Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of PTFGRN Expression on the Proteomic Profile of A431 Cells and Determination of the PTGFRN Interactome

ABSTRACT: The exact molecular mechanisms by which PTGFRN influences cancer progression are still unknown. Our laboratory set out to investigate how PTGFRN knockdown affected the expression of other proteins. We also carried out co-immunoprecipitation experiments using a monoclonal anti-PTGFRN antibody. We employed mass spectrometry-based proteomics for both experiments to identify proteins that were associated with PTGFRN.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Mehari Weldemariam

LAB HEAD: Maureen A. Kane

PROVIDER: PXD048092 | Pride | 2024-06-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20230627_JM_A431cell_pellets_and_Co-IP_8C7_4x3_combined.msf	Msf
	20230627_JM_A431cell_pellets_and_Co-IP_8C7_4x3_combined.pdResult	Other
	20230627_JM_IP_strap_205min_1ug_8C7-1.raw	Raw
	20230627_JM_IP_strap_205min_1ug_8C7-2.raw	Raw
	20230627_JM_IP_strap_205min_1ug_8C7-3.raw	Raw

Items per page:

1 - 5 of 15

Publications

Effect of PTFGRN Expression on the Proteomic Profile of A431 Cells and Determination of the PTGFRN Interactome.

Marquez Jorge J Weldemariam Mehari M MM Dong Jianping J Hayashi Jun J Kane Maureen A MA Serrero Ginette G

ACS omega 20240315 12

Prostaglandin F2 receptor negative regulator (PTGFRN) is a transmembrane protein whose expression has been previously implicated in cancer metastasis. However, the exact molecular mechanisms by which PTGFRN influences cancer progression are still unknown. As such, our laboratory set out to investigate how PTGFRN knockdown affected the expression of other proteins. We also carried out coimmunoprecipitation experiments using a monoclonal anti-PTGFRN antibody. We employed mass spectrometry-based pr ...[more]

PMID: 38559916

Similar Datasets

Effects of prenylcysteine oxidase 1 (PCYOX1) silencing on HepG2 cell secretome

Project description:We performed a label free mass spectrometry-based proteomic analysis to investigate the effects of PCYOX1 silencing on the secretome of human HepG2 cells

2021-10-12 | PXD022302 | Pride

Reanalysis of Pandey lab's draft of the human proteome

Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.

2015-03-10 | E-PROT-1 | biostudies-arrayexpress

Easy and Accessible Workflow for Label-Free Single-Cell Proteomics

Project description:Single cell proteomics (SCP) can provide information that is unattainable through either bulk-scale protein measurements or single-cell profiling of other omes. Maximizing proteome coverage often requires custom instrumentation, consumables and reagents for sample processing and separations, which limits accessibility of SCP to a small number of specialized laboratories. Commercial platforms have become available for SCP cell isolation and sample preparation, but the high cost of these platforms and the technical expertise required for their operation place them out of reach of many interested laboratories. Here, we assessed the new HP D100 Single Cell Dispenser for label-free SCP. The low-cost instrument proved highly accurate and reproducible for dispensing reagents in the 200 nL to 2 µL range. We used the HP D100 to isolate and prepare single cells for SCP within 384-well PCR plates. When the well plates were immediately centrifuged following cell dispensing and again after reagent dispensing, we found that ~97% of wells that were identified in the instrument software as containing a single cell indeed provided proteome coverage expected of a single cell. The D100 Single Cell Dispenser combined with one-step sample processing provides a very rapid easy-to-use workflow for SCP with no reduction in proteome coverage relative to a nanowell-based workflow. The commercial well plates also facilitate autosampling with commercial instrumentation. Single cell samples were analyzed using home-packed 30-µm-i.d. nanoLC columns as well as commercially available 50-µm-i.d. columns. The commercial columns led to identification of ~35% fewer identified proteins. However, combined with the well plate-based preparation platform the presented workflow provides fully commercial and relatively low cost alternative for SCP sample preparations and separations, which should greatly broaden accessibility of SCP to other laboratories.

