potential biological markers for assessing stem cells and early embryo development.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Stem Cell

SUBMITTER: E Com

LAB HEAD: Charles Pineau

PROVIDER: PXD035768 | Pride | 2023-03-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Naive Pluripotent and Trophoblastic Stem Cell Lines as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project.

Girard Océane O Lavigne Régis R Chevolleau Simon S Onfray Constance C Com Emmanuelle E Schmit Pierre-Olivier PO Chapelle Manuel M Fréour Thomas T Lane Lydie L David Laurent L Pineau Charles C

Journal of proteome research 20221129 4

The Chromosome-centric Human Proteome Project (C-HPP) aims at identifying the proteins as gene products encoded by the human genome, characterizing their isoforms and functions. The existence of products has now been confirmed for 93.2% of the genes at the protein level. The remaining mostly correspond to proteins of low abundance or difficult to access. Over the past years, we have significantly contributed to the identification of missing proteins in the human spermatozoa. We pursue our search ...[more]

PMID: 36445260

Similar Datasets

Proteomics of endometriosis

Project description:This project aims at comparing endometrium from women with and without endometriosis during the secretory phase of menstrual cycle. The present results constitute a first step towards identifying potential diagnosis biomarkers and may provide a better understanding of endometriosis especially the etiology of the disease.

2022-04-01 | PXD012981 | Pride

To identify the nuclear partner(s) of TYRO3 in colon cells using LC-Quadrupole Time-of-Flight Mass Spectrometry.

Project description:Colorectal cancer (CRC) is one of the most common death-related cancers worldwide. Aberrant expression of oncogenes is regarded as a predominant factor in CRC development. In our study, we found that TYRO3 intracellular domain nuclear translocation promotes CRC cell proliferation, metastasis, and tumor progression. To identify downstream effector that transmits the cellular functions of nuclear TYRO3, we performed nuclear TYRO3 co-immunoprecipitation.

2023-05-10 | PXD029743 | Pride

nitric oxide-reducing microbial community metaproteomics

Project description:Here, we successfully used NO as the direct electron acceptor for the enrichment of a microbial community in a continuous bioreactor. The enrichment culture, mainly comprised of two new organisms from the Sterolibacteriaceae family, grew on NO reduction to N2 and formate oxidation, with virtually no accumulation of N2O. The microbial growth kinetics of the enrichment culture as well as its affinity for different N-oxides were determined. In parallel, using metagenomics, metatranscriptomics, and metaproteomics, the biochemical reactions underlying the growth of these microorganisms on NO were investigated. This study demonstrates that microorganisms thrive and can be enriched on NO, and presents new opportunities to study microbial growth on this highly energetic and climate-active molecule that may have been pivotal in the evolution of aerobic respiration.

2023-06-09 | PXD037586 | Pride

Proteomic and cellular responses against mutagenesis

Project description:Endogenous stress represents a major source of genome instability, but is in essence difficult to apprehend. Incorporation of labeled radionuclides into DNA constitutes a tractable model to analyze cellular responses to endogenous attacks. Here we show that incorporation of [3H]thymidine into CHO hamster cells generates oxidative-induced mutagenesis, but, with a peak at low doses. Proteomic analysis showed that the cellular global response differs between low and high levels of endogenous stress. In particular, these results confirmed the involvement of proteins implicated in redox homeostasis and DNA damage signaling pathways. Induced-mutagenesis was abolished by the anti-oxidant N-acetyl cysteine and plateaued, at high doses, upon exposure to L-buthionine sulfoximine, which represses cellular detoxification. The [3H]thymidine-induced mutation spectrum revealed mostly base substitutions, exhibiting a signature specific for low doses (GC>CG and AT>CG). Consistently, the enzymatic activity of the base excision repair protein APE-1 is induced at only medium or high doses. Collectively, the data reveal that a threshold of endogenous stress must be reached to trigger cellular detoxification and DNA repair programs; below this threshold, the consequences of endogenous stress escape cellular surveillance, leading to high levels of mutagenesis. Therefore, low doses of endogenous local stress can jeopardize genome integrity more efficiently than higher doses.

2016-07-15 | PXD003542 | Pride

Characterization of ISG65-Cd3 complex

Project description:Identification of disulfide bonds of ISG65 protein and hydrogen-deuteium exchange with mass spectrometry for characterization of protein-protein interaction area.

2023-05-10 | PXD033606 | Pride

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 disease specific mechanisms and vulnerabilities.

Project description:Coronaviruses constitute a constant threat as documented by the recent emergence of SARS-CoV-2 that has caused more than 2,5 million deaths worldwide. Despite this our understanding of coronaviruses and how they interact with their host is very limited. Here we describe a novel phage display library for the discovery of viral short linear interaction motifs (SLiMs) from RNA viruses that mediate binding to human host factors. We utilize this library to uncover the unique patterns of viral SLiMs mediating SARS-CoV-2 - host factor interactions. This established a specific interaction between the human G3BP1/2 proteins and an xFG peptide motif in the viral nucleocapside (N) protein that when disrupted reduce viral replication and infection. We show that the N protein through this xFG motif modulates the G3BP1/2 host interactome by competing with numerous cellular xFG containing proteins and inhibits G3BP1/2 mediated stress granule formation. Collectively our work outlines a strategy for system-wide understanding of viral-host factor interactions that provides both mechanistic insight and pinpoints therapeutically relevant interactions for development of novel antiviral strategies.

2021-10-29 | PXD025410 | Pride

Moonlighting chaperone 1 activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa

Project description:Pseudomonas aeruginosa is a major cause of nosocomial infections and also leads to severe exacerbations in cystic fibrosis or chronic obstructive pulmonary disease. Three intertwined quorum sensing systems control virulence of P. aeruginosa, with the rhl circuit playing the leading role in late and chronic infections. The majority of traits controlled by rhl transcription factor RhlR depend on PqsE, a dispensable thioesterase in Pseudomonas Quinolone Signal (PQS) biosynthesis that interferes with RhlR through an enigmatic mechanism likely involving direct interaction of both proteins. Here we show that PqsE and RhlR form a 2:2 protein complex that, together with RhlR agonist N-butanoyl-L-homoserine lactone (C4-HSL), solubilizes RhlR and thereby renders the otherwise insoluble transcription factor active. We determined crystal structures of the complex and identified residues essential for the interaction. To corroborate the chaperone like activity of PqsE, we designed stability-optimized variants of RhlR that bypass the need for C4-HSL and PqsE in activating PqsE/RhlR-controlled processes of P. aeruginosa. Together, our data provide insight into the unique regulatory role of PqsE and lay groundwork for developing new P. aeruginosa-specific pharmaceuticals.

2023-03-11 | PXD038000 | Pride

Bacteriocin producing Enterococcus faecium

Project description:Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from foodstuffs

2023-03-11 | PXD037241 | Pride

Palaeoproteomics species identification of Toteng remains

Project description:This project has two main objectives: 1. Identify the best suited decalcification protocol for bones and teeth from African archaeological sites; 2. Provide species identification of the remains based on UHPLC-MS/MS data.

2018-09-14 | PXD010725 | Pride

Comparison of bone demineralization protocols for paleoproteomics applications

Project description:Protocols for bone protein extraction adapted for radiocarbon dating were compared for their capability of being used also for paleoproteomics applications. Eight extraction protocols were tested on modern and archaeological bones. Molecular characterization of the extracts was performed by shot-gun proteomics. The effect of each extraction protocol on species identification through database searchnig was evaluated.

2018-12-11 | PXD010775 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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