Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PACTS-assisted thermal proteome profiling identifies peptide-interacting proteins

ABSTRACT: The interaction between peptide ligands and protein receptors induced significant abundance changes of the target proteins, which was a signature to indicate the interaction and provide complementary information for the current thermal proteome profiling (TPP) technique

ORGANISM(S): Homo Sapiens

SUBMITTER: Chenxi Jia

PROVIDER: PXD031246 | iProX | Wed Jan 26 00:00:00 GMT 2022

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

PACTS-Assisted Thermal Proteome Profiling for Use in Identifying Peptide-Interacting Proteins.

Zhao Ting T Tian Jingya J Wang Xiankun X Hao Yanan Y Xu Mengting M Zhao Yuanyuan Y Liu Xinyue X Chen Yali Y Jia Chenxi C

Analytical chemistry 20220429 18

Bioactive peptides play important roles in various biological processes. However, the traditional methods for profiling the peptide-interacting proteins require modifications to the peptide molecules, often leading to false identifications. We found that the interaction between peptide ligands and protein receptors induced significant changes in the abundance of the interacting proteins, which is a signature indicating the interaction and providing complementary information for use in the classi ...[more]

PMID: 35485935

Similar Datasets

Integration of Thermal Proteome Profiling with phosphoproteomic and transcriptomic data via mechanistic network models decodes the molecular response to PARP inhibition

Project description:The deregulation of complex diseases often spans multiple molecular processes. A multimodal functional characterization of these processes can shed light on the disease mechanisms and the effect of drugs. Thermal Proteome Profiling (TPP) is a mass-spectrometry based technique assessing changes in thermal protein stability that can serve as proxies of functional changes of the proteome. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a framework for causal integration of multi-omics, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover known mechanistic consequences of PARP inhibition in ovarian cancer cells on cell cycle and DNA damage response in detail and to uncover new insights into drug response mechanisms related to interferon and hippo signaling. We found that TPP complements the other omics data and allowed us to obtain a network model with higher coverage of the main underlying mechanisms. These results illustrate the added value of TPP, and more generally the power of network models to integrate the information provided by different omics technologies. We anticipate that this strategy can be used to broadly integrate functional proteomics with other omics to study complex molecular processes.

2024-04-10 | GSE243208 | GEO

Drug target deconvolution in Plasmodium falciparum using thermal proteomics profiling

Project description:Early identification of a compound’s mode of action can greatly benefit the discovery process. Thermal proteomics profiling (TPP) is a powerful, unbiased tool that can be used to identify potential ligands of protein targets. TPP takes advantage of the fact that a ligand binding to its target protein can significantly stabilise that protein, increasing its melting temperature (Tm). We previously optimised this technique for use in drug target deconvolution in the kinetoplastid parasite, Leishmania donovani1 and here report the optimisation and validation of TPP in the malaria-causing parasite P. falciparum.

2022-10-13 | PXD025182 | Pride

Thermal Proteome Profiling Datasets for smarTPCA

Project description:Chemical biology and the application of small molecules has proven to be a potent perturbation strategy especially for the functional elucidation of proteins, their networks and regulators. In recent years, the cellular thermal shift assay (CETSA) and its proteome-wide extension, thermal proteome profiling (TPP), have proven to be effective tools for identifying interactions of small molecules with their target proteins as well as off-targets in living cells. Here, we asked the question if isothermal dose-response (ITDR) CETSA can be exploited to characterize secondary effects downstream of the primary binding event, such as changes in post-translational modifications or protein-protein interactions (PPI). Applying ITDR-CETSA to MAPK14 kinase inhibitor treatment of living HL-60 cells, we found similar dose-responses for the direct inhibitor target and its known interaction partners MAPKAPK2 and MAPKAPK3. Extension of the dose-response similarity comparison to the proteome wide level using TPP with compound concentration range (TPP-CCR) revealed not only the known MAPK14 interaction partners MAPKAPK2 and MAPKAPK3, but also the potentially new intracellular interaction partner MYLK. We are confident that dose-dependent small molecule treatment in combination with ITDR-CETSA or TPP-CCR similarity assessment will not only allow discrimination between primary and secondary effects, but also provide a novel method to study PPI in living cells without perturbation by protein modification, which we named "small molecule arranged thermal proximity coaggregation" (smarTPCA).

2022-06-09 | PXD032942 | Pride

Thermal Proteome Profiling (TPP) of l-Cysteine–Treated Arabidopsis Mitochondrial Proteins

Project description:This project investigates the thermal stability of isolated mitochondrial proteins from Arabidopsis thaliana cell cultures following L-cysteine treatment, using Thermal Proteome Profiling (TPP). Shotgun proteomics was employed to identify and quantify proteins after thermal treatment. Quantitative data (iBAQ values) were subsequently analyzed using a custom R script (available on GitHub: “MeCuP”) to identify candidate proteins that exhibit changes in thermal stability due to interaction with L-cysteine.

2025-05-29 | PXD064096 | Pride

LL10000 hybridization

Project description:The screening of a previously reported fluorescein labelled 10,000 member PNA encoded peptide library allowed information on the interaction between the peptide-ligands and the cell surface receptors to be extracted, identified new peptide ligands for cell surface receptors, and gave crucial information about consensus sequences. A novel indirect amplification of the PNA signal by amplification of the PNA-complementary DNA library was developed to screen PNA-encoded peptide library against D54, HEK293T, and HEK293T-CCR6 cells. This work generates a new approach to biological discovery and an expansion of modern microarray techniques. In addition, the microarray approach facilitates screening for differences in surface-receptor ligands and/or receptor expression between various cell types including diseased and normal cells.

2011-11-08 | E-MEXP-3104 | biostudies-arrayexpress

Tissue Thermal Proteome Profiling

Project description:We introduce tissue Thermal Proteome Profiling (tissue-TPP) which enables the discovery of drug targets and off-targets as well as measurements of target occupancy in tissue samples derived from dosed animals. Here we report the first proteome-wide thermal stability map of tissues and organ-specific target profiles of the non-covalent histone deacetylase inhibitor, panobinostat. In addition, we devised blood-CETSA/TPP to monitor target and off-target engagement directly in whole blood.

2020-01-07 | PXD016277 | Pride

Tissue Thermal Proteome Profiling

2020-01-07 | PXD015373 | Pride

Tissue Thermal Proteome Profiling

2020-01-07 | PXD015458 | Pride

Tissue Thermal Proteome Profiling

2020-01-07 | PXD015427 | Pride

Tissue Thermal Proteome Profiling

2020-01-07 | PXD015397 | Pride