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ProteomicsCritical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.
Environmental meta-omics is rapidly expanding as sequencing capabilities improve, computing technologies become more accessible, and associated costs are reduced. The in situ snapshots of marine microbial life afforded by these data provide a growing knowledge of the functional roles of communities ...
ORGANISM(S): marine metagenome 
2019-01-25 | PXD006688 | Pride
Metaproteomics  ocean metaproteomics 
ProteomicsMetaproteomics of viral concentrates at deep chlorophyll maximum of Scouth China Sea
Marine viral concentrates (VCs) contains a substantial amount of non-cellular biological particles, e.g. viruses, gene transfer agents (GTAs) and membrane vesicles that are ecological significant. Metagenomic sequencing of VCs has been extensively applied to study the diversity and function potentia...
ORGANISM(S): environmental samples <unclassified> 
2018-05-02 | PXD007174 | Pride
Virua 56 kda selenium-binding protein Viral concentrates Metaproteomics 
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 
ProteomicsDiel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
Diel cycle is of enormous biological importance in that it imposes temporal structure on ecosystem productivity. In the world oceans, microorganisms form complex communities that carry out about half of photosynthesis and the bulk of life-sustaining nutrient cycling. Within these natural microbial a...
ORGANISM(S): Marine Metagenome 
2020-03-06 | PXD017373 |
ProteomicsPlastics investigated can be mineralized by bacteria naturally occurring within the marine environment
Biodegradable plastics are one possible solution for reducing plastic waste, yet the mechanisms and organisms involved in their degradation in the aquatic environment remain understudied. In this study, we have enriched a microbial community from North Sea water and sediment, capable of growing on t...
ORGANISM(S): Alcanivorax Thalassobius sp. 
2023-11-22 | PXD038098 | Pride
Marine environment Biodegradable plastic Metaproteomics 
ProteomicsMetaproteomics analyses of three chronically petroleum-polluted sites
Crude oil is the one of the most important natural assets of humankind, yet it is a major environmental pollutant, in particular, in marine environments. One of the largest crude oil polluted areas in the word is the semi-enclosed Mediterranean Sea, where the metabolic potential of indigenous popula...
ORGANISM(S): environmental samples 
2015-07-24 | PXD001490 | Pride
Marine Crude oil Hydrocarbon Microbiology Sediment Pollution Metaproteomics 
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 
ProteomicsMetaproteomics of the marine gutless oligochaete Olavius algarvensis and its symbionts to determine stable isotope fingerprints using Direct Protein-SIF
We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. We validated and tested the method extensively using pure cultures (PXD006762) and mock communities (PXD00...
ORGANISM(S): Olavius algarvensis Gamma 3 endosymbiont Chromatiales bacterium OalgGamma1 Olavius algarvensis Olavius algarvensis Delta 4 endosymbiont Olavius algarvensis Delta 1 endosymbiont Olavius algarvensis Gamma 1 endosymbiont Spirochaeta sp. ELBA 
2018-05-21 | PXD007510 | Pride
Lc-ms/ms Metaproteome Symbiosis Stable carbon isotope fingerprinting Metaproteomics Symbiont P-sif Protein-sif Stable isotopes 
UnknownNovel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics.
Not available
S-EPMC10882806 | biostudies-literature
ProteomicsGenome-informed extracellular metaproteomic datasets of natural seawater microbial communities exposed to amorphous and semi-crystalline polyhydroxyalkanoates
This dataset contains bottom-up LC-MS/MS data from culture-supernatant-derived extracellular protein fractions of natural seawater microbial communities incubated under three conditions: a polymer-free control (Marine Blank), amorphous polyhydroxyalkanoate (aPHA), and semi-crystalline polyhydroxyalk...
ORGANISM(S): marine metagenome 
2026-09-06 | PXD083733 | Pride
Metaproteomics Semi-crystalline pha Alcanivorax Amorphous pha Natural seawater Extracellular proteome Polyhydroxyalkanoate 
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