Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of proteins binding "ubiquitin like" activity based probes

ABSTRACT: HA antibody beads were used to pulldown HA proteins in a cell lysate. The HA protein is an activty based probe (consisting of a small protein and a warhead) and was spiked into the cell lysate. 35, 156, 149 and 61 are different probes. Experiments were performed with and without pretreatment of the cell lysate with IAA an alkylating agent which should reduce the binding between the probe and its targets in cell lysate (cysteine based proteases).

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Petra Janning

PROVIDER: MSV000090802 | MassIVE | Tue Nov 29 07:48:00 GMT 2022

SECONDARY ACCESSION(S): PXD038455

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Pull-Down of UCHL1 from living cells with small molecule probes GK13S, GK13R, and GK16S (1 uM)

Project description:UCHL1 was enriched from HEK293 cells (Homo Sapiens) using a probe (PullDown via NeutrAvidin beads). Protein enrichment as a function of substance addition was studied in comparison to a DMSO control.

2022-08-01 | MSV000090045 | MassIVE

Pull-Down of UCHL1 from living cells with small molecule probes GK13S, GK13R, and GK16S (5 uM)

2022-08-01 | MSV000090044 | MassIVE

Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases [II]

Project description:We adapted the Aldehyde reactive probe (ARP; O-(biotinylcarbazoylmethyl) hydroxylamine) pulldown method to map ALKBH1 dependent targets in a transcriptome-wide manner.

2022-06-28 | GSE202814 | GEO

NAIA for cysteine profiling in HepG2 cells, protein target identification of covalent ligand and studying cysteine oxidative modifications

Project description:New cysteine probes, N-acryloylindole-alkynes (NAIAs), have been developed. We have applied NAIA-5 for cysteine profiling in HepG2 cell lysates, and the results have been compared to the conventional cysteine probe iodoacetamide-alkyne (IAA). NAIA-5 allows identification of more ligandable Cys than IAA in our experiment, and more interesting, a unique pool of Cys which have not been profiled previously by any reported cysteine probe. We have further utilized NAIA-5 for covalent ligand screening experiment. This allows us to discover hit compounds targeting the newly identified cysteines and proteins. One of the hit compounds, CL1, demonstrated good bioactivity by arresting cell cycle at G1 phase through targeting proteins associated with cell cycle and regulations. In addition, NAIA-5 has been successfully coupled with NAI compound for studying cysteine oxidative modifications in HepG2 cells by MS experiments.

2023-06-14 | PXD041264 | Pride

Screen for Ferry-associated RNAs

Project description:Goal: Identification of RNAs that are associated with the novel Ferry complex Methods: We performed a GST pulldown experiment, where GST-Ferry and GST were incubated with a HEK 293 cell lysate and extensively washed prior to elution. Subsequently, RNA was extracted from the elution and sequenced. Results: We identifed around 17 588 different transcripts and found a set of 252 mRNAs that are specifically enriched in the GST-Ferry sample. Conclusions: The Ferry complex seems to interact with a specific subset of mRNAs

2023-04-27 | GSE173422 | GEO

RNA-Seq of A375 cells treated with tetracycline-based crosslinking probes to identify binding sites for the tetracycline analogs Col-3 and doxycycline on the human ribosome

Project description:Following the identification of the 80S ribosome as a putative target of the tetracycline analogs Col3 and doxycycline, we next sought to identify the precise binding sites for these tetracyclines within the ribonucleoprotein complex. We incorporated dual bioorthogonal handles into tetracycline-based probes, containing both a photoactive diazirine to enable direct probe crosslinking to the human ribosome and an azide handle to allow selective enrichment of crosslinked biomolecules via copper-free click chemistry. The Col-3 and doxycycline probes were each incubated with A375 cells, followed by irradiation at 365 nm to induce photolysis of the diazirine moiety and subsequent crosslinking to adjacent ribosomal components. Pulldown and RNA-Seq of the crosslinked RNAs from our experiments were used to identify enrichment of reverse transcription (RT) stops at ribosomal RNA sites caused by local crosslinking of our probes. This RNA-Seq based RT stop enrichment analysis was compared to results using an non-specific aniline control probe and untreated controls.

2018-08-30 | E-MTAB-7147 | biostudies-arrayexpress

Pulldown CG42797 vs S2 cell lysate

Project description:Pulldown of CG42797 protein vs S2 cell lysate. Stage diging protocol trypsin digestion.

2022-02-17 | PXD025809 | Pride

Genome-wide ZNF410 binding sites identified by CUT&RUN in HUDEP-2, human CD34+ HSPCs and MEL cells.

Project description:We examined the chromatin occupancy of ZNF410 by conducting CUT&RUN. We used an HA antibody to probe for epitope tagged ZNF410 in HUDEP-2 cells. We used a ZNF410 antibody to probe for endogenous ZNF410 in HUDEP-2 cells, human CD34+ hematopoietic stem and progenitor cell (HSPC) derived erythroid precursors and mouse erythroleukemia (MEL) cells.

2021-02-05 | GSE166221 | GEO

WASH pulldown proteomics analysis

Project description:Affinity pulldown-paired quantitative proteomic analysis of HA-YFP-NLS.WASH interactors.

2022-02-17 | PXD026512 | Pride

Peptide probes containing a non-hydrolyzable phosphotyrosine-mimetic residue as a tool for tyrosine phosphatomics

Project description:Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate intracellular tyrosine phosphorylation levels, and their dysfunction is associated with various diseases. However, due to the low abundance of PTPs in cells, comprehensive analysis requires an enrichment step prior to liquid chromatography/tandem mass spectrometry (LC/MS/MS). In this study, we designed and synthesized peptide probes for PTP pulldown assay using a non-hydrolyzable phosphotyrosine mimetic, 4-[difluoro(phosphono)methyl]-L-phenylalanine (F2Pmp). We found that different F2Pmp probes can enrich different PTPs, depending on the probe sequence. Furthermore, proteins containing a Src homology 2 (SH2) domain were enriched together. Importantly, probes containing phosphotyrosine instead of F2Pmp failed to enrich PTPs due to dephosphorylation during the pulldown step. This enrichment approach using peptides containing F2Pmp could be a generic tool for tyrosine phosphatome analysis without the use of antibodies.

2021-10-27 | PXD025038 | JPOST Repository

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