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ProteomicsToward industrial C8 production: Oxygen intrusion drives renewable n caprylate production from ethanol and acetate via intermediate metabolite production
Previous bioreactor studies achieved high volumetric n caprylate (i.e., n octanoate) production rates and selectivities from ethanol and acetate with chain elongating microbiomes. However, the metabolic pathways from the substrates to n caprylate synthesis were unclear. We operated two n caprylate p...
ORGANISM(S): bioreactor metagenome 
2025-05-24 | PXD054148 | Pride
N caprylate Bioreactor Metaproteomic 
ProteomicsA Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 3
Many diseases have been associated with gut microbiome abnormalities. The root cause of such diseases is not only due to bacterial dysbiosis, but also to change in bacterial functions, which are best studied by proteomic approaches. Although bacterial proteomics is well established, metaproteomics i...
ORGANISM(S): Homo sapiens (Human) mouse gut metagenome 
2022-02-16 | PXD021928 | Pride
Mus musculus Taxonomy Metaproteomics Metagenome 
ProteomicsPhosphoproteome dynamics of Streptomyces rimosus during submerged growth and antibiotic production
Streptomyces rimosus is an industrial streptomycete, best known as a producer of oxytetracycline, one of the most widely used antibiotics. Despite the significant contribution of Streptomyces species to the pharmaceutical industry, most omics analyses have only been conducted on the model organism, ...
ORGANISM(S): Streptomyces rimosus 
2022-08-22 | PXD034565 | Pride
Streptomyces rimosus Phosphoproteome Peptide dimethylation labeling Proteome Pellet fragmentation Oxytetracycline production 
ProteomicsTemporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-dependent Mitophagy
Mitophagy, the selective degradation of mitochondria by autophagy, affects defective mitochondria following damage or stress. At the onset of mitophagy, parkin ubiquitylates proteins on mitochondrial outer membrane (MOM). While the role of parkin at the onset of mitophagy is well understood, less is...
ORGANISM(S): Homo sapiens (Human) 
2022-01-17 | PXD027586 | Pride
Quantitative proteomics Mitochondria Mitophagy Ubiquitin Parkin 
ProteomicsExploration of phosphoproteins in Acinetobacter baumannii
Acinetobacter baumannii is a multidrug-resistant bacterium that has gained significant attention in recent years due to its involvement in a growing number of hospital-acquired infections. The World Health Organization has classified it as a critical priority pathogen, underscoring the urgent need f...
ORGANISM(S): Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) 
2025-09-03 | PXD064268 | Pride
Acinetobacter baumannii  phosphorylation  post-translational modification  proteomic  biofilm  virulence 
ProteomicsPhotoferrotroph R. palustris TIE-1
The underlying adaptations required by anoxygenic phototrophs to oxidize Fe(II), a potential stressor, are not well constrained. We used quantitative proteomics to compare cells of the photoferrotroph Rhodopseudomonas palustris TIE-1 grown photoautotrophically with Fe(II) or H2, and photoheterotroph...
ORGANISM(S): Rhodopseudomonas palustris TIE-1 
2018-06-25 | PXD009629 | Pride
Anoxygenic photosynthesis Oxidation Iron Photoferrotroph 
ProteomicsProteome dynamics in persisting and resuscitating bacterial cells
Bacterial persister cells become transiently tolerant to antibiotics by restraining their growth and metabolic activity. Detailed molecular characterization of bacterial persistence is hindered by low count of persisting cells and the need for their isolation. Here we used sustained addition of stab...
ORGANISM(S): Escherichia coli 
2021-07-30 | PXD018153 | Pride
Hipb Resuscitation Hipa Persistence Escherichia coli 
ProteomicsQuantitative proteomics links the intermediate filament nestin to vemurafenib resistance in melanoma cell lines
Targeted inhibition of mutated kinases using selective MAP kinase inhibitors in malignant melanoma often results in temporary improvement of the metastatic disease followed by rapid development of resistance. To gain insights in molecular processes that govern resistance, we performed SILAC-based qu...
ORGANISM(S): Homo sapiens (Human) 
2019-05-14 | PXD010683 | Pride
Cytoskeletal proteins Mass spectrometry Drug resistance Melanoma 
ProteomicsA Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 1
Many diseases have been associated with gut microbiome abnormalities. The root cause of such diseases is not only due to bacterial dysbiosis, but also to change in bacterial functions, which are best studied by proteomic approaches. Although bacterial proteomics is well established, metaproteomics i...
ORGANISM(S): mouse gut metagenome 
2022-02-15 | PXD020695 | Pride
Mus musculus Taxonomy Metaproteomics Metagenome 
ProteomicsA Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 5
The intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behaviour. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although prote...
ORGANISM(S): Eukaryota (eucaryotes) Bacteria Archaea Viruses 
2022-02-17 | PXD027306 | Pride
Mus musculus Taxonomy Metaproteomics Metagenome 
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