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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 the Resistant Starch-fed Chronic Kidney Disease Rats
Background- Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by ...
ORGANISM(S): Rattus norvegicus (Rat) 
2018-12-18 | PXD008845 | Pride
Chronic kidney disease Resistant starch Rat Gut microbiome Metaproteomics 
ProteomicsMetaproteomics of Human Breast Milk and Formula-fed Neonatal Piglets
The benefits of breastfeeding infants are well characterized, including those on the immune system. However, determining the mechanism by which human breast milk (HBM) elicits effects on immune response requires investigation in an appropriate animal model. In the current study we used neonatal pigl...
ORGANISM(S): Sus scrofa domesticus (domestic pig) 
2021-11-03 | PXD025432 | Pride
Gut microbiome Microbiome-host interactions Metaproteomics 
UnknownUltra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases.
Not available
S-EPMC12274446 | biostudies-literature
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 
ProteomicsA Metaproteomics Approach to Elucidate Host and Pathogen Protein Expression during Catheter-Associated Urinary Tract Infections
Long term-catheterization leads inevitably to a catheter-associated bacteriuria caused by multispecies bacterial biofilms growing on and in the catheters. The overall goal of the presented study was (I) to unravel bacterial community structure and function of such an uropathogenic biofilm and (II) t...
ORGANISM(S): Morganella Homo sapiens (Human) Morganella Pseudomonas sp. 
2015-02-17 | PXD000164 | Pride
Metaproteomics 
UnknownNovoLign: metaproteomics by sequence alignment.
Not available
S-EPMC11530927 | biostudies-literature
ProteomicsIsobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic
Quantitative metaproteomics is a relatively new research field by applying proteomics technique to study microbial proteins of microbiome, and holds the great potential to truly quantify the functional proteins actually expressed by microbes in the biological environment such as gastrointestinal tra...
ORGANISM(S): Mus musculus (Mouse) 
2018-12-17 | PXD011735 | Pride
Isobaric labeling Metapro-iq Metaproteomics Gut microbiome Arsenic Tandem mass tags Label free 
ProteomicsEvaluating sequence alignment for metaproteomics applications
This dataset was utilized to assess the performance of a novel de novo metaproteomics pipeline, which performs sequence alignment of de novo sequences from complete metaproteomics experiments. Traditionally, metaproteomics data annotation relies on database searching that requires sample-specific da...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-10-10 | PXD050548 | Pride
Microbial proteomics Sequence alignment De novo sequencing Metaproteomics 
ProteomicsDeep gut metaproteomics - A deep metaproteomics approach for the study of human microbiomes
Stool samples were collected from 4 children and subjected to deep gut metaproteomics analysis for in-depth understanding the functional compositions of human gut mcirobiome.
ORGANISM(S): human gut metagenome 
2017-08-10 | PXD005619 | Pride
Strain Microbiome Deep Metaproteomics 
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