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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 
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 
ProteomicsProteomic analysis of sulfur-respiring haloarchaea from hypersaline lakes
Dimitry Y. Sorokin et al., (2021, Russian Academy of Sciences, Russia and Delft University of Technology, The Netherlands) describe the isolation and physiological and genomic properties of a fifth functional group of sulfur-respiring haloarchaea enriched from hypersaline lake sediments with CO as t...
ORGANISM(S): Archaea 
2022-12-25 | PXD028241 | Pride
Shotgun discovery proteomics Haloarchaea Qe plus 
ProteomicsInvestigation of fermentation process of a Lactobacillus suebicus
Investigation of fermentation process of a Lactobacillus suebicus strainan grown in anaerobic batch and chemostat cultures.
ORGANISM(S): Lactobacillus suebicus 
2019-10-30 | PXD015964 | Pride
Lc-ms/ms Lactobacillus suebicus Discovery proteomics 
ProteomicsA systematic evaluation of common yeast whole cell lysate proteomics sample preparation protocols
The continuing ‘desire’ in obtaining more quantitative and detailed information from cellular proteomics experiments in regards to proteome coverage and protein modifications asks for a systematic investigation of the protein extraction and digestion protocols, in particular when working with unicel...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-03-31 | PXD026806 | Pride
Yeast Shotgun proteomics Ms artefacts Modifications Sample preparation 
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 
ProteomicsInvestigating the autotrophic and mixotrophic metabolism of an anammox bacterium
Anaerobic ammonium oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving an...
ORGANISM(S): Candidatus Kuenenia stuttgartiensis 
2021-07-30 | PXD016171 | Pride
Metabolism Anammox Shot-gun proteomics Microbial proteomics 
ProteomicsSmall extracellular vesicles-delivered LSD1 promotes gastric cancer cell stemness
Although there are plenty of researches about nucleic acid in small extracellular vesicles (sEVs), properties of proteins identified as sEVs’ cargos and the mechanism of their action in recipient cell are poorly understood. Here, we show that lysine specific demethylase 1 (LSD1), the first identifie...
ORGANISM(S): Homo sapiens (Human) 
2021-12-22 | PXD020223 | Pride
Small extracellular vesicles  lsd1  stemness  gastric cancer 
ProteomicsMetaproteomic profiling of a granule-forming Ca. Accumulibacter enrichment
Extracellular proteins play key roles in microbial biofilm and aggregate formation, yet remain poorly understood. Using two advanced metaproteomic techniques, this study identified and classified 387 extracellular proteins potentially involved in aggregate formation, including filamentous and cell s...
ORGANISM(S): Candidatus Accumulibacter phosphatis 
2025-02-21 | PXD057220 | Pride
Shotgun proteomics Ca. accumulibacter phosphatis Granular biofilm Secretome 
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 
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