Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2011-06-30

AUTHORS

Warwick B Dunn, David Broadhurst, Paul Begley, Eva Zelena, Sue Francis-McIntyre, Nadine Anderson, Marie Brown, Joshau D Knowles, Antony Halsall, John N Haselden, Andrew W Nicholls, Ian D Wilson, Douglas B Kell, Royston Goodacre,

ABSTRACT

Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography–mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography–MS (GC-MS) and ultraperformance liquid chromatography–MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control–based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described. More... »

PAGES

1060-1083

References to SciGraph publications

  • 2008-07-14. GC-MS with ethyl chloroformate derivatization for comprehensive analysis of metabolites in serum and its application to human uremia in ANALYTICAL AND BIOANALYTICAL CHEMISTRY
  • 2005-03. Comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC × GC-TOF) for high resolution metabolomics: biomarker discovery on spleen tissue extracts of obese NZO compared to lean C57BL/6 mice in METABOLOMICS
  • 2007-09-12. Proposed minimum reporting standards for chemical analysis in METABOLOMICS
  • 2010-05-06. Global metabolic profiling procedures for urine using UPLC–MS in NATURE PROTOCOLS
  • 2006-08-24. Phospholipid capture combined with non-linear chromatographic correction for improved serum metabolite profiling in METABOLOMICS
  • 2010-05-02. Metabolic oxidation regulates embryonic stem cell differentiation in NATURE CHEMICAL BIOLOGY
  • 2000-11. Metabolite profiling for plant functional genomics in NATURE BIOTECHNOLOGY
  • 2009-07-21. Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules' in BMC BIOINFORMATICS
  • 2007-06-28. Serum metabolomics reveals many novel metabolic markers of heart failure, including pseudouridine and 2-oxoglutarate in METABOLOMICS
  • 2008-12-28. Environmental metabolomics: a critical review and future perspectives in METABOLOMICS
  • 2006-11-28. Statistical strategies for avoiding false discoveries in metabolomics and related experiments in METABOLOMICS
  • 2005-06-10. Metabolic footprinting and systems biology: the medium is the message in NATURE REVIEWS MICROBIOLOGY
  • 2002-01. Metabolomics – the link between genotypes and phenotypes in PLANT MOLECULAR BIOLOGY
  • 2008-09-28. Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy in NATURE BIOTECHNOLOGY
  • 2003-05-12. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting in NATURE BIOTECHNOLOGY
  • 2008-04-20. Human metabolic phenotype diversity and its association with diet and blood pressure in NATURE
  • 2006-12-13. MathDAMP: a package for differential analysis of metabolite profiles in BMC BIOINFORMATICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nprot.2011.335

