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ProteomicsMetaProSIP protein-SIP data - MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics
MetaProSIP offers an automated high-throughput solution for 13C or 15N protein-SIP experiments. Labeled peptides are identified based on their unlabeled isotopologues. It calculates incorporation of heavy isotopes (RIA), the labeling ratio (LR) between proteins as well as additional shape properties...
ORGANISM(S): uncultured bacterium 
2014-11-27 | PXD000382 | Pride
Protein-sip Metaprosip 
UnknownProteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.
Not available
S-EPMC11313024 | biostudies-literature
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 
ProteomicsProteomics of biphenyl labelling study
protein based stable isotope probing was performed for identifying microorganisms actually responsible for biphenyl biodegradation in soil environment.
ORGANISM(S): soil metagenome 
2022-02-16 | PXD023646 | Pride
Soil 13c-labelled peptides 
ProteomicsA clinic responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice
Growing evidence supports the gut microbiota as a promising target for enhancing the efficacy of cancer immunotherapy. However, the success of microbiota-targeting interventions has been limited, partly due to interindividual microbial heterogeneity. Here, we designed and constructed a defined cons...
ORGANISM(S): Firmicutes bacterium HGW-Firmicutes-5 
2026-01-14 | PXD064618 | Pride
ProteomicsStable Isotope Probing Deuterium LC-MS/MS
Competition between commensal and pathogenic microbes for monosaccharides derived from mucus layer O-glycans as nutrient sources has been proposed as a mechanism by which the gut microbiota counteracts pathogen colonization. However, our understanding of the microbial interactions that determine com...
ORGANISM(S): Escherichia coli 
2020-09-09 | PXD015215 | Pride
Stable isotope probing Nutrient competition Mucosal sugars Colonization resistance Metaproteomics 
ProteomicsPure and mixed crude extracts of Thauera aromatica K172 and Pseudomonas putida KT2440 for benchmarking GroEL-proteotyping
This dataset has been used to establish GroEL-proteotyping, a targeted proteotyping approach for assessing bacterial community compositions using the taxonomic marker protein GroEL. This dataset contains raw data of two experiments: 1. Pure cultures of T. aromatica (sample names: TA, TB, TC) and P. ...
ORGANISM(S): Thauera aromatica K172 Pseudomonas putida KT2440 
2023-10-27 | PXD046460 | Pride
Shotgun proteomics Taxonomic profiling Chaperon Sds-page Proteotyping Chaperonin Metaproteomics 
ProteomicsInvestigating the autotrophic and mixotrophic metabolism of an anammox bacterium
Anaerobic ammonium oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving an...
ORGANISM(S): Candidatus Kuenenia stuttgartiensis 
2021-07-30 | PXD016171 | Pride
Metabolism Anammox Shot-gun proteomics Microbial proteomics 
ProteomicsMAA-SIP biomethanisation with hydrogen addition
By using metagenome resolved protein stable isotope probing (protein-SIP) through incubations of identical reactors with 13C labelled bicarbonate over a period of 48 hours, the study aims to map differences in the metabolic behaviour of the microbial community during anaerobic digestion.
ORGANISM(S): anaerobic digester metagenome 
2021-12-05 | PXD027519 | Pride
Biomethanisation Anaerobic digestion Protein-sip Metagenomics Wood-ljungdahl pathway Anaplerotic carbon fixation 
ProteomicsProtein-SIP of cellulose-fed reactors
In this study we examined an anaerobic digester reactor fed with cellulose in order to identify cellulose degrading microorganisms using a culture independent approach. A metagenome was linked to the newly synthesized proteins involved by cellulose, by investigation of labelled proteins (Protein-SIP...
ORGANISM(S): anaerobic digester metagenome 
2022-03-23 | PXD027303 | Pride
Stable isotope probing Microbial communities Anaerobic digestion Lignocellulosic biomass Metaproteomics Stable isotope probing 
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