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ProteomicsDevelopment of in planta chemical cross-linking-based quantitative interactomics in Arabidopsis
An in planta chemical cross-linking-based quantitative interactomics (IPQCX-MS) workflow has been developed to investigate in vivo protein-protein interactions and alteration in protein structures in a model organism, Arabidopsis thaliana. A chemical cross-linker, azide-tag-modified disuccinimidyl p...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2018-08-14 | PXD008161 | Pride
Arabidopsis thaliana Ecl2 In planta quantitative interactomics Ipqcx-ms In vivo cross-linking 4c proteomic workflow 
ProteomicsTrioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks
Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MSn analysis...
ORGANISM(S): Mus musculus (Mouse) 
2025-05-30 | PXD063825 | Pride
Tsto Xl-ms Lc-msn 
ProteomicsTrioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks
Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MSn analysis...
ORGANISM(S): Homo sapiens (Human) 
2025-05-30 | PXD054551 | Pride
Tsto Xl-ms Cross-linking mass spectrometry 
ProteomicsIn vivo protein interaction network analysis reveals porin-localized toxin inactivation in antibiotic resistant bacteria
The nosocomial pathogen Acinetobacter baumannii is a frequent cause of hospital acquired infections worldwide, and a challenge for treatment due to its evolved resistance to antibiotics, including carbapenems. To gain insight on A. baumannii antibiotic resistance mechanisms, we analyzed the protein...
ORGANISM(S): Acinetobacter baumannii AB5075 
2016-12-22 | PXD004236 | Pride
Acinetobacter baumannii Chemical cross-linking Protein-protein interactions Antibiotic resistance Carbapenem 
ProteomicsA3G-Vif-CBFB-CRL5 Cross-Linking with DSSO
Here we use an optimization cross-linking mass spectrometry (XL-MS) pipeline for the structural characterization of a dynamic HIV-host protein complex. Using DSSO-based XL-MS analysis, residue-protein proximity restraints based on functional genetics, and integrative modeling, we define the structu...
ORGANISM(S): Homo sapiens (Human) Human immunodeficiency virus 
2021-11-03 | PXD025391 | Pride
Xl-ms Dsso Apobec3g Hiv vif Integrative modeling 
ProteomicsExpanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS
In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here we present a gas-phase sepa...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Gallus gallus (Chicken) Equus caballus (Horse) 
2020-07-22 | PXD019926 | Pride
Faims Whole proteome Cross-linking mass spectrometry Xl-ms Orbitrap fusion lumos Cx-ms 
ProteomicsThe catalytic activity of TCPTP is auto-regulated by its intrinsically disordered tail and activated by Integrin alpha-1
T-Cell Protein Tyrosine Phosphatase (TCPTP, PTPN2) is a non-receptor type protein tyrosine phosphatase that is ubiquitously expressed in human cells. TCPTP is a critical component of a variety of key signaling pathways that are directly associated with the formation of cancer and inflammation. Thus,...
ORGANISM(S): Homo sapiens (Human) 
2021-11-10 | PXD029256 | Pride
Tcptp Ptpn2 Intermolecular cx-ms Intramolecular cx-ms 
UnknownIntra- and inter-molecular cross-linking of peptide ions in the gas phase: reagents and conditions.
Not available
S-EPMC3241442 | biostudies-literature
ProteomicsCombining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines
Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interact...
ORGANISM(S): Mus musculus (Mouse) 
2024-09-17 | PXD055943 | Pride
Mouse Cross-linking Mitochondria 
ProteomicsFAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation
Protein-protein interactions (PPIs) underpin nearly all cellular processes; therefore, mapping PPI and protein-protein association networks is critical for understanding how biological systems function in health and disease. However, many functionally relevant PPIs are transient and mediated by weak...
ORGANISM(S): Homo sapiens (Human) 
2026-05-27 | PXD064228 | Pride
Faims Cross-linking mass spectrometry Structural biology Interactomics 
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