    DOI

    http://dx.doi.org/10.1038/nprot.2011.335

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1015396743

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21720319


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/03", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Chemical Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0301", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Analytical Chemistry", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Blood Chemical Analysis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chromatography, Liquid", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gas Chromatography-Mass Spectrometry", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mass Spectrometry", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metabolomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Plasma", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Serum", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Centre for Advanced Discoveries and Experimental Therapeutics, Manchester Biomedical Research Centre and School of Biomedicine, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.454377.6", 
              "name": [
                "Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
                "Centre for Advanced Discoveries and Experimental Therapeutics, Manchester Biomedical Research Centre and School of Biomedicine, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Dunn", 
            "givenName": "Warwick B", 
            "id": "sg:person.01042634342.49", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042634342.49"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Medicine, Katz Group Centre for Pharmacy & Health, University of Alberta, Edmonton, Alberta, Canada", 
              "id": "http://www.grid.ac/institutes/grid.17089.37", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
                "Department of Medicine, Katz Group Centre for Pharmacy & Health, University of Alberta, Edmonton, Alberta, Canada"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Broadhurst", 
            "givenName": "David", 
            "id": "sg:person.01140423003.13", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01140423003.13"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Begley", 
            "givenName": "Paul", 
            "id": "sg:person.0747502723.50", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0747502723.50"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zelena", 
            "givenName": "Eva", 
            "id": "sg:person.01300177150.05", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300177150.05"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Francis-McIntyre", 
            "givenName": "Sue", 
            "id": "sg:person.0671021450.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0671021450.18"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Anderson", 
            "givenName": "Nadine", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Brown", 
            "givenName": "Marie", 
            "id": "sg:person.01016430011.14", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01016430011.14"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Computer Science, The University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Computer Science, The University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Knowles", 
            "givenName": "Joshau D", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Halsall", 
            "givenName": "Antony", 
            "id": "sg:person.01157062742.50", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157062742.50"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Investigative Preclinical Toxicology, GlaxoSmithKline, Hertfordshire, UK", 
              "id": "http://www.grid.ac/institutes/grid.418236.a", 
              "name": [
                "Department of Investigative Preclinical Toxicology, GlaxoSmithKline, Hertfordshire, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Haselden", 
            "givenName": "John N", 
            "id": "sg:person.01247330464.11", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247330464.11"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Investigative Preclinical Toxicology, GlaxoSmithKline, Hertfordshire, UK", 
              "id": "http://www.grid.ac/institutes/grid.418236.a", 
              "name": [
                "Department of Investigative Preclinical Toxicology, GlaxoSmithKline, Hertfordshire, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nicholls", 
            "givenName": "Andrew W", 
            "id": "sg:person.0762101646.16", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0762101646.16"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Clinical Pharmacology, Drug Metabolism and Pharmacokinetics, AstraZeneca, Cheshire, UK", 
              "id": "http://www.grid.ac/institutes/grid.417815.e", 
              "name": [
                "Department of Clinical Pharmacology, Drug Metabolism and Pharmacokinetics, AstraZeneca, Cheshire, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wilson", 
            "givenName": "Ian D", 
            "id": "sg:person.010010573072.33", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010010573072.33"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kell", 
            "givenName": "Douglas B", 
            "id": "sg:person.01032405132.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032405132.18"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
              "id": "http://www.grid.ac/institutes/grid.5379.8", 
              "name": [
                "Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK", 
                "School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Goodacre", 
            "givenName": "Royston", 
            "id": "sg:person.01007611374.40", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007611374.40"
            ], 
            "type": "Person"
          }, 
          {}
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1186/1471-2105-10-227", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010131855", 
              "https://doi.org/10.1186/1471-2105-10-227"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11306-006-0037-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014281361", 
              "https://doi.org/10.1007/s11306-006-0037-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1013713905833", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027843923", 
              "https://doi.org/10.1023/a:1013713905833"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11306-005-1108-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037718367", 
              "https://doi.org/10.1007/s11306-005-1108-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11306-006-0028-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046195559", 
              "https://doi.org/10.1007/s11306-006-0028-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt823", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051888256", 
              "https://doi.org/10.1038/nbt823"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature06882", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002778922", 
              "https://doi.org/10.1038/nature06882"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/81137", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045090002", 
              "https://doi.org/10.1038/81137"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00216-008-2220-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050870590", 
              "https://doi.org/10.1007/s00216-008-2220-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1500", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033238111", 
              "https://doi.org/10.1038/nbt.1500"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro1177", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044547329", 
              "https://doi.org/10.1038/nrmicro1177"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11306-008-0152-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003660520", 
              "https://doi.org/10.1007/s11306-008-0152-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11306-007-0063-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043894656", 
              "https://doi.org/10.1007/s11306-007-0063-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nchembio.364", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020884064", 
              "https://doi.org/10.1038/nchembio.364"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nprot.2010.50", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036792816", 
              "https://doi.org/10.1038/nprot.2010.50"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-7-530", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017234046", 
              "https://doi.org/10.1186/1471-2105-7-530"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11306-007-0082-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023480149", 
              "https://doi.org/10.1007/s11306-007-0082-2"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2011-06-30", 
        "datePublishedReg": "2011-06-30", 
        "description": "Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography\u2013mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography\u2013MS (GC-MS) and ultraperformance liquid chromatography\u2013MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control\u2013based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/nprot.2011.335", 
        "inLanguage": "en", 
        "isAccessibleForFree": false, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2758011", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1037502", 
            "issn": [
              "1754-2189", 
              "1750-2799"
            ], 
            "name": "Nature Protocols", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "7", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "6"
          }
        ], 
        "keywords": [
          "multiple analytical batches", 
          "chromatography-MS", 
          "gas chromatography-MS", 
          "liquid chromatography-MS", 
          "thousands of metabolites", 
          "analytical batches", 
          "mass spectrometry", 
          "gas chromatography", 
          "sample preparation", 
          "large-scale metabolic profiling", 
          "liquid chromatography", 
          "metabolic profiling", 
          "large-scale metabolomics studies", 
          "biological systems", 
          "reproducible detection", 
          "biofluid collection", 
          "chromatography", 
          "experimental workflow", 
          "metabolomics studies", 
          "single biofluid", 
          "spectrometry", 
          "compounds", 
          "biofluids", 
          "preparation", 
          "batch", 
          "quantitation", 
          "samples", 
          "signal correction", 
          "drug perturbations", 
          "metabolites", 
          "metabolome", 
          "human samples", 
          "profiling", 
          "detection", 
          "plasma", 
          "method", 
          "essential role", 
          "platform", 
          "influence", 
          "identification", 
          "serum", 
          "system", 
          "procedure", 
          "thousands", 
          "hundreds", 
          "study", 
          "protocol", 
          "workflow", 
          "changes", 
          "data", 
          "perturbations", 
          "role", 
          "data acquisition", 
          "tissue samples", 
          "quality assurance", 
          "metabolism", 
          "correction", 
          "differences", 
          "metabolic changes", 
          "integration", 
          "collection", 
          "assurance", 
          "environmental influences", 
          "years", 
          "integration of data", 
          "acquisition", 
          "disease", 
          "genetic differences", 
          "months", 
          "Chromatography\u2013mass spectrometry (MS) platforms", 
          "spectrometry (MS) platforms", 
          "plasma-based metabolic profiling", 
          "quality control\u2013based robust LOESS signal correction", 
          "control\u2013based robust LOESS signal correction", 
          "robust LOESS signal correction", 
          "LOESS signal correction"
        ], 
        "name": "Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry", 
        "pagination": "1060-1083", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1015396743"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/nprot.2011.335"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "21720319"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/nprot.2011.335", 
          "https://app.dimensions.ai/details/publication/pub.1015396743"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-11-01T18:16", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_554.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/nprot.2011.335"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.335'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.335'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.335'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.335'


