ArticleNature protocols2010
Protein-based stable isotope probing.
Article in Nature protocols, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 100 citations in OpenAlex.
- Aerith: Visualization and Annotation of Isotopic Enrichment Patterns of Peptides and Metabolites with Stable Isotope Labeling from Proteomics and Metabolomics.Analytical chemistry · 2025Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Unravelling metabolic cross-feeding in a yeast-bacteria community usingMolecular systems biology · 2023Article
- Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments.The ISME journal · 2023Article
- DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome.Microbiology spectrum · 2022Article
- Review
- NanoSIP: NanoSIMS Applications for Microbial Biology.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization.Nature communications · 2020Article
- Molecular Ecology of Isoprene-Degrading Bacteria.Microorganisms · 2020Review
- A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology.Frontiers in microbiology · 2020Review
- Advancing functional and translational microbiome research using meta-omics approaches.Microbiome · 2019Review
- The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Capturing the genetic makeup of the active microbiome in situ.The ISME journal · 2017Review
- Heavy Sugar and Heavy Water Create Tunable Intact Protein Mass Increases for Quantitative Mass Spectrometry in Any Feed and Organism.Analytical chemistry · 2016Article
- Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics.The ISME journal · 2016Article
- In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry.Environmental microbiology · 2014Article
- Quantification of peptide m/z distributions from 13C-labeled cultures with high-resolution mass spectrometry.Analytical chemistry · 2014Article
- Article
- Microbial minorities modulate methane consumption through niche partitioning.The ISME journal · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon ((13)C)- or nitrogen ((15)N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and the sequence information from peptide analysis obtained by mass spectrometry delivers phylogenetic information about the microorganisms responsible for the metabolism of the particular substrate. In this article, we provide guidelines for incubating microbial cultures with labeled substrates and a protocol for protein-SIP. The protocol guides readers through the proteomics pipeline, including protein extraction, gel-free and gel-based protein separation, the subsequent mass spectrometric analysis of peptides and the calculation of the incorporation of stable isotopes into peptides. Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.