2023-10-09 | PXD043355 | Pride

A streamlined data analysis pipeline for the identification of sites of citrullination

Project description:Citrullination is an enzyme-catalyzed post-translational modification (PTM) that is essential for a host of biological processes including gene regulation, programmed cell death, and organ development. While this PTM is required for normal cellular functions, aberrant citrullination is a hallmark of numerous autoimmune disorders as well as cancer. Although aberrant citrullination is linked to human pathology, the exact role of citrullination in disease remains poorly characterized, in part because of the challenges associated with identifying the specific arginine residues that are citrullinated. Tandem mass spectrometry is the most precise method to uncover sites of citrullination, however, due to the small mass shift (+0.984 Da) that results from citrullination, current database search algorithms commonly misannotate spectra leading to a high number of false-positive assignments. To address this challenge, we developed an automated workflow to rigorously and rapidly mine proteomic data to unambiguously identify the sites of citrullination from complex peptide mixtures. The crux of this streamlined workflow is the ionFinder software program, which classifies citrullination sites with high confidence based on the presence of diagnostic fragment ions. These diagnostic ions include the neutral loss of isocyanic acid, which is a dissociative event that is unique to citrulline residues. Using the ionFinder program, we have mapped the sites of autocitrullination on purified protein arginine deiminases (PADs 1-4) and mapped the global citrullinome in a PAD2 over-expressing cell line. The ionFinder algorithm is a highly versatile, user-friendly, and open-source program that is agnostic to the type of instrument and mode of fragmentation that is used.

2021-11-25 | PXD027358 | Pride

Geographical origin and antigenicity of venom. Intraspecies proteomic and immunological analysis of Naja mossambica venom.

Project description:The main objective of the project is to find the reason why antivenoms commonly used in treatments of Naja mossambica bites are not effective in Eswatini and Mozambique, whereas they exhibit normal activity in other countries of southern Africa. The main hypothesis here assumes that intra-species differences in protein composition of venoms from different part of the continent are the main cause of observed diversity in antivenom efficacy. In the course of the project, there is also a plan to identify the specific toxins that differ analyzed venoms in reactivity towards antivenom immunoglobulins.

2024-03-15 | PXD043647 | Pride

Proteomic landscape of atypical antipsychotics clinical response in blood plasma from schizophrenia patients

Project description:Antipsychotics are the main line of treatment for schizophrenia, despite being effective only in about 50% of patients. Additionally, serious side effects may cause medication drop-out, aggravated by a lack of understanding about how these drugs act at molecular level. As proteomics is a suitable tool for studying multifactorial disorders, the main goal was to unravel signaling pathways in blood plasma associated with a positive treatment outcome for the atypical antipsychotics olanzapine and risperidone. Blood plasma was collected from schizophrenia patients six weeks after treatment (T6), and patients were classified as good or poor responders to olanzapine or risperidone, and then samples were compared to each patient's baseline (T0). All samples were analyzed using label-free quantitative shotgun proteomics. Samples were depleted of the 14 most abundant proteins in plasma, were digested, and then submitted to M-Class two-dimensional nano-liquid chromatography, coupled online to a Synapt G2-Si mass spectrometer. Data was obtained in MSE mode (data- independent acquisition) in combination with ion-mobility (HDMSE). The proteins found to be differentially abundant in good responders compared to poor responders for risperidone and olanzapine were functionally analyzed in silico using Ingenuity® Pathway Analysis and were found to be mostly involved with immune system functions. This data can contribute to better understand the biochemical signaling peripherally triggered by antipsychotic medication, and can eventually be used to help improve treatment outcome by predicting patient response as well as through the development of new medication or a combination of drugs that act on the immune system to reduce the duration of poor response periods in patients suffering with schizophrenia.

