Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global profiling of the C.elegans redoxome

ABSTRACT: We used several state-of-the-art site-centric chemoproteomics to systematically map three distinct types of redox forms (-SH, -SOH, and -SO2H) in C.elegans and quantify their dynamic changes in response to a short-term oxidative stress.

INSTRUMENT(S): Q Exactive HF, Q Exactive

ORGANISM(S): Caenorhabditis Elegans

SUBMITTER: Jing Yang

LAB HEAD: Jing Yang

PROVIDER: PXD018575 | Pride | 2021-01-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	0000_HF5_YangJing_Fuling_20170715_ALK-SO2H_50per_F1_R1.raw	Raw
	0000_HF5_YangJing_SRui_20170715_ALK_3_50per_F1_R1.raw	Raw
	QE_Plus_YangJing_FL_Ce_SOH_1_100per_20180421.raw	Raw
	QE_Plus_YangJing_FL_Ce_SOH_2_100per_20180421.raw	Raw
	QE_Plus_YangJing_FL_IPM-SH_01_50per_20171202.raw	Raw

Items per page:

1 - 5 of 13

Publications

Global profiling of distinct cysteine redox forms reveals wide-ranging redox regulation in C. elegans.

Meng Jin J Fu Ling L Liu Keke K Tian Caiping C Wu Ziyun Z Jung Youngeun Y Ferreira Renan B RB Carroll Kate S KS Blackwell T Keith TK Yang Jing J

Nature communications 20210303 1

Post-translational changes in the redox state of cysteine residues can rapidly and reversibly alter protein functions, thereby modulating biological processes. The nematode C. elegans is an ideal model organism for studying cysteine-mediated redox signaling at a network level. Here we present a comprehensive, quantitative, and site-specific profile of the intrinsic reactivity of the cysteinome in wild-type C. elegans. We also describe a global characterization of the C. elegans redoxome in which ...[more]

PMID: 33658510

Similar Datasets

pChem_benchmarking_dataset_lysinome_profiling

Project description:Data sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. Data were produced from the IPM-based QTRP (quantitative thiol reactivity profiling) applications in various species, incData sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. Data were produced from the lysinome profiling experiments using amine-reactive probes as indicated, including STP and NHS, both with a clickable alkyne handle.

2022-12-16 | PXD027789 | Pride

pChem_benchmarking_dataset_QTRP_diff_ratios

Project description:Data sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. Data were produced from the IPM-based QTRP (quantitative thiol reactivity profiling) experiments where light and heavy IPM-tagged samples mixed in different ratios (L/H = 1:10, 1:5, 1:2, 1:1, 2:1, 5:1 and 10:1). IPM is a clickable thiol reactive reagent with the iodoacetamide warhead.

2022-12-16 | PXD027762 | Pride

pChem_benchmarking_dataset_QTRP_diff_instruments

2022-12-16 | PXD027758 | Pride

pChem_benchmarking_dataset_QTRP_diff_species

Project description:Data sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. Data were produced from the IPM-based QTRP (quantitative thiol reactivity profiling) applications in various species, including Arabidopsis thaliana, Escherichia coli, Homo sapiens, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Psedomonas syringae, and Mus musculus. IPM is a clickable thiol reactive reagent with the iodoacetamide warhead.

2024-09-24 | PXD027767 | Pride

pChem_benchmarking_dataset_redoxome

Project description:Data sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. Data were produced from the redoxome profiling experiments using oxoform-specific probes as indicated, including SOH probes (DYn-2, BTD, WYneC/O/N) and SO2H probe (DiaAlk). All these probes contain a clickable alkyne handle.

2023-02-27 | PXD027764 | Pride

pChem_benchmarking_dataset_QTRP_diff_species

Project description:Data sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. Data were produced from the IPM-based QTRP (quantitative thiol reactivity profiling) applications in various species, including Arabidopsis thaliana, Escherichia coli, Homo sapiens, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Psedomonas syringae, and Mus musculus. IPM is a clickable thiol reactive reagent with the iodoacetamide warhead.

2022-12-16 | PXD030064 | Pride

Defining the hydrogen peroxide-dependent redoxome in human cells

Project description:Protein cysteinyl residues are the mediators of hydrogen peroxide (H2O2)-dependent redox signaling. However, site-specific mapping of the selectivity and dynamics of these redox reactions in cells poses a major analytical challenge. Here we describe a chemoproteomic platform to systematically and quantitatively analyze the reactivity of thousands of cysteines toward H2O2 in human cells. We identified >900 H2O2-sensitive cysteines, which are defined as the H2O2-dependent redoxome. Although redox sites associated with antioxidative and metabolic functions are consistent, most of the H2O2-dependent redoxome varies dramatically between different cells. Structural analyses reveal that H2O2-sensitive cysteines are less conserved than their redox-insensitive counterparts and display distinct sequence motifs, structural features, and potential for crosstalk with lysine modifications. Notably, our chemoproteomic platform also provides an opportunity to predict oxidation-triggered protein conformational changes. The data are freely accessible as a resource at http://redox.ncpsb.org/OXID/.

2021-02-18 | PXD006657 | Pride

Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes

2017-08-25 | PXD007153 | Pride

Multiplexed thiol reactivity profiling for target discovery of electrophilic natural products

Project description:Electrophilic groups, such as Michael acceptors, expoxides, are common motifs in natural products (NPs). Electrophilic NPs can act through covalent modification of cysteinyl thiols on functional proteins, and exhibit potent cytotoxicity and anti-inflammatory/cancer activities. Here we describe a new chemoproteomic strategy, termed multiplexed thiol reactivity profiling (MTRP), and its use in target discovery of electrophilic NPs. We demonstrate the utility of MTRP by identifying cellular targets of gambogic acid, an electrophilic NP that is currently under evaluation in clinical trials as anticancer agent. Moreover, MTRP enables simultaneous comparison of seven structurally diversified -unsaturated -lactones, which provides insights into the relative proteomic reactivity and target preference of diverse structural scaffolds coupled to a common electrophilic motif and reveals various potential druggable targets with liganded cysteines. We anticipate that this new method for thiol reactivity profiling in a multiplexed manner will find broad application in redox biology and drug discovery.

2017-10-12 | PXD007575 | Pride

A Paal-Knorr agent for chemoproteomic profiling of targets of isoketals in cells

Project description:Natural systems produce various γ-dicarbonyl-bearing compounds that can covalently modify lysine in protein targets via the classic Paal-Knorr reaction. Among them is a unique class of lipid-derived electrophiles - isoketals that exhibit high chemical reactivity and critical biological functions. However, it remains unknown about their target selectivity and profiles in complex proteomes. Here we report a Paal-Knorr agent, 4-oxonon-8-ynal (herein termed ONAyne), for a proteome-wide selectivity survey and quantitative reactivity profiling of the γ-dicarbonyl warhead. Furthermore, combined with quantitative chemoproteomics in a competitive format, ONAyne permitted global, in situ, and site-specific profiling of targeted lysine residues of two specific isomers of isoketals, levuglandin (LG) D2 and E2. The functional analyses reveal that LGs-derived adduction drives inhibition of malate dehydrogenase MDH2 and exhibits a crosstalk with two epigenetic marks on histone H2B in macrophages. Our approach should be broadly useful for target profiling of bioactive γ-dicarbonyls in diverse biological contexts.

2022-02-15 | PXD028270 | 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