{
  "abstract": "Metabolomics enables the profiling of small-molecule metabolites, thereby capturing the biochemical state of a living organism at a given moment and making it possible to monitor the organism's cellular responses to stimuli. This technique has become a powerful tool in pharmaceutical research, the food industry, and microbial research. Metabolomics aims to obtain an unbiased metabolic profile; however, this is complicated by compound instability, the requirement for complex and often extensive sample processing, and nonlinear responses in mass spectrometry. Therefore, correcting for metabolite loss and mass-spectrometry-related artifacts is essential; this is typically achieved through relative quantification against an isotopically labeled internal standard for each metabolite of interest. This article describes a method to produce ¹³C-labeled yeast extract and its use as internal standard for metabolomics. More specifically, it provides step-by-step protocols for the fed-batch fermentation, quenching, metabolite extraction, and LC-MS and GC-MS characterization of the internal standard. It also includes a protocol explaining how to use the internal standard for the quantification of metabolites in yeast samples. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Trial run-fed-batch fermentation Support Protocol 1: Dry weight determination Basic Protocol 2: Quenching and washing of the cell samples and metabolite extraction Basic Protocol 3: Identification of intracellular metabolites using LC-MS Basic Protocol 4: Identification of intracellular metabolites using GC-MS Basic Protocol 5: Real run-fed-batch fermentation Basic Protocol 6: LC-MS characterization of the internal standard Basic Protocol 7: GC-MS characterization of the internal standard Basic Protocol 8: Quantification of metabolites in yeast samples.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.",
    "These authors contributed equally to this work."
  ],
  "article_type": "other",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Miriam Cammaert"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Rosalie Wouters"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Jitske van Ede"
    },
    {
      "affs": [
        0
      ],
      "name": "Erik de Hulster"
    },
    {
      "affs": [
        0
      ],
      "name": "Christiaan Mooiman"
    },
    {
      "affs": [
        0
      ],
      "name": "Patricia van Dam"
    },
    {
      "affs": [
        0
      ],
      "name": "Martin Pabst"
    },
    {
      "affs": [
        0
      ],
      "name": "Walter van Gulik"
    },
    {
      "affs": [
        0
      ],
      "name": "Pascale Daran-Lapujade"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/365p1f6j0h6s0.bib",
  "cited_by": 0,
  "doi": "10.1002/cpz1.70470",
  "fulltext_url": "https://europepmc.org/articles/PMC13729820",
  "id": "365p1f6j0h6s0",
  "issns": [
    "2691-1299"
  ],
  "landing_url": "https://europepmc.org/article/MED/42975294",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Chemical Biology"
    ],
    [
      "heading",
      "Protocol"
    ],
    [
      "openalex",
      "1312|Metabolomics and Mass Spectrometry Studies"
    ]
  ],
  "openalex": "W7164906046",
  "pdf_url": "https://europepmc.org/articles/PMC13729820?pdf=render",
  "pmcid": "PMC13729820",
  "pmid": "42975294",
  "published": "2026-11-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/365p1f6j0h6s0.ris",
  "sources": [
    {
      "first_seen": "2026-11-04T15:20:47Z",
      "native_id": "MED:42975294",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42975294"
    },
    {
      "first_seen": "2026-11-07T12:22:33Z",
      "native_id": "PMC13729820",
      "source": "pmc",
      "url": "https://doi.org/10.1002/cpz1.70470"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "heading:Chemical Biology",
      "subfield": "chemical-biology"
    }
  ],
  "title": "A Protocol for Lab-Scale Production of ¹³C-Labeled Yeast Extract as Internal Standard for Metabolomics and Quantification of Intracellular Metabolites.",
  "title_text": "A Protocol for Lab-Scale Production of ¹³C-Labeled Yeast Extract as Internal Standard for Metabolomics and Quantification of Intracellular Metabolites.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T12:22:33Z",
  "url": "https://research.draconitic.com/paper/365p1f6j0h6s0",
  "venue": "Current protocols",
  "versions": []
}