Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiplexed isobaric quantitative cross-linking reveals drug-induced interactome changes in breast cancer cells

ABSTRACT: In vivo application of an extended set of six iqPIR reagents (6-plex iqPIR) allowing multiplexed quantitative interactome analysis of up to six biological samples in a single LC-MS acquisition. Multiplexed iqPIR is demonstrated on MCF-7 breast cancer cells treated with five different Hsp90 inhibitors revealing large scale protein conformational and interaction changes specific to the molecular class of the inhibitors.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Helisa Wippel

LAB HEAD: James E. Bruce

PROVIDER: PXD029350 | Pride | 2023-03-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	100721_MCF7_6plex_hsp90_SEC_DDA_F1_5_biorep1_1.raw	Raw
	100721_MCF7_6plex_hsp90_SEC_DDA_F1_5_biorep1_2.raw	Raw
	100721_MCF7_6plex_hsp90_SEC_DDA_F1_5_biorep1_3.raw	Raw
	100721_MCF7_6plex_hsp90_SEC_F10_biorep1_1.raw	Raw
	100721_MCF7_6plex_hsp90_SEC_F10_biorep1_2.raw	Raw

Items per page:

1 - 5 of 40

Publications

Multiplexed Isobaric Quantitative Cross-Linking Reveals Drug-Induced Interactome Changes in Breast Cancer Cells.

Wippel Helisa H HH Chavez Juan D JD Keller Andrew D AD Bruce James E JE

Analytical chemistry 20220202 6

The study of protein structures and interactions is critical to understand their function. Chemical cross-linking of proteins with mass spectrometry (XL-MS) is a rapidly developing structural biology technique able to provide valuable insight into protein conformations and interactions, even as they exist within their native cellular environment. Quantitative analysis of cross-links can reveal protein conformational and interaction changes that occur as a result of altered biological states, env ...[more]

PMID: 35107270

Similar Datasets

Multiplexed isobaric quantitative Protein Interaction Reporter (iqPIR) cross-linking on standard proteins

Project description:Initial demonstration of multiplexed isobaric quantitative Protein Interaction Reporter technology using two multiplexed samples consisting of 5 cross-linked standard proteins including alcohol dehydrogenase 1 (ADH1_YEAST), albumin (ALBU_BOVIN), cytochrome c (CYC_BOVIN), hemoglobin (HBA_HUMAN), and myoglobin (MYG_HORSE).

2023-03-11 | PXD026037 | Pride

Age induced interactome remodeling in muscle mitochondria

Project description:A novel quantitative crosslinking mass spectrometry technique (qXL-MS) was applied to elucidate interactome changes in aged murine skeletal muscle mitochondria that contribute to age-related mitochondrial functional decline. Reported here are results from initial investigations of murine muscle mitochondrial interactomes that enable identification of statistically significant changes associated with aging. Newly developed isobaric quantitative protein interaction reporter (iqPIR) technologies15 enabled reproducible detection of age-related mitochondrial interactome changes. Muscle mitochondria from young and old mice were isolated, cross-linked with iqPIR molecules, young and old mitochondrial samples were paired, process and analyzed to quantify age-related mitochondrial interactome changes. In parallel, mitochondria were also subjected to additional measurements of mitochondrial protein yield, functional measurements including oxygen consumption rates on Complex I and Complex II substrates, and citrate synthase activity.

2024-05-23 | PXD031643 | Pride

Quantitative Analysis of Samples Labeled with Multiplex iqPIR Cross-Linkers

Project description:The isobaric quantitative protein interaction reporter (iqPIR) has now been extended to six channels, enabling quantitation of cross-links from six different samples simultaneously. To analyze data for such cross-linkers, the two-channel mode of quantitative analysis was extended to accommodate any number of channels with defined isotope peak offsets. The HeLa 1:1:1:1:1 data was used for the development of the quantitation method of the 6-plex iqPIR.

2023-03-11 | PXD025796 | Pride

quantitative crosslinking of ADP treated mitochondria isolated from HEK293 cells

Project description:Acute treatment of isolated mitochondria with 1.5 mM ADP. Crosslinking and quantitative comparison to non-treated control using iqPIR technology for quantitative crosslinking.

