Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The identification of novel peptides in bivalves.

ABSTRACT: The identification of novel peptides in bivalves by LC-MS/MS.

ORGANISM(S): Cellular Organisms

SUBMITTER: Yoshio Kodera

PROVIDER: PXD031105 | JPOST Repository | Fri Jan 20 00:00:00 GMT 2023

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Cfnym001_001_Penshell_Vg_DS85K_Fra12_3uL_T65.mgf	Mgf
	Cfnym001_001_Penshell_Vg_DS85K_Fra12_3uL_T65.mzid	Mzid
	Cfnym001_001_Penshell_Vg_DS85K_Fra12_3uL_T65.raw	Raw
	Cfnym001_002_Penshell_Vg_DS85K_Fra13_3uL_T65.mgf	Mgf
	Cfnym001_002_Penshell_Vg_DS85K_Fra13_3uL_T65.mzid	Mzid

Items per page:

1 - 5 of 15

Similar Datasets

Identification of targets of the protein disulfide reductase thioredoxin

Project description:Identification of targets of the protein disulfide reductase thioredoxin using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and thiol specific differential labeling with isotope-coded affinity tags (ICAT). Reduction of specific target disulfides is quantified by measuring ratios of cysteine residues labeled with the heavy (13C) and light (12C) ICAT reagents in peptides derived from tryptic digests of Trx-treated and non-treated samples. Keywords: protein, LC-MS/MS, ICAT

2008-11-20 | GSE11650 | GEO

Improved prediction of endogenous HLA-associated epitopes based on mono-allelic mass spectrometry profiling

Project description:LC-MS/MS-based identification of HLA-peptides is poised to provide a deep understanding of the rules underlying antigen presentation. However, a key obstacle limiting the utility of MS data is the ambiguity arising from the co-expression of multiple HLA alleles. Here, we introduce a strategy for profiling the HLA ligandome one allele at a time. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing a novel spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of novel binding motifs, and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a scalable strategy for systematically learning the rules of endogenous antigen presentation.

2017-02-21 | GSE93315 | GEO

Identification of Vaccinia Virus HLA Class I Peptides Presented by the Immune System

Project description:Seeking to identify HLA class I peptides that originate from vaccinia virus proteins to understand the mechanism of immune protection. Note that vaccinia-infected B cells will still continue to present (primarily) a wide variety of peptides originating from endogenous proteins; this data set contains evidence for more than 5000 such peptides. The objective and challenge is to detect and identify the peptides that originate from the pathogen (vaccinia virus) in the presence (background) of this large number of endogensous 'self' peptides. Keywords: Peptide search results from multiple injections of multiple strong cation exchange fractions combined into one set of results.

2009-08-31 | GSE10549 | GEO

Identification of HELLS as a Novel DNA G-quadruplex Helicase

Project description:Guanine quadruplexes (G4s) are unique secondary structures of nucleic acids with functions in many biological processes. Understanding the biological functions of DNA G4s requires the knowledge about their recognitions by cellular proteins. Affinity pull-down coupled with LC-MS/MS analysis was previously employed to identify G4-binding proteins (G4BPs); the approach, however, has limitations in capturing weak and transient interactions, potentially leading to false-positives. Here, we developed a photoclick chemistry-based method, in combination with LC-MS/MS, for uncovering G4BPs. By incorporating a photoactivatable ortho-nitrobenzylamine (o-NBA) moiety into G4 DNA probes and employing UVA irradiation along with stringent washing, we identified 99 proteins enriched with G4 structures derived from the human telomere. We further validated the abilities of one of these proteins, HELLS, in binding and resolving G4 structures both in vitro and in chromatin. Together, we developed a photoclick chemistry-based approach for identifying novel G4BPs. Our work led to the discovery of new G4BPs, and uncovered novel functions of HELLS in recognizing and unwinding G4 structures in vitro and in cells.

2025-04-01 | GSE263592 | GEO

Identification of HELLS as a Novel DNA G-quadruplex Helicase [ChIP-Seq]

2025-04-01 | GSE271227 | GEO

Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance

Project description:Although evidence accumulates on the role of plant peptides in the response to external conditions, the number of peptide-encoding genes in the genome is still underestimated. In order to identify novel oxidative stress-induced peptides in Arabidopsis thaliana a tiling array analysis (GeneChipM-BM-. Arabidopsis Tiling 1.0R Arrays ) was performed on mRNA extracted from leaves treated with paraquat (PQ), an reactive oxygen species inducer and water (control), resulting in the identification of 92,844 and 86,272 transcriptionally active regions (TARs), respectively. Normalized log signals were obtained using the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. ON and OFF probes were selected using a treshold, based on positive controls. Next, groups of 4-13 successive ON probes were combined into short TARs and a selection was made of TARs having an average signal intensity at least 2.6-fold higher after PQ treatment compared to the control treatment, resulting in 176 TARS induced by PQ. paraquat treated A. thaliana leaves (2 replicates) vs control (water) treated A. thaliana leaves (2 replicates), (4 samples in total)

2013-08-31 | E-GEOD-49001 | biostudies-arrayexpress

Proteogenomics-based identification of the repertoire of human MHC class I-associated peptides

Project description:We have develop a proteogenomics-based approach for identification of human MHC class I-associated peptides, including those deriving from polymorphisms, mutations and non-canonical reading frames

2016-12-22 | GSE67174 | GEO

Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance

Project description:Although evidence accumulates on the role of plant peptides in the response to external conditions, the number of peptide-encoding genes in the genome is still underestimated. In order to identify novel oxidative stress-induced peptides in Arabidopsis thaliana a tiling array analysis (GeneChip® Arabidopsis Tiling 1.0R Arrays ) was performed on mRNA extracted from leaves treated with paraquat (PQ), an reactive oxygen species inducer and water (control), resulting in the identification of 92,844 and 86,272 transcriptionally active regions (TARs), respectively. Normalized log signals were obtained using the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. ON and OFF probes were selected using a treshold, based on positive controls. Next, groups of 4-13 successive ON probes were combined into short TARs and a selection was made of TARs having an average signal intensity at least 2.6-fold higher after PQ treatment compared to the control treatment, resulting in 176 TARS induced by PQ.

2013-08-31 | GSE49001 | GEO

Project description:LC-MS/MS(Lipid metabolomics)

| PRJNA1297903 | ENA

Identification and characterization of novel proteins associated with CHD4

Project description:CHD (chromodomain helicase DNA binding protein) family is composed of nine members of chromatin remodeling factors that regulate chromatin structure in an ATP-dependent manner. Among them, CHD4 contributes to many basic cellular functions during development mainly through multiple proteins interacting with CHD4 including NuRD (nucleosome remodeling and deacetylase activities) complex, which contains histone deacetylase HDAC1/2. However, functions of CHD4 that are not mediated by NuRD complexes have also been found, implying the existence of unknown proteins that are associated with CHD4. In the present study, we generated CHD4 FLAG-tag knock-in cells in HeLa-S3 and HEK293T cells and sought proteins bound to CHD4 with the use of immunoprecipitation and liquid chromatography and tandem MS (LC-MS/MS) analysis. We found that LCORL (ligand dependent nuclear receptor corepressor like) and NOL4L (nucleolar protein 4 like) were reproducibly identified as a novel CHD4 interactors. RNA-sequencing analysis of HEK293T cells depleted of CHD4, LCORL, and NOL4L revealed consistent upregulation of genes related to the Notch pathway. Our results thus suggest that both NOL4L and LCORL may cooperate with CHD4 to suppress the Notch pathway in mammalian cells.

2022-01-01 | GSE190369 | GEO

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