Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LiP-MS on HEK293 lysate treated with rapamycin

ABSTRACT: Limited proteolysis coupled to mass spectrometry (LiP-MS) is a structural proteomics technique that can be used to identify the targets of small molecules. This is achieved by incubating lysate with the drug of interest, which induces structural changes such as occupation of the binding site or changes and protein-protein interactions. This is followed by a limited proteolysis step in which the unspecific protease proteinase K is added to the treated lysate. The protease preferentially cleaves accessible and flexible regions of the proteins, thus generating peptides that reflect the changes in surface accessibility caused by the treatment with the small molecule. Here we treated HEK293 cell lysate with rapamycin and identify the known main target FKBP1A. This data is intended to be used as a model dataset for LiP-MS data evaluation and was created as part of the IMI EUbOPEN project.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Viviane Reber

LAB HEAD: Matthias Gstaiger

PROVIDER: PXD035183 | Pride | 2023-04-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

LiP-MS on HEK293 lysate treated with Probe Candidate TR06189215 and Negative Control TR03633723

Project description:Limited proteolysis coupled to mass spectrometry (LiP-MS) is a structural proteomics technique that can be used to identify the targets of small molecules. This is achieved by incubating lysate with the drug of interest, which induces structural changes such as occupation of the binding site or changes and protein-protein interactions. This is followed by a limited proteolysis step in which the unspecific protease proteinase K is added to the treated lysate. The protease preferentially cleaves accessible and flexible regions of the proteins, thus generating peptides that reflect the changes in surface accessibility caused by the treatment with the small molecule. Here we treated HEK293 cell lysate with the candidate probe TR06189215 and the corresponding negative control TR03633723 to profile target engagement and other structural effects. This project is part of the IMI EUbOPEN project and was performed in collaboration with Kilian Huber (University of Oxford).

2023-04-26 | PXD041099 | Pride

LiP-MS on HEK293 lysate treated with Probe Candidate TR05481366 and Negative Control TR05302201

Project description:Limited proteolysis coupled to mass spectrometry (LiP-MS) is a structural proteomics technique that can be used to identify the targets of small molecules. This is achieved by incubating lysate with the drug of interest, which induces structural changes such as occupation of the binding site or changes and protein-protein interactions. This is followed by a limited proteolysis step in which the unspecific protease proteinase K is added to the treated lysate. The protease preferentially cleaves accessible and flexible regions of the proteins, thus generating peptides that reflect the changes in surface accessibility caused by the treatment with the small molecule. Here we treated HEK293 cell lysate with the candidate probe TR05481366 and the corresponding negative control TR05302201 to profile target engagement and other structural effects. This project is part of the IMI EUbOPEN project and was performed in collaboration with Kilian Huber (University of Oxford).

2023-09-01 | PXD041100 | Pride

LiP-MS on HEK293 lysate treated with Probe Candidate TR05267290 and Negative Control TR05706192

Project description:Limited proteolysis coupled to mass spectrometry (LiP-MS) is a structural proteomics technique that can be used to identify the targets of small molecules. This is achieved by incubating lysate with the drug of interest, which induces structural changes such as occupation of the binding site or changes and protein-protein interactions. This is followed by a limited proteolysis step in which the unspecific protease proteinase K is added to the treated lysate. The protease preferentially cleaves accessible and flexible regions of the proteins, thus generating peptides that reflect the changes in surface accessibility caused by the treatment with the small molecule. Here we treated HEK293 cell lysate with the candidate probe TR05267290 and the corresponding negative control TR05706192 to profile target engagement and other structural effects. This project is part of the IMI EUbOPEN project and was performed in collaboration with Kilian Huber (University of Oxford).

2023-09-01 | PXD041098 | Pride

LiP-MS on Purified CAMKK1 treated with Staurosporine

Project description:Limited proteolysis coupled to mass spectrometry (LiP-MS) is a structural proteomics technique that can be used to identify the targets of small molecules. This is achieved by incubating protein with the drug of interest, which induces structural changes such as occupation of the binding site or changes and protein-protein interactions. This is followed by a limited proteolysis step in which the unspecific protease proteinase K is added to the treated protein sample. The protease preferentially cleaves accessible and flexible regions of the protein, thus generating peptides that reflect the changes in surface accessibility caused by the treatment with the small molecule. Here we treated affinity-purified CAMKK1 kinase inhibitor Staurosporine. The data were generated as part of the IMI EUbOPEN project.

2023-04-26 | PXD041089 | Pride

Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using Limited Proteolysis

Project description:Conformational changes in proteins can lead to disease. Thus, methods for identifying conformational changes in proteins can further improve our understanding and facilitate detection of disease states. Here we combine limited proteolysis (LiP) with Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) to characterize breast cancer-related conformational changes in proteins on the proteomic scale. Studied here are the conformational properties of proteins in two cell culture models of breast cancer, including the MCF-10A and MCF-7 cell lines. The SILAC-LiP approach described here identified ~200 proteins with cell-line dependent conformational changes, as determined by their differential susceptibility to proteolytic digestion using the non-specific protease, proteinase K. The protease susceptibility profiles of the proteins in these cell lines were compared to thermodynamic stability and expression level profiles previously generated for proteins in these same breast cancer cell lines. The comparisons revealed that there was little overlap between the proteins with protease susceptibility changes and the proteins with thermodynamic stability and/or expression level changes. Thus, the large-scale conformational analysis described here provides unique insight into the molecular basis of the breast cancer phenotypes in this study.

2016-12-23 | PXD005210 | Pride

Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using Limited Proteolysis

2017-03-29 | MSV000080770 | MassIVE

A map of protein-metabolite interactions reveals principles of chemical communication

Project description:Application of a novel mass spectrometry-based high-throughput workflow (LiP-SMap) and data resource based on limited proteolysis (LiP) of complex samples. Proteome-wide limited proteolysis sites were obtained in different conditions to infer ligand-induced and protein-protein interaction induced conformational changes. This information was used to identify unknown ligand binding proteins, small molecule-protein binding sites and the remodeling of protein complexes directly in cells.

2018-01-04 | PXD006543 | Pride

Aging-Associated Changes in CSF Protein Abundances and Structures Revealed by a Modified LiP-MS Screen

Project description:We performed LiP-MS on CSF from young and old mice with a modified analysis pipeline. We found 38 protein groups that change in abundance with aging, most dominantly immunoglobulins of the IgM subclass. We discovered six high-confidence candidates that appeared to change in structure with aging.

2022-08-22 | PXD031174 | Pride

Structural basis of calmodulin modulation of the rod cyclic nucleotide-gated channel (LiP-MS)

Project description:The aim of the project was to characterize structural changes that occur on the rod cyclic nucleotide-gated channel upon interaction with calmodulin (CaM) directly in the native membrane.

2023-04-06 | PXD038768 | Pride

Oxygen deficiency of the human bowel

Project description:Primary objectives: This study aims at (further) revealing the pathophysiology of intestinal IR in man, with a specific interest for the role of proteases and protease-activated receptor-2 (PAR-2), cellular and inflammatory changes, barrier function and intestinal permeability, microscopic mucosal changes and gene expression patterns. An important element will be the determination of the effects of protease- and MMP inhibitors. By these means we hope to identify preventive and therapeutic strategies for patients with intestinal IR. Primary endpoints: The primary endpoint in this study is inflammation (neutrophil influx, complement activation, interleukins, TNF-α, COX 1-2) and protease activity in tissue as well as in blood plasma.

| 2533504 | ecrin-mdr-crc

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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