2022-07-29 | PXD031644 | Pride

Analysis of bilirubin-induced bovine serum albumin stability using protein denaturation and quantitative cross-linking mass spectrometry

Project description:We report the combination of protein-denaturation stability principles with quantitative cross-linking mass spectrometry using isobaric quantitative protein interaction reporter technologies. This method enables the evaluation of ligand-induced protein engagement through analysis of cross-link relative ratios across chemical denaturation. We found ligand-stabilized cross-linked lysine pairs in bovine serum albumin (BSA) and ligand bilirubin map to known binding sites Sudlow Site I and subdomain IB.

2024-07-03 | PXD036649 | Pride

Transcription profiling of mouse SCIDs subcutaneously injected with human Farage DLBCL cells. When tumors reached 1 cm in diameter, four mice were administered PU-H71 (75mg/kg) by intra-peritoneal injectionThe purine scaffold HSP90 inhibitor PU-H71 induces specific changes in gene expression in DLBCL xenografts.

Project description:Heat shock protein 90 (Hsp90) is an emerging therapeutic target in cancer. We report that Hsp90 inhibitors selectively kill DLBCLs that are biologically dependent on the BCL6 transcriptional repressor. We examined the pharmacokinetics, toxicity and efficacy of PUH71, a recently developed purine scaffold Hsp90 inhibitor. PUH71 preferentially accumulated in tumors vs. normal tissues, and unlike the widely used benzoquinone Hsp90 inhibitors, displayed no signs of organ toxicity. PUH71 selectively and potently induced the regression of BCL6-dependent DLBCLs in vivo, through reactivation of key BCL6 target genes and apoptosis. Experiment Overall Design: Six SCID mice were subcutaneously injected with human Farage DLBCL cells. When tumors reached 1 cm in diameter, four mice were administered PU-H71 (75mg/kg) by intra-peritoneal injection and two mice served as no-treatment controls. Animals were sacrificed by cervical dislocation under anesthesia at 6 and 12 h after the administration of PU-H71.

2009-11-28 | E-GEOD-13401 | biostudies-arrayexpress

Human Cell Lines Interactomics Comparison

Project description:Quantitative comparison of human cell lines (HEK293, HeLa, MCF7) using acrosslinking mass spectrometry

2024-09-16 | PXD025923 | Pride

Transcription profiling of Arabidopsis plants after heat shock or treatment with HSP90 inhibitors (geldanamycin and radicicol)

Project description:Effect of heat shock or HSP90 inhibitors (geldanamycin and radicicol) on wild type Arabidopsis thaliana.

2007-06-01 | E-ATMX-12 | biostudies-arrayexpress

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics.

Project description:Quantitative mass spectrometry-based proteomics is highly versatile but not easily multiplexed. Isobaric labeling strategies allow mass spectrometry-based multiplexed proteome quantification; however, ratio distortion owing to protein quantification interference is a common effect. We present a two-proteome model (mixture of human and yeast proteins) in a sixplex isobaric labeling system to fully document the interference effect, and we report that applying triple-stage mass spectrometry (MS3) almost completely eliminates interference.

| S-EPMC3205343 | biostudies-literature

Multiplexed Cross-Linking with Isobaric Quantitative Protein Interaction Reporter Technology.

Project description:Chemical cross-linking with mass spectrometry (XL-MS) has emerged as a useful technique for interrogating protein structures and interactions. When combined with quantitative proteomics strategies, protein conformational and interaction dynamics can be probed. Quantitative XL-MS has been demonstrated with the use of stable isotopes incorporated metabolically or into the cross-linker molecules. Isotope-labeled cross-linkers have primarily utilized deuterium and rely on MS1-based quantitation of precursor ion extracted ion chromatograms. Recently the development and application of isobaric quantitative protein interaction reporter (iqPIR) cross-linkers were reported, which utilize 13C and 15N isotope labels. Quantitation is accomplished using relative fragment ion isotope abundances in tandem mass spectra. Here we describe the synthesis and initial evaluation of a multiplexed set of iqPIR molecules, allowing for up to six cross-linked samples to be quantified simultaneously. To analyze data for such cross-linkers, the two-channel mode of iqPIR quantitative analysis was adapted to accommodate any number of channels with defined ion isotope peak mass offsets. The summed ion peak intensities in the overlapping channel isotope envelopes are apportioned among the channels to minimize the difference with respect to the predicted ion isotope envelopes. The result is accurate and reproducible relative quantitation enabling direct comparison among six differentially labeled cross-linked samples. The approach described here is generally extensible for the iqPIR strategy, accommodating future iqPIR reagent design, and enables large-scale in vivo quantitative XL-MS investigation of the interactome.

| S-EPMC9014865 | biostudies-literature

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