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ProteomicsUrine recirculation prolongs normothermic kidney perfusion for via more optimal metabolic homeostasis – a proteomics study
We describe a proteomics analysis to determine the molecular differences between normothermically perfused (normothermic machine perfusion, NMP) human kidneys with urine recirculation (URC) and urine replacement (UR). Proteins were extracted from 16 kidney biopsies with URC (n=8 donors after brain d...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021507 | Pride
Proteomics Mass spectrometry Nephrology Kidney transplantation Ischemia reperfusion injury Organ perfusion Iri 
ProteomicsActivity-based profiling of deubiquitylating enzymes
This set is a repackaging of PXD031848 (described in https://doi.org/10.3390/ijms23063263: "ABPP-HT*-Deep Meets Fast for Activity-Based Profiling of Deubiquitylating Enzymes Using Advanced DIA Mass Spectrometry Methods") to make each LC-MS/MS experiment individually downloadable and to include TIMSC...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-07-24 | MSV000095426 | MassIVE
ProteomicsTransplant Model Ischemic Conditioning Causes Tissue Leakage and Suppressed Inflammation in a Porcine Kidney
Background: Remote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the Ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regim...
ORGANISM(S): Sus scrofa domesticus (domestic pig) 
2022-04-04 | PXD025273 | Pride
Remote ischaemic conditioning Kidney transplantation Transcriptomics Inflammation Proteomics Integrative omics 
ProteomicsComprehensive landscape of active deubiquitinating enzymes profiled by advanced chemoproteomics
Enzymes that bind and process ubiquitin, a small 76 amino acid protein, have been recognized as pharmacological targets in oncology, immunological disorders and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire ...
ORGANISM(S): Homo sapiens (Human) 
2019-11-12 | PXD014391 | Pride
Proteomics Mass spectrometry Deubiquitylating enzymes Chemical biology Isoforms Ubiquitin specific proteases 
ProteomicsMultifaceted disruption to cholesterol homeostasis upon loss of the mEMC
The mammalian Endoplasmic Reticulum Membrane protein Complex (mEMC) is an evolutionarily conserved hetero-oligomer whose function and mechanism of action remain elusive. Here we identify a multi-layered contribution of the mEMC to post-translational regulation of cholesterol homeostasis. Mammalian c...
ORGANISM(S): Homo sapiens (Human) 
2019-01-02 | PXD006603 | Pride
Soat1 Squalene synthase Srebp-2 Endoplasmic reticulum 
ProteomicsABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA mass spectrometry methodsABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA mass spectrometry methods
Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and...
ORGANISM(S): Homo sapiens (Human) 
2022-04-04 | PXD031848 | Pride
Data-independent acquisition mass spectrometry (dia) Drug discovery Proteomics Activitomics Mass spectrometry Chemical biology Deubiquitylating enzymes Ubiquitin Activity-based probes 
ProteomicsProximity proteomics reveals UCH-L1 as an essentialregulator of NLRP3-mediated IL-1β production in humanmacrophages and microglia
Activation of the NACHT, LRR family pyrin domain containing 3 (NLRP3) inflammasome complex is an essential innate immune signalling mechanism. To reveal how NLRP3 inflammasome assembly and activation are controlled, in particular by components of the ubiquitin system, proximity labelling, affinity p...
ORGANISM(S): Homo sapiens (Human) 
2024-04-24 | PXD045862 | Pride
Affinity purification-mass spectrometry Apex2 proximity labelling Nlrp3 inflammasome 
ProteomicsA quantitative label-free analysis of the extracellular proteome of human supraspinatus reveals damage to the pericellular and elastic fibre niches in torn and aged tendons
Tears of the human supraspinatus tendon are common and often cause painful and debilitating loss of function. Progressive failure of the tendon leading to structural abnormality and tearing is accompanied by numerous cellular and extra-cellular matrix (ECM) changes in the tendon tissue. This proteom...
ORGANISM(S): Homo sapiens (Human) 
2018-07-03 | PXD006466 | Pride
Human Label-free Supraspinatus 
ProteomicsLipid metabolism modulation is associated with molecular injury and kidney dysfunction in a rat ischemia model
Due to organ shortage, the transplantation community are increasingly using kidney from deceased donors such as donation after circulatory death (DCD) and donation after brain death (DBD). However, DCD donation have increased delayed graft function compared to DBD, an underline mechanism is still no...
ORGANISM(S): Rattus rattus (Black rat) 
2020-07-06 | PXD005101 | Pride
Metabolomics Lipid metabolism Β-oxidation Kidney transplantation Ischaemia reperfusion injury (iri) Proteomics Fatty acids Gcxgc-ms 
ProteomicsDeep analysis of the USP18-dependent ISGylome and proteome unveils important roles for USP18 in tumour cell antigenicity and radiosensitivity
The deubiquitylating enzyme USP18 is a major negative regulator of the interferon (IFN) signalling cascade. IFN pathways contribute to resistance to conventional chemotherapy, radiotherapy, and immunotherapy and are often upregulated in certain tumours, including breast, lung, and colon tumours. USP...
ORGANISM(S): Homo sapiens (Human) 
2022-02-15 | PXD018299 | Pride
Human Cancer Deisgylating enzyme Proteomics Usp18 Isg15 Immunotherapy 
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