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UnknownLINA: A Linearizing Neural Network Architecture for Accurate First-Order and Second-Order Interpretations.
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S-EPMC9032252 | biostudies-literature
ProteomicsMediterranean grassland soil C-N compound turnover is mediated by genomically novel organisms, depth stratified, and rainfall dependent
integrated soil metagenomics and metaproteomics to study grassland soil microbial communities
ORGANISM(S): soil bacterium TS1114R 
2019-03-27 | PXD013110 | Pride
C-n compound Microbial communities Soil Metaproteomics 
ProteomicsQuantitative Tracking of Isotope Flows in Proteomes of Microbial Communities
Stable isotope probing (SIP) has been used to track nu- trient flows in microbial communities, but existing pro- tein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per samp...
ORGANISM(S): Escherichia coli 
2024-06-14 | PXD041958 | Pride
Proteomics 15n labeling Stable isotope Sip 
ProteomicsSipros Ensemble Improves Database Searching and Filtering for Complex Metaproteomics
Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased dis...
ORGANISM(S): Escherichia coli 
2018-02-09 | PXD007587 | Pride
Machine learning Metaproteomics Database searching 
ProteomicsProteomics for Newport Estuary Samples
Microorganisms are key contributors to biogeochemical flux in estuarine ecosystems. In this study, we conducted proteogenomic characterization of microbial communities from estuarine ecosystems.
ORGANISM(S): Escherichia coli 
2018-07-04 | PXD008093 | Pride
Estuarine microorganisms Proteomics 
ProteomicsAnaerobic synthetic microbial communities
Anaerobic microbial communities play a critical role in biogeochemical cycles through complex networks of interactions that influence community structure, stability, and functionality. This study investigates the metabolic interactions within synthetic communities composed of a cellulolytic bacteriu...
ORGANISM(S): Methanothrix soehngenii GP6 Clostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10) Methanospirillum hungatei JF-1 Desulfovibrio vulgaris str. Hildenborough 
2025-09-22 | PXD056517 | Pride
Sulfate-reducing bacteria Cellulose degrader Methanogen 
ProteomicsAngelo soil proteomics - Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
integration of metagenomics, metaproteomics, and metabolomics to study soil microbial community.
ORGANISM(S): metagenomes 
2016-12-23 | PXD004965 | Pride
Soil proteomics 
ProteomicsFungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acidic environments
Proteins from acid mine drainage microbial communities were extracted, trypsine digested and identified with LC-MS/MS analysis.
ORGANISM(S): uncultured microorganism 
2016-03-15 | PXD003541 | Pride
Fungi Nitrogen and carbon cycling Microbial community Lc-ms/ms 
ProteomicsCharacterization of Mortierella elongata/Candidatus Glomeribacter sp. symbiotic system
Proteins from Mortierella elongata/Candidatus Glomeribacter sp. symbiotic system were extracted, trypsine digested and identified with LC-MS/MS analysis.
ORGANISM(S): Candidatus Glomeribacter Mortierella elongata AG-77 
2017-03-29 | PXD003240 | Pride
Mortierella elongata Candidatus glomeribacter sp. Endosymbiosis Lc-ms/ms 
Proteomics2014 Panama soil proteomics - Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil
integrating metagenomics and metaproteomics to study microbial communities that have undergone long-term P addition experiment
ORGANISM(S): metagenomes 
2018-01-08 | PXD005910 | Pride
Proteomics Microbial community Soil 
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