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ProteomicsAP-SWATH analysis reveals a direct involvement of VCP/p97 in integrated stress response signalling through CReP/PPP1R15B degradation
The ubiquitin-directed AAA-ATPase VCP/p97 facilitates degradation of misfolded proteins in diverse cellular stress response pathways. Resolving the complexity of dynamic interactions with hosts of accessory proteins and substrates has therefore been a major challenge. Here, we used affinity-purifica...
ORGANISM(S): Homo sapiens (Human) 
2018-04-04 | PXD007876 | Pride
Integrated stress response Ap-swath P97 
ProteomicsIn vivo and in vitro proteome analysis of HIV-1 infected, human CD4+ T cells
Host directed therapies against HIV-1 are thought to be critical for long term containment of the HIV-1 pandemic but remain elusive. Since HIV-1 infects and manipulates important effectors of both the innate and adaptive immune system, identifying modulations of the host cell systems in humans durin...
ORGANISM(S): Homo sapiens (Human) 
2017-02-28 | PXD005234 | Pride
Cd4 t cell Hiv Swath 
ProteomicsThe Proteome Landscape of Chronic Lymphocytic Leukemia
Many functional consequences of mutations on tumor phenotypes in chronic lymphocytic leukemia (CLL) are only partially known. This is in part due to missing information on the proteome of CLL. We profiled the proteome of 49 diverse CLL samples with data-independent acquisition mass spectrometry (DIA...
ORGANISM(S): Homo sapiens (Human) 
2021-09-27 | PXD022216 | Pride
Leukemia Diapasef Cll 
ProteomicsMultilayered Regulation of Autophagy by the Atg1 Kinase Orchestrates Spatial and Temporal Control of Autophagosome Formation
Autophagy is a conserved intracellular degradation pathway exerting various cytoprotective and homeostatic functions by utilizing de novo double membrane vesicle (autophagosome) formation to target a wide range of cytoplasmic material for vacuolar/lysosomal degradation. The Atg1 kinase is one of its...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-10-11 | PXD029047 | Pride
Metabolism Protein phosphatases Protein kinases Signalling Phosphorylation Ubiquitin-like proteins Autophagy Atg8 lipidation 
ProteomicsEnterococcus faecalis V583, Part 1
Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption ...
ORGANISM(S): Enterococcus faecalis (Streptococcus faecalis) 
2016-12-06 | PXD001576 | Pride
Swath Ph_shift Efv583 
ProteomicsEnterococcus faecalis V583 - data analysis
Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption ...
ORGANISM(S): Enterococcus faecalis (Streptococcus faecalis) 
2016-12-06 | PXD002869 | Pride
Swath Ph_shift Efv583 
ProteomicsBuilding high-quality assay libraries for targeted analysis of SWATH MS data
Targeted proteomics by selected/multiple reaction monitoring or, on a larger scale, by SWATH MS relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of critical importance. Here we present a detailed protocol that has been successfu...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2015-01-26 | PXD001126 | Pride
Yeast Assay library Swath Spectral library 
ProteomicsMulti-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Quantitative proteomics employing mass spectrometry has become an indispensable tool in basic and applied life science research. Methods based on data-dependent acquisition have proved extremely valuable for qualitative proteome analysis but historically have struggled to achieve reproducible quanti...
ORGANISM(S): Homo sapiens (Human) 
2020-02-19 | PXD004886 | Pride
Reproducibility Proteomics Swath-ms 
OtherAssessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.
Data from ProteomeXchange, PXD ID: PXD002534. File: GR_130129_20_OT3_NT_L3MBTL2_FAB_31_G11_2_HEK293.mzXML. Published as part of Nat Methods. 2015 Jun 29 . From the Abstract: {{i}} ... We describe a mass spectrometry-based standard operating procedure for scoring immunoprecipitation antibody quality...
ORGANISM(S): Homo_sapiens_viruses, Human_female 
GPM32320016573 | GPMDB
Resource Reanalysis 
UnknownA progeria mutation reveals functions for lamin A in nuclear assembly, architecture, and chromosome organization.
Not available
S-EPMC2779830 | biostudies-literature
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