Name: Limitation in Protein-SIP - Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP)
Keywords: Not available

OmicsDI

Browse
Submit Data
Databases
API
Help

Dataset Information

261 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Limitation in Protein-SIP - Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP)

ABSTRACT: Mass spectra of Ps. fluorescens grown on partially 13C-labeled galactose. Peptide and protein identification of 1-DE bands.

INSTRUMENT(S): LTQ Orbitrap, instrument model

ORGANISM(S): Pseudomonas Fluorescens

SUBMITTER: Martin Taubert

PROVIDER: PRD000456 | Pride | 2014-08-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP).

Taubert Martin M Baumann Sven S von Bergen Martin M Seifert Jana J

Analytical and bioanalytical chemistry 20110807 6

One of the features of protein-based stable isotope probing is the parallel identification of differentially labeled peptide forms and the accurate calculation of their relative isotope abundances. The level of incorporation is informative of the metabolic activity of the species that synthesized the said protein and peptide. To model the carbon flux in a microbial community, an accurate assessment is crucial. Since the initial processes in carbon consumption are one of the most interesting obje ...[more]

PMID: 21822970

Similar Datasets

Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy.

Project description: Not available

| S-EPMC5725960 | biostudies-literature

Mock microbial community with spike-ins of 13C-labeled Escherichia coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description: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, 5 and 10%) of fully labeled 13C glucose (13C1-6) and spiked-in into a mock microbial community consisting of 32 species of bacteria, archaea, eukaryote and bacteriophages (UNEVEN Community described in Kleiner et al. 2017 Nat Communications 8(1):1558). The community also contained unlabeled E. coli cells and labeled/unlabeled E. coli cells in the spike-in sample were at a 1:1 ratio. Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C1-6 glucose were added 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-12-30 | PXD024174 | Pride

The effect of Iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5: iron(III) chloride

Project description:Transcriptomic profiling of Pseudomonas fluorescens Pf-5 comparing iron(III) chloride supplemented grown culture against non-iron treated grown culture in M9 minimal media

2011-05-16 | GSE29320 | GEO

The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5: iron(II) chloride

Project description:Transcriptomic profiling of Pseudomonas fluorescens Pf-5 comparing iron(II) chloride supplemented grown culture against non-iron treated grown culture in M9 minimal media

2011-05-16 | GSE29319 | GEO

13C-DNA-SIP Distinguishes the Prokaryotic Community That Metabolizes Soybean Residues Produced Under Different CO2 Concentrations.

Project description: Not available

| S-EPMC6798031 | biostudies-literature

Probing the limits to positional information.

Project description: Not available

| S-EPMC2253670 | biostudies-literature

Mixing of Escherichia coli cells labeled with 13C glucose with unlabeled E. coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description: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-carbon 13C glucose (13C2) or fully-labeled 13C glucose (13C1-6). Labeled cells were subsequently mixed with unlabeled E. coli cells in fixed ratios (50%, 90%, 95%, 99%). Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C2 or 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-12-30 | PXD024287 | Pride

Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities using protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset was obtained from the authors of Starke et al. (2020, Journal of Proteomics 222: 103791, https://doi.org/10.1016/j.jprot.2020.103791). Sample labels: 1 - High fiber diet inoculum 2 - High protein diet inoculum 3,4,5 - High fiber + unlabeled water 6,7,8 - High protein + unlabeled water 9,10,11 - High fiber + 25% of 99.9 atom% D2O 12,13,14 - High protein + 25% of 99.9 atom% D2O 15,16,17 - High fiber + 25% of 99.0 atom% H218O 18,19,20 - High protein + 25% of 99.0 atom% H218O Direct quote from the original article describing the dataset. “…the impact of specific diets on a defined microbial community derived from a human fecal sample was to be determined. The defined community was chosen to provide a stable in vitro setup that could be useful for future microbiome research. Briefly, the microbial community was grown in a heavy fiber and a heavy protein diet in addition to 25% heavy water, either as D2O or H218O. A dosage of 25% isotopically labeled water was chosen by trial-and-error to yield sufficient incorporation into protein but avoid the reduction of activity of individual organisms. A difference in growth medium formulation, representing a high-fiber diet and a high-protein diet, was utilized to evaluate shifts in microbial activity. We chose to assess these diets because high-protein, low-carbohydrate interventions represent a popular weight-loss strategy and because we expected a strong effect on the synthesis of amino acids by this comparison. After an incubation time of 12 h, the proteins were analyzed for label-free quantitation (metaproteomics) and incorporation of isotopes (protein-SIP), each in triplicates….”

2022-12-30 | PXD024291 | Pride

Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.

Project description: Not available

| S-EPMC7852690 | biostudies-literature

Probing the ultimate limits of plasmonic enhancement.

Project description: Not available

| S-EPMC3649871 | biostudies-literature