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ProteomicsMembrane proteomics of Caldalkalibacillus thermarum TA2.A1
Alkaliphilic microorganisms are similar to mesophilic counterparts with exception to membrane proteins. Detection of membrane proteins is difficult due to hydrophobicity and low absolute abundance. Caldalkalibacillus thermarum TA2.A1 is of interest due to growth from pH 7.5 to pH 10. Combination of ...
ORGANISM(S): Caldalkalibacillus thermarum TA2.A1 
2023-07-11 | PXD042369 | Pride
Qe plus Membrane proteome Caldalkalibacillus thermarum Shotgun proteomics 
ProteomicsProteomics on proteins from freshwater anaerobic methanotrophs that forms cytochrome nanowires
Anaerobic methanotrophic archaea are key components of the biological methane filter, but progress in understanding their physiology has been limited by the lack of axenic cultures. This study establishes near-axenic electrode-grown cultures of a freshwater anaerobic methanotroph, proposed as Candid...
ORGANISM(S): Candidatus Methanoperedens 
2026-08-28 | PXD072602 | Pride
Anme-2 archaea Extracellular cytochrome nanowires Anaerobic methane oxidation Extracellular electron transfer cryo-electron microscopy 
ProteomicsAnammox enrichment culture glycoproteomics
The physiology of the planctomycetal anammox bacteria makes them particularly special because they share features with all three domains of life. Anammox bacteria have been reported recently to produce surface-layer proteins, which represent the outermost layer and provide structure, shape and prote...
ORGANISM(S): Candidatus Kuenenia stuttgartiensis Candidatus Brocadia sapporoensis 
2021-08-05 | PXD021600 | Pride
Mass binning Microbial glycoproteomics Anammox bacteria Metaproteomics 
ProteomicsAerobic heterotrophic denitrification
Roothans et al., analyzed heterotrophic denitrification processes that can be an important source of nitrous oxide. We employed planktonic nitrification-inhibited denitrifying enrichment cultures under alternating oxic-anoxic conditions. The dynamic conditions resulted in a general presence of the d...
ORGANISM(S): Escherichia coli 
2024-07-17 | PXD042057 | Pride
N2o Heterotrophic denitrification Shotgun proteomics 
ProteomicsProteomic analysis chain-elongating microorganisms
The study by Allaart et al. (2023) investigates whether different environmental conditions can alter chain-elongating microbial communities to exhibit different catabolic stoichiometries. In support of the study, we provide whole-cell lysate shotgun proteomics data that compare the tested conditions...
ORGANISM(S): Escherichia coli 
2023-10-24 | PXD040972 | Pride
Chain-elongation Shotgun proteomics Label free quantification Clostridium kluyveri 
ProteomicsProteomics on extracellular fractions of polyphosphate accumulating organisms from wastewater treatment plant
Polyphosphate accumulating organisms are responsible for enhanced biological phosphate removal from wastewater, where they grow embedded in a matrix of extracellular polymeric substances. Little is known about the composition and dynamics of those proteins and their production by the different micro...
ORGANISM(S): Escherichia coli 
2022-12-25 | PXD036522 | Pride
Qe plus Extracellular protein fractions Polyphosphate accumulating organisms Wastewater treatment plants 
ProteomicsSalt stress in freshwater anaerobic methane-oxidizing archaea
Maider J. Echeveste Medrano and colleagues characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. The study performed metaproteomics, gene expression profiles and dedicated metabolomics to identify the pathways involved in the salt stress response...
ORGANISM(S): Candidatus Methanoperedens nitroreducens 
2024-07-17 | PXD048239 | Pride
Salt stress Methane-oxidizing archaea Shotgun proteomics Metaproteomics 
ProteomicsMetaomic study on the ecophysiological cascade underlaying seasonal N2O emissions
Nina Roothans et al.(2024) combined long-term, metagenomically resolved metaproteomics and ex situ kinetic characterizations to elucidate the ecophysiology of an N2O-emitting wastewater treatment plant community. The integration of these data enabled the identification of a cascade of environmental ...
ORGANISM(S): Microthrix Candidatus Accumulibacter phosphatis Nitrosomonas sp. Nitrospira sp. 
2025-02-21 | PXD051095 | Pride
Wastewater treatment plants Microbes Shotgun proteomics Metaproteomics 
ProteomicsWastewater metaproteomics: tracking microbial and human protein biomarkers
This study showcases the application of metaproteomics to generate a comprehensive proteomic profile from municipal wastewater. We developed a streamlined sample preparation protocol and a data-processing pipeline that integrates de novo sequencing to customize large public sequence databases for in...
ORGANISM(S): Escherichia coli 
2025-12-15 | PXD059455 | Pride
Metaproteomics Wastewater-based epidemiology Wastewater Gut microbes Biomarkers 
ProteomicsProteome dynamics during transition from exponential to stationary phase in yeast
Glycolysis is the central pathway for sugar metabolism in most living organisms. The single celled eukaryote yeast is a widely used model organism for higher eukaryotes in which the regulation of glycolysis is widely studied. S. cerevisiae is one of the few eukaryotic organisms that can efficiently ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-04-15 | PXD031412 | Pride
Growth Yeast Tmt quantification Orbitrap qe plus Glycolysis 
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