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ProteomicsHuman stomach LC-MSMS China Human Proteome Project
With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptide characterization, where peptide backbones and N-glycan moieties are selective...
ORGANISM(S): Homo sapiens (Human) 
2020-05-11 | PXD016865 | Pride
Human Lc-msms Hcd Stepped nces Stomach 
ProteomicsOptimized TMT-based quantitative cross-linking mass spectrometry strategy for large-scale interactomic studies
Cross-linking mass spectrometry is a powerful method for the investigation of protein-protein interactions from highly complex samples. XL-MS combined with tandem mass tag labeling holds the promise of large-scale PPI quantification. However, a robust and efficient TMT-based XL-MS quantification met...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Bacteria 
2022-04-07 | PXD031114 | Pride
Faims Hek Ratio distortion E. coli Mass spectrometry Lumos Dsso Xl-ms Interactome Stepped hcd Cross-linking Interference Sps 
ProteomicsOptimized fragmentation improves the identification of peptides cross-linked using MS-cleavable reagents
Cross-linking mass spectrometry (XLMS) is becoming increasingly popular, and current advances are widening the applicability of the technique so that it can be utilized by non-specialist laboratories. Specifically, the use of novel mass spectrometry-cleavable (MS-cleavable) reagents dramatically red...
ORGANISM(S): Bos taurus (Bovine) Cicer arietinum (Chickpea) (Garbanzo) Streptococcus pyogenes serotype M2 Candida albicans (Yeast) Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) Escherichia coli Equus caballus (Horse) 
2019-02-01 | PXD011861 | Pride
Xlms Cross-linking Cleavable cross-linking reagents Dsso Stepped-hcd 
UnknownOptimization of Higher-Energy Collisional Dissociation Fragmentation Energy for Intact Protein-Level Tandem Mass Tag Labeling.
Not available
S-EPMC10164041 | biostudies-literature
MetabolomicsSimultaneously discovering the fate and biochemical effects of pharmaceuticals through untargeted metabolomics
Untargeted metabolomics is an established approach in toxicology for characterising endogenous metabolic responses to xenobiotic exposure. Detecting the xenobiotic and its biotransformation products as part of the metabolomics analysis provides an opportunity to simultaneously gain deep insights int...
2023-07-03 | MTBLS2746 | MetaboLights
ProteomicsReconstitution of 3’-processing of mammalian pre-mRNA reveals a central role of RBBP6
The 3’ ends of almost all eukaryotic mRNAs are generated in an essential two-step processing reaction, endonucleolytic cleavage of an extended precursor followed by the addition of a poly(A) tail. By reconstituting the reaction from overproduced and purified proteins, we provide a minimal list of fo...
ORGANISM(S): Homo sapiens (Human) 
2022-03-04 | PXD031227 | Pride
Cpsf 3’-processing Xl-ms Rbbp6 
ProteomicsProteome-Wide Photo-Crosslinking Enables Residue-Level Visualization of Protein Interaction Networks in vivo
Crosslinking mass spectrometry (XL-MS) is emerging as a unique method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of crosslinkers that can form li...
ORGANISM(S): Escherichia coli 
2023-12-07 | PXD036884 | Pride
Heterobifunctional crosslinker Escherichia coli Xl-ms Diazirine Cleavable crosslinker Photo-crosslinking Proteome-wide Nhs-carbamate 
ProteomicsComparative glycomics study on the surface of SKOV3 versus IOSE80 cell lines
Both SKOV3 and IOSE80 cells were cultured and extracted the proteins. With sequential digestion by trypsin, enriched by Zwitterionic Hydrophilic Interaction chromatography (ZIC-HILIC), the intact N-glycopeptides were then isotopic diethyl labelled and analyzed using C18-RPLC-MS/MS (HCD).
ORGANISM(S): Homo sapiens (Human) 
2023-03-10 | PXD030927 | Pride
Skov3 iose80 
ProteomicsIntact extracellular vesicle cross-linking on vesicles derived from MDA-MB-231 and LM2 cells
The development of any pharmaceutical requires characterization of the compound, usually be several techniques. Therefore, characterizing the protein content and biochemical state of EVs is of great importance for their useif they are to be used as biopharmaceuticals. Structural characterization of ...
ORGANISM(S): Homo sapiens (Human) 
2022-11-08 | PXD029591 | Pride
Tnbc Evs Xl-ms Structural proteomics Cx-ms 
ProteomicsNon-native entanglement protein misfolding observed in all-atom simulations and supported by experimental structural ensembles
Several mechanisms are known to cause monomeric protein misfolding. Coarse-grained simulations have predicted an additional mechanism exists involving off-pathway, non-covalent lasso entanglements, which are long-lived kinetic traps and structurally resemble the native state. Here, we examine whethe...
ORGANISM(S): Escherichia coli 
2025-08-11 | PXD066083 | Pride
Structural mass spectrometry Non-native entanglement 
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