Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PChem_benchmarking_dataset_lysinome_profiling

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: jixiang he

LAB HEAD: Jing Yang

PROVIDER: PXD027789 | Pride | 2022-12-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HFX_YangJing_HJX_NHS100_20210607_R1.raw	Raw
	HFX_YangJing_HJX_NHS100_20210607_R1.xlsx	Xlsx
	HFX_YangJing_HeJiXiang_STP-1_20210515_R1.raw	Raw
	HFX_YangJing_HeJiXiang_STP-1_20210515_R1.xlsx	Xlsx

Items per page:

1 - 4 of 4

Similar Datasets

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_instruments

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. The IPM-based QTRP (quantitative thiol reactivity profiling) data sets were recorded on different LC-MS/MS instruments from three vendors. IPM is a clickable thiol reactive reagent with the iodoacetamide warhead.

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.

2022-12-16 | PXD030064 | 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_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_initial_test_negative_data

Project description:we will acquire three types of data sets as negative controls from 1) probe-free samples (i.e., regular proteomics sample), 2) probe-labeled samples without isotope-coding, and 3) probe-free samples treated with isotope reagents (i.e., without probe labeling, peptides cannot be isotopically labeled).

2022-12-16 | PXD032376 | Pride

pChem_benchmarking_dataset_initial_test_negative_data_20220318

2022-12-16 | PXD032392 | Pride

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

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/.

2017-08-25 | PXD007153 | Pride

Defining the hydrogen peroxide-dependent redoxome in human cells

2021-02-18 | PXD006657 | 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