     

    This table displays all metadata directly associated to this object as RDF triples.

    349 TRIPLES      22 PREDICATES      127 URIs      102 LITERALS      15 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/nprot.2011.335 schema:about N131a69a81c134d2681fccc140a4a3373
    2 N26ef87ee362a45408d215733889da6f5
    3 N7a403cc0cb9146e9ab9f6971c0ddb854
    4 N943df59860c94146a3ca67261aa26f9f
    5 Nac144e7a36214586a3cce1419593645e
    6 Nae9bdfa063f14817ac02220ccbcb8854
    7 Ndf2f4dadc3324f24b3eeda5618ff7c7d
    8 Nf6c80f9c812e40d2a8300f1b8b849c3c
    9 anzsrc-for:03
    10 anzsrc-for:0301
    11 schema:author N2d66859a5e7f4cc7838ef498f3ea0b70
    12 schema:citation sg:pub.10.1007/s00216-008-2220-8
    13 sg:pub.10.1007/s11306-005-1108-2
    14 sg:pub.10.1007/s11306-006-0028-0
    15 sg:pub.10.1007/s11306-006-0037-z
    16 sg:pub.10.1007/s11306-007-0063-5
    17 sg:pub.10.1007/s11306-007-0082-2
    18 sg:pub.10.1007/s11306-008-0152-0
    19 sg:pub.10.1023/a:1013713905833
    20 sg:pub.10.1038/81137
    21 sg:pub.10.1038/nature06882
    22 sg:pub.10.1038/nbt.1500
    23 sg:pub.10.1038/nbt823
    24 sg:pub.10.1038/nchembio.364
    25 sg:pub.10.1038/nprot.2010.50
    26 sg:pub.10.1038/nrmicro1177
    27 sg:pub.10.1186/1471-2105-10-227
    28 sg:pub.10.1186/1471-2105-7-530
    29 schema:datePublished 2011-06-30
    30 schema:datePublishedReg 2011-06-30
    31 schema:description Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography–mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography–MS (GC-MS) and ultraperformance liquid chromatography–MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control–based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.
    32 schema:genre article
    33 schema:inLanguage en
    34 schema:isAccessibleForFree false
    35 schema:isPartOf Na7265dfe7da4431995f3d472965c708d
    36 Nd7aa9e59b8034037ae243dee378e5a47
    37 sg:journal.1037502
    38 schema:keywords Chromatography–mass spectrometry (MS) platforms
    39 LOESS signal correction
    40 acquisition
    41 analytical batches
    42 assurance
    43 batch
    44 biofluid collection
    45 biofluids
    46 biological systems
    47 changes
    48 chromatography
    49 chromatography-MS
    50 collection
    51 compounds
    52 control–based robust LOESS signal correction
    53 correction
    54 data
    55 data acquisition
    56 detection
    57 differences
    58 disease
    59 drug perturbations
    60 environmental influences
    61 essential role
    62 experimental workflow
    63 gas chromatography
    64 gas chromatography-MS
    65 genetic differences
    66 human samples
    67 hundreds
    68 identification
    69 influence
    70 integration
    71 integration of data
    72 large-scale metabolic profiling
    73 large-scale metabolomics studies
    74 liquid chromatography
    75 liquid chromatography-MS
    76 mass spectrometry
    77 metabolic changes
    78 metabolic profiling
    79 metabolism
    80 metabolites
    81 metabolome
    82 metabolomics studies
    83 method
    84 months
    85 multiple analytical batches
    86 perturbations
    87 plasma
    88 plasma-based metabolic profiling
    89 platform
    90 preparation
    91 procedure
    92 profiling
    93 protocol
    94 quality assurance
    95 quality control–based robust LOESS signal correction
    96 quantitation
    97 reproducible detection
    98 robust LOESS signal correction
    99 role
    100 sample preparation
    101 samples
    102 serum
    103 signal correction
    104 single biofluid
    105 spectrometry
    106 spectrometry (MS) platforms
    107 study
    108 system
    109 thousands
