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ProteomicsSoil Metaproteomics LC-MS
Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of microbial populations (metaproteomics), yet not the...
ORGANISM(S): Escherichia coli 
2022-03-01 | PXD009773 | Pride
Shotgun Lc-ms Metaproteomics Climate change Soil 
ProteomicsSoil Metaproteome - proteome data analysis
Phosphorus (P) limitation will play a key role in the productivity of agriculture in the coming decades. Struvite is an ammonium magnesium phosphate mineral that can be recovered from wastewater-treatment plants and can be considered as an alternative source of P. However, the impact of struvite on ...
ORGANISM(S): Escherichia coli 
2019-03-13 | PXD009595 | Pride
Lc-ms Agriculture Soil microbiome 
ProteomicsSoil metaproteomics using DNA RNA protein co-extraction method
Soil is an inherently complex matrix and as such, we believe when performing culture-independent microbial community analyses using the 'omics' suite of tools, all biomolecules investigated should be co-extracted from the same biological sample. To this end, we developed a robust, cost-effective DNA...
ORGANISM(S): environmental samples 
2019-07-15 | PXD007077 | Pride
Soil metaproteomics lc ms/ms 
ProteomicsWetland soil incubation treated with sulfate and oxygen
To unravel complex dynamics of environmental disturbance and microbial metabolic activities, we set up laboratory microcosms to investigate the effects of SO42- and O2 alone or in combination on microbial activities and interactions, as well as the resulting fate of carbon within wetland soil. We us...
ORGANISM(S): soil metagenome 
2024-05-19 | PXD047453 | Pride
Soil microbiome Lc-ms/ms 
ProteomicsSoil metaproteome and pH effects
Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here ...
ORGANISM(S): Escherichia coli 
2018-07-26 | PXD010526 | Pride
Soil metaproteome Ph effects Land use Lc-ms/ms 
ProteomicsEnhancing Peptide Identification in Metaproteomics through Curriculum Learning in Deep Learning
Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from si...
ORGANISM(S): soil metagenome human gut metagenome marine metagenome 
2025-10-20 | PXD067277 | Pride
Lc-ms/ms Marine Human gut Soil 
ProteomicsMoisture Modulates Soil Reservoirs of Active DNA and RNA viruses
Global proteomics analyses to identify viral proteins in the soil microbiome. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.
ORGANISM(S): Environmental Samples <bacteria> (ncbitaxon:48479) 
MSV000086144 | MassIVE
ProteomicsAddressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage
Investigation of LC-MS/MS approaches to improve soil metaproteome depth of coverage for a Kansas prairie native soil
ORGANISM(S): environmental samples 
2018-11-21 | PXD008895 | Pride
Metaproteome Soil 
ProteomicsStructure and function of the topsoil metaproteome across global biomes: a survey of the topsoil metaproteome across global biomes
Herein, we evaluated the changes in biological functions in soils across global biomes through the identification and quantification of proteins. This knowledge is essential to provide one stepforward in soil microbial ecology in order to decipher the cellular and molecular mechanisms employed by so...
ORGANISM(S): Escherichia coli 
2023-02-24 | PXD018448 | Pride
Survey Soil metaproteomics Lc-ms Topsoil Global microbiomes 
ProteomicsRhizosphere bacterial community in re-used cover crop root channels initiate responses against drought
Plant growth and development depends on the availability of nutrients and water resources in the soil. The increased frequencies of drought events over recent years have affected nutrient availability soil systems. Crops reutilising winter cover crop root channels allows access to resources from dis...
ORGANISM(S): soil metagenome 
2025-09-22 | PXD062138 | Pride
Cover crop  root channel re-use  bacterial community  drought  soil types  metaproteomics 
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