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ProteomicsDe novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition
Dataset generated and used in "De novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition". For more information, see SDRF.sdrf.tsv
ORGANISM(S): Candidatus Kuenenia stuttgartiensis Bacteria 
2025-09-08 | PXD057215 | Pride
De novo peptide sequencing Protein-based stable isotope probing 
ProteomicsGroEL-proteotypbing-based stable isotope probing of Thauera aromatica K172, Pseudomonas putida KT2440, and Escherichia coli BL21(DE3)
This dataset has been used to establish GroEL-SIP, coupling a targeted proteotyping approach for assessing bacterial community compositions using the taxonomic marker protein GroEL with stable isotope probing to link the identified taxa to substrate assimilation. This dataset contains raw data of fo...
ORGANISM(S): Thauera aromatica K172 Escherichia coli BL21(DE3) Pseudomonas putida KT2440 Bacteria 
2024-10-17 | PXD048255 | Pride
Protein-sip Stable isotope probing Groel-proteotyping 
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 
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 
ProteomicsIdentification of TBBPA-degraders in anaerobic bioreactor at environmentally relevant concentrations by combined protein-based stable isotope probing and metagenomics
The aim of this study was to identify TBBPA-degrading organisms in a complex microbial community by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). Firstly, the degradation kinetics were evaluated in order to simulate the decrease of re...
ORGANISM(S): anaerobic digester metagenome 
2022-09-12 | PXD030335 | Pride
Anaerobic digestion Stable isotope probing Tetrabromobisphenol a Metaproteomics 
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 
ProteomicsStable isotope probing with 13C-labeled bicarbonate/proteomics of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada
In this work we used stable isotope probing/proteomics to study uptake of carbon sources by members of the cyanobacterial consortium. The database for protein identification was obtained from assembled metagenomes.
ORGANISM(S): Phormidium sp. OSCR 
2022-01-21 | PXD028578 | Pride
Heterotrophs Stable isotope probing Cyanobacteria 
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 
GenomicsMicrobial community in Anaerobic reactor
Identification of protein-degraders in an anaerobic digester by protein stable isotope probing combined with metagenomics
PRJNA1132705 | ENA
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 
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