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ProteomicsEvaluation of mass spectrometry MS/MS spectra for the presence of isopeptide crosslinked peptides
Isopeptide crosslinked proteins can be the product of transglutaminase or of exposure to organophosphorus toxicants (OP). Transglutaminase links glutamine to lysine with loss of ammonia. OP toxicants induce a link between glutamic acid and lysine with loss of water. Our goal was to establish crit...
ORGANISM(S): Sus scrofa domesticus (domestic pig) 
2021-07-12 | PXD026790 | Pride
Transglutaminase Dansyl cadaverine Isopeptide Dansyl-aminohexyl qqiv Protein prospector Map-rich tubulin Neurodegenerative disease Crosslinks 
ProteomicsRNF2_PCGF4_CBX8 crosslinked with BS3
Recombinant PRC1 complex consisting of RNF2, PCGF4 and CBX8 was crosslinked with BS3 to identify complex structure
ORGANISM(S): Homo sapiens (Human) 
2024-12-30 | PXD049094 | Pride
Xl-ms Prc1 Cbx8 Polycomb 
ProteomicsA synthetic crosslinked peptide library for benchmarking crosslinking mass spectrometry search engines
We have created a synthetic crosslinked peptide library to benchmark crosslinking mass spectrometry search engines. The unique benefit of the library is knowing which identified crosslinks are true and which are false. The data collected from mass spectrometry measurements of the peptide library wer...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2020-07-28 | PXD014337 | Pride
Crosslinking mass spectrometry peptide library 
GenomicsPDAP1 RIP in UV-crosslinked human T cells
PDAP1 RIP in UV-crosslinked human T cells
PRJNA761680 | ENA
ProteomicsLight-induced orthogonal fragmentation of crosslinked peptides
Crosslinking mass spectrometry provides pivotal information on the structure and interaction of proteins. MS-cleavable crosslinkers are regarded as a cornerstone for the analysis of complex mixtures. Yet they fragment under similar conditions as peptides, leading to mixed fragmentation spectra of th...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2023-08-28 | PXD040267 | Pride
Clms Cleavable crosslinker Crosslinking Uvpd 
ProteomicsIdentification of MS-Cleavable and Non-Cleavable Chemically Crosslinked Peptides with MetaMorpheus
The present work describes a novel search program for the detection of both MS-cleavable and non-cleavable crosslinked peptides and it is the first software program reported with both capacities. The search strategy has been implemented in the computer program MetaMorpheus, which has a user-friendly...
ORGANISM(S): Escherichia coli 
2018-07-16 | PXD009000 | Pride
Proteomics Ms-cleavable chemical crosslink Protein-protein interactions Ion index 
ProteomicsCTCF ChIP-MS from crosslinked chromatin in mouse embryonic stem cells (mESCs) and motor neurons (MNs)
To identify CTCF partners and co-localizing proteins from crosslinked chromatin in mESCs and MNs in endogenous conditions. The goal is to identify proteins within each sample with respect to wild-type control for each.
ORGANISM(S): Mus musculus (Mouse) 
2022-02-15 | PXD030543 | Pride
Mouse Crosslinked chromatin Ctcf chip-ms Ctcf partners Lc-ms/ms 
ProteomicsSystematic Discovery of Deeply Conserved Plant Protein Complexes, DSSO-crosslinked soy (Glycine max)
The associated files are mass spec data from size exclusion chromatography fractions that were subsequently crosslinked with DSSO. The starting material was a native extract prepared from soy sprouts (Glycine max). The mass spectrometry used a data-dependent MS2-MS3 method to identify crosslinks.
ORGANISM(S): Glycine max 
2019-10-28 | PXD013704 | Pride
Cross link Xlinkx Cl-ms Glycine max Dsso Xl-ms Cf-ms Soy Sec 
ProteomicsThe Human RNA-Binding Proteome and Its Dynamics during Translational Arrest
The data presented here was produced using XRNAX - a novel extraction method for protein-crosslinked RNA from UV-crosslinked cells. We apply XRNAX for three proteomic downstream applications. First, we purify ribonucleotide-crosslinked peptides from XRNAX extracts and use their identification as dir...
ORGANISM(S): Homo sapiens (Human) 
2018-12-06 | PXD010520 | Pride
Uv-crosslinking Nucleotide-crosslinked peptides Xrnax Protein-crosslinked rna extraction Rna-binding proteins Arsenite stress Translational arrest Human rna-binding proteome Ribophagy 
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data
We applied 4-thiouridine to cultured cells expressing the FLAG/HA-tagged RNA-binding proteins (RBPs) followed by UV 365 nm irradiation. The crosslinked RNA-protein complexes were isolated by immunoprecipitation, and the covalently bound RNA was partially digested with RNase T1 and radiolabeled. The ...
ORGANISM(S): Homo sapiens 
2010-05-21 | E-GEOD-21918 | biostudies-arrayexpress
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