2020-06-01 | PXD015049 | Pride

Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics

Project description:We investigated the compatibility of tube-gel with alternatives to SDS-based buffers allowing notably the extraction of proteins in various pH conditions. We also explored the use of photopolymerization to extend the number of possibilities, as it is compatible with a wide range of pH and is non-oxydative. To achieve this goal, we compared six extraction buffers in combination with two polymerization conditions to further optimize tube-gel protocol and evaluate its versatility.

2018-06-06 | PXD008656 | Pride

Multi-OMICS data of a Hyper IgD Syndrome family

Project description:The aim of this study was to understand why two siblings carrying both the same homozygous causal mutation for the auto-inflammatory disease hyper IgD show opposite phenotypes, i.e. the first being asymptomatic, the second presenting all classical characteristics of the disease. As compared to studies of a single omics type, the multi-omics approach becomes a method of choice to resolve complex traits. Here we combined exome, proteome and transcriptome analysis in the two siblings and identified a single gene - STAT1 - harboring a rare missense variant and showing mRNA and protein abundances significantly more important in the symptomatic than the asymptomatic sister. This mutation was shown to be a gain of function mutation involved in an increased activation of the JAK/STAT pathway which is known to play a critical role in inflammatory diseases and for which specific bio-therapies exist. Pathway analysis based on information from differentially expressed transcripts and proteins confirmed the central role of STAT1 in the proposed regulatory network leading to an increased inflammatory phenotype in the symptomatic sibling. In addition, we provide a proteogenomics analysis pipeline that takes advantage of subject-specific genomic and transcriptomic information to improve protein identifications. In conclusion, this study demonstrates the power of a multi-omics approach to uncover potentially clinically actionable targets for a personalized therapy.

2019-10-24 | PXD009063 | Pride

Normal human mitral valve proteome: a preliminary investigation by gel-based and gel-free proteomic approaches

Project description:The mitral valve is a highly complex structure which regulates blood flow from the left atrium to the left ventricle (LV) avoiding a significant forward gradient during diastole or regurgitation during systole. The integrity of the mitral valve is also essential for the maintenance of normal LV size, geometry, and function. Significant advances in the comprehension of the biological, functional, and mechanical behavior of the mitral valve have recently been made. However, current knowledge of protein components in the normal human mitral valve is still limited and complicated by the low cellularity of this tissue and the presence of high abundant proteins from the extracellular matrix. We employed here an integrated proteomic approach to analyse the protein composition of the normal human mitral valve and reported confident identification of 422 proteins, some of which have not been previously described in this tissue. In particular, we described the ability of pre-MS separation technique based on liquid-phase IEF and SDS-PAGE to identify the largest number of proteins. These initial results provide a valuable basis for future studies aimed at analysing in depth the mitral valve protein composition and at investigating potential pathogenetic molecular mechanisms.

2016-08-18 | PXD004397 | Pride

SARS-CoV-2 infects brain astrocytes of COVID-19 patients and impairs neuronal viability

Project description:COVID-19 patients may exhibit neuropsychiatric and neurological symptoms. We found that anxiety and cognitive impairment are manifested by 28-56% of SARS-CoV-2-infected individuals with mild respiratory symptoms and are associated with altered cerebral cortical thickness. Using an independent cohort, we found histopathological signs of brain damage in 25% of individuals who died of COVID-19. All of the affected brain tissues exhibited foci of SARS-CoV-2 infection and replication, particularly in astrocytes. Infection of neural stem cell-derived astrocytes changed energy metabolism, altered key proteins and metabolites used to fuel neurons and for biogenesis of neurotransmitters, and elicited a secretory phenotype that reduces neuronal viability. Our data support the model where SARS-CoV-2 reaches the brain, infects astrocytes and triggers neuropathological changes that contribute to the structural and functional alterations in the brain of COVID-19 patients.

2022-09-01 | PXD023781 | 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