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ProteomicsMock microbial community with spike-ins of 13C-labeled Escherichia coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)
This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms in microbial communities after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with different percentages (1...
ORGANISM(S): Escherichia coli 
2022-12-30 | PXD024174 | Pride
13c Carbon 13 Stable isotope probing Stable isotope Protein-sip 1d-lc 
ProteomicsMetaproteomics to study metabolic handoffs in the Idas modiolaeformis symbiosis
The goal of this study was to identify the key functions of the six main symbionts that are hosted in gills of the marine bivalve, Idas modiolaeformis, which lives at deep-sea hydrocarbon seeps and wood falls in the Eastern Atlantic Ocean and the Mediterranean Sea. These symbionts include the main a...
ORGANISM(S): Bacteria Idas modiolaeformis 
2023-07-20 | PXD040273 | Pride
Mollusk Chemosynthesis Metaproteome Symbiosis Metagenomics Bacteria-animal symbiosis Bivalve Metagenome 1d-lc-ms/ms Deep-sea Metaproteomics 
ProteomicsCa. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani are metabolically versatile.
The goal of this study was to identify the key functions of Candidatus Thiodiazotropha gloverae symbionts that are hosted in the gills of the lucinind clams, Lucinoma kazani, found at the deep-sea hydrocarbon seeps in the eastern Mediterranean Sea. These symbionts (Cromatiales, Sedimenticolaceae) ar...
ORGANISM(S): Candidatus Thiodiazotropha sp. Lucinoma kazani 
2025-05-26 | PXD051186 | Pride
Chemosynthesis 1d-lc Metaproteome Symbiosis Diazotrophs Metaproteomics 
ProteomicsAn omics-based metabolic model of methane-driven denitrification by aerobic methanotrophic bacteria
Methylomonas denitrificans is the first characterized organism that couples methane oxidation to nitrate reduction in pure culture without a partner. The aim of this study is to develop a metabolic model of methane driven nitrate respiration using a multi-level omics approach. Samples of M. denitrif...
ORGANISM(S): Methylomonas denitrificans 
2025-09-17 | PXD004041 | Pride
Methane Denitrification Omics Hypoxic Methylomonas Respiration Methanotroph Nitrous oxide Nitrate 
ProteomicsQuantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics
In this study we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We also compared metaproteomics based quantification to other quantification methods, namely metagenomics and 16S rRNA gene amplicon sequencing. The metagenomic and 1...
ORGANISM(S): Eukaryota (eucaryotes) Bacteria Archaea Viruses 
2017-05-12 | PXD006118 | Pride
1d-lc Metaproteome Microbiome Metagenomics 2d-lc Mock community Biomass assessment Metaproteomics 
ProteomicsLabeling Escherichia coli to saturation with 2.5 % of 15N ammonium in two conditions (aerobic and anaerobic) for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)
This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with 2.5 % of 15N-labeled NH4Cl and grown either anaer...
ORGANISM(S): Escherichia coli 
2022-02-16 | PXD024288 | Pride
Nitrogen 15 Stable isotope probing Stable isotope 15n Protein-sip 1d-lc Metaproteomics Lc-ms/ms 
ProteomicsLabeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of fully 13C labeled glucose for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)
This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of ful...
ORGANISM(S): Bacillus subtilis subsp. subtilis Escherichia coli 
2022-12-30 | PXD023693 | Pride
13c Carbon 13 Stable isotope probing Stable isotope Protein-sip 1d-lc 
ProteomicsMixing of Escherichia coli cells labeled with 13C glucose with unlabeled E. coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)
This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli cultures were labeled with different percentages (1% or 10%) of either single...
ORGANISM(S): Escherichia coli 
2022-12-30 | PXD024287 | Pride
13c Carbon 13 Stable isotope probing Stable isotope Protein-sip 1d-lc Metaproteomics Lc-ms/ms 
ProteomicsLabeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of 13C2 labeled glucose for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)
This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of sin...
ORGANISM(S): Escherichia coli Bacillus subtilis subsp. subtilis 6051-HGW 
2022-12-30 | PXD024285 | Pride
13c Carbon 13 Stable isotope probing Stable isotope Protein-sip 1d-lc Metaproteomics Lc-ms/ms 
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 
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