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ProteomicsPhosphoproteomic analysis of T cell receptor stimulation-induced changes in human primary CD4+CD25- T cells in the absence or presence of regulatory T cells.
This is an addition to dataset PXD004291. This data were only used for confirmation of certain phosphopetides. The dataset was not included in inital analysis due to suboptimal sample preparation.
ORGANISM(S): Homo sapiens (Human) 
2017-08-28 | PXD006142 | Pride
T-cells Phosphoproteomics 
ProteomicsPhosphoproteomic analysis of T cell receptor stimulation-induced changes in human primary CD4+CD25- T cells in the absence or presence of regulatory T cells.
Regulatory T cells (Tregs) suppress other immune cells and are indispensable for human health, yet the molecular mechanisms of suppression remain incompletely understood. Tregs can suppress proliferation and cytokine production of CD4+CD25- conventional T cells (Tcons). We previously demonstrated th...
ORGANISM(S): Homo sapiens (Human) 
2017-08-28 | PXD004291 | Pride
Co-cultures Regulatory t cells (tregs) Ti-imac Human cd4+ t cells Phosphoproteomics 
ProteomicsWidespread protein histidine phosphorylation in bacteria
For decades, extreme difficulties in analyzing histidine phosphorylation have limited the study of phosphohistidine signaling. Here we report a method revealing widespread and abundant protein histidine phosphorylation in E. coli. Our new approach generated the largest E. coli phosphoproteome datase...
ORGANISM(S): Escherichia Coli 
2017-12-07 | PXD008369 | JPOST Repository
ProteomicsDirect comparison of the hinge-cleaving proteases IgdE and BdpK for LC-MS based IgG1 clonal profiling
Human antibodies are heterogeneous molecules, primarily due to clonal sequence variations. Analytical techniques to assess antibody levels quantitatively, like ELISA assays, lack the power to determine abundances at the clonal level. Recently, we introduced an LC-MS-based approach that can distingui...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-08-17 | MSV000092676 | MassIVE
ProteomicsChanges in the ATP synthase interactome in mitochondrial dysfunction by crosslinking mass spectrometry
Mitochondrial oxidative phosphorylation (OXPHOS) comprises a series of multi-subunit protein complexes that operate in coordination with the tricarboxylic acid (TCA) cycle to generate ATP. Although these systems are metabolically interconnected, complex II is generally regarded as the only direct st...
ORGANISM(S): Mus musculus (Mouse) 
2026-05-18 | PXD071441 | Pride
Atp synthase  mitochondrial dysfunction  tca cycle  crosslinking mass spectrometry  oxphos 
ProteomicsProteomic analysis of T cell differentiation
T helper cells (Th) play an important role guarding, regulating and modulating immune responses. The different Th lineages fulfill different tasks in response to infections. The two best defined subtypes are Th1 (involved in cellular immunity) and Th2 (humoral immunity). The cytokine environment aft...
ORGANISM(S): Mus musculus (Mouse) 
2019-02-14 | PXD004532 | Pride
Th2 Th1 Murine cd4+ t- cells Q exactive Scx 
ProteomicsSpectral quality guided optimization of hybrid EAciD fragmentation on the ZenoTOF 7600 system
Systematically optimized N-glycoproteomics method combining EAD and CID on the ZenoTOF 7600. Several dynamic CID parameters were optimized, next EAD was added using different kinetic energy values. Optimization was performed on glycopeptide enriched human plasma. After optimization, the method was ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-07-15 | MSV000098519 | MassIVE
ProteomicsAnalysis of intact mannose-6-phosphate glycopeptides
We have repurposed standard phosphoproteomics workflow based on Fe3+IMAC for enrichment ofmannose-6-phosphate modified glycopeptides. This worklfow was used to profile lysosomal acid hydrolases in HeLa and CHO cell lines. We have combined this approach with CRISPR/Cas9 KO of acid phosphatases 2 and ...
ORGANISM(S): Homo sapiens (Human) Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus) 
2018-12-18 | PXD010333 | Pride
Imac Hela M6p Glycopeptide Cho 
ProteomicsComplexome Profiling of Lrpprc KO and WT mouse heart mitochondria
Complexome profiling was performed to address the changes in composition of ATP synthase assemblies upon knockout of Lrpprc in mouse heart.
ORGANISM(S): Mus musculus (Mouse) 
2026-05-20 | PXD075583 | Pride
Proteomics"In-gel cross-linking mass spectrometry (IGX-MS) of proteins and protein complexes"
Cross-linking mass spectrometry has developed into an important method to study protein structures and interactions. The in-solution cross-linking workflows involve time and sample consuming steps and do not provide sensible solutions for differentiating cross-links obtained from co-occurring protei...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Escherichia coli 
2020-12-14 | PXD020014 | Pride
Bn-page/ cross-linking/ protein complexes/ complement/ protein modeling 
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