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ProteomicsCalculating coefficients of variation for data independent acquisition-based proteomics
Reanalysis of the Kawashima et al dataset with DIA-NN and Spectronaut. By using different settings this shows how the CVs can be altered by the software parameters.
ORGANISM(S): Homo sapiens (Human) 
2024-05-20 | PXD052403 | Pride
Intensity Proteomics Cv Coefficient of variation 
ProteomicsTissue adaptation is the dominant driver of the proteomic landscape of intestinal intraepithelial lymphocytes
Intestinal intraepithelial T lymphocytes (T-IEL) patrol the single layer of epithelial cells lining the gut, and consist of both induced T-IEL, derived from systemic antigen-experienced lymphocytes, and natural IEL, that are developmentally targeted to the intestine. To gain functional insights into...
ORGANISM(S): Mus musculus (Mouse) 
2021-03-15 | PXD023140 | Pride
Tmt T cells Lymph nodes Lymphocytes Iel 
ProteomicsOptimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples
Data independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be ...
ORGANISM(S): Candida albicans (Yeast) Mus musculus (Mouse) 
2023-10-11 | PXD045958 | Pride
Data quality Spectronaut False positives Immunology C. albicans Mouse Infection Dia Xic Multi-species 
ProteomicsHipSci: the iPSC proteomic compendium
Human induced pluripotent stem cell (iPSC) technology holds great potential for therapeutic and research purposes, by providing improved models of disease and for studying mechanisms regulating differentiation. The Human Induced Pluripotent Stem Cell Initiative (HipSci) was established to generate l...
ORGANISM(S): Homo sapiens (Human) 
2019-07-25 | PXD010557 | Pride
Dda Ipsc Proteomics Homo sapiens Human Orbitrap Fusion Stem cells Tmt 
ProteomicsMass Spectrometry identifies temporal changes and hallmarks of Delayed Recovery in the COVID19 Neutrophil proteomes
High-resolution mass spectrometry and the parallel quantitative evaluation of thousands of proteins has been used to characterise the proteomes of peripheral blood neutrophils from >200 individuals. This work has comprehensively mapped neutrophil molecular changes associated with mild versus severe ...
ORGANISM(S): Homo sapiens (Human) 
2022-08-17 | PXD036082 | Pride
Proteomics Long covid Dia Interferon Mass spectrometry Human Covid19 Neutrophil 
ProteomicsMass Spectrometry identifies temporal changes and hallmarks of Delayed Recovery in the COVID19 Neutrophil proteomes part2
Mass Spectrometry identifies temporal changes and hallmarks of Delayed Recovery in the COVID19 Neutrophil proteomes MTD project_description High-resolution mass spectrometry and the parallel quantitative evaluation of thousands of proteins has been used to characterise the proteomes of peripheral bl...
ORGANISM(S): Homo sapiens (Human) 
2022-08-17 | PXD036089 | Pride
Proteomics Long covid Dia Interferon Mass spectrometry Human Covid19 Neutrophil 
ProteomicsSuper-killer CTLs are generated by single gene deletion of Bach2
Bach2 codes for a transcriptional regulator exerting major influences on T cell mediated immune regulation. Effector CTLs derived from in vitro activation of murine CD8+ T cells showed increased proliferative and cytolytic capacity in the absence of BACH2. Before activation, BACH2-deficient CD8+ T c...
ORGANISM(S): Mus musculus (Mouse) 
2022-09-02 | PXD036457 | Pride
T cell Proteomics Bach2 Cd8 Ctl Tmt 
ProteomicsHypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity
The long-term impact of systemic hypoxia resulting from Acute Respiratory Distress Syndrome (ARDS) on the function of short-lived innate immune cells is unclear. We show that patients 3-6 months after recovering from ARDS have persistently impaired circulating neutrophil effector functions and an in...
ORGANISM(S): Homo sapiens (Human) 
2025-09-22 | PXD065461 | Pride
Epigenetics Neutrophil Hypoxia Reprogramming 
ProteomicsHypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity
The long-term impact of systemic hypoxia resulting from Acute Respiratory Distress Syndrome (ARDS) on the function of short-lived innate immune cells is unclear. We show that patients 3-6 months after recovering from ARDS have persistently impaired circulating neutrophil effector functions and an in...
ORGANISM(S): Homo sapiens (Human) 
2025-09-22 | PXD065519 | Pride
Epigenetics Neutrophil Hypoxia Reprogramming 
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