    110 thousands of metabolites
    111 tissue samples
    112 workflow
    113 years
    114 schema:name Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry
    115 schema:pagination 1060-1083
    116 schema:productId N36d03aa3fa2b45759176335818324e67
    117 Nb5be457288824cc79c094c3d5af5642f
    118 Ne4c1d4ff46514598aec98fdbb2352bf1
    119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015396743
    120 https://doi.org/10.1038/nprot.2011.335
    121 schema:sdDatePublished 2021-11-01T18:16
    122 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    123 schema:sdPublisher N99c40ea5a9df4e6a9c1c65a6738ee210
    124 schema:url https://doi.org/10.1038/nprot.2011.335
    125 sgo:license sg:explorer/license/
    126 sgo:sdDataset articles
    127 rdf:type schema:ScholarlyArticle
    128 N041919586549453da6acab2c03f41864 rdf:first sg:person.01300177150.05
    129 rdf:rest Ne6f725c3ff8547f38225c29f0b894461
    130 N131a69a81c134d2681fccc140a4a3373 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    131 schema:name Gas Chromatography-Mass Spectrometry
    132 rdf:type schema:DefinedTerm
    133 N26ef87ee362a45408d215733889da6f5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    134 schema:name Chromatography, Liquid
    135 rdf:type schema:DefinedTerm
    136 N2b90ea1cb549458ca9c2097efb2fdfd2 rdf:first Nd51959fb74124aada4305c95f327ffed
    137 rdf:rest Na41cc5d1aa244bc4bf7cb1df3d8a4feb
    138 N2d66859a5e7f4cc7838ef498f3ea0b70 rdf:first sg:person.01042634342.49
    139 rdf:rest Nf4db881e0ef34bef937692d069a9ca76
    140 N3023a43f63f54ae3bebed9c7ad315401 rdf:first sg:person.01032405132.18
    141 rdf:rest Nf231f5bdb1814df8b938ece0dcd2c99b
    142 N36d03aa3fa2b45759176335818324e67 schema:name dimensions_id
    143 schema:value pub.1015396743
    144 rdf:type schema:PropertyValue
    145 N4c3a2b9020184ad9a295ecd8a8498c9a rdf:first sg:person.0762101646.16
    146 rdf:rest Nc02941be1dfe462ba123acb39f093bd4
    147 N50da15b489d34722a429b6f49d663e82 rdf:first N44ab9c742e0144618e94d45d391443c3
    148 rdf:rest rdf:nil
    149 N5a9cbc19057e4a788207e44c0b0d149d schema:affiliation grid-institutes:grid.5379.8
    150 schema:familyName Anderson
    151 schema:givenName Nadine
    152 rdf:type schema:Person
    153 N5c7fe0fbd1ce4d749fabc25fc3fc89ab rdf:first sg:person.01247330464.11
    154 rdf:rest N4c3a2b9020184ad9a295ecd8a8498c9a
    155 N7a403cc0cb9146e9ab9f6971c0ddb854 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    156 schema:name Plasma
    157 rdf:type schema:DefinedTerm
    158 N943df59860c94146a3ca67261aa26f9f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    159 schema:name Blood Chemical Analysis
    160 rdf:type schema:DefinedTerm
    161 N99c40ea5a9df4e6a9c1c65a6738ee210 schema:name Springer Nature - SN SciGraph project
    162 rdf:type schema:Organization
    163 Na41cc5d1aa244bc4bf7cb1df3d8a4feb rdf:first sg:person.01157062742.50
    164 rdf:rest N5c7fe0fbd1ce4d749fabc25fc3fc89ab
    165 Na7265dfe7da4431995f3d472965c708d schema:volumeNumber 6
    166 rdf:type schema:PublicationVolume
    167 Nac00d2c3c1ae49a980ed91c88106b304 rdf:first sg:person.01016430011.14
    168 rdf:rest N2b90ea1cb549458ca9c2097efb2fdfd2
    169 Nac144e7a36214586a3cce1419593645e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    170 schema:name Serum
    171 rdf:type schema:DefinedTerm
    172 Nae9bdfa063f14817ac02220ccbcb8854 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    173 schema:name Mass Spectrometry
    174 rdf:type schema:DefinedTerm
    175 Nb007eef629224453a479097711ce22b9 rdf:first sg:person.0747502723.50
    176 rdf:rest N041919586549453da6acab2c03f41864
    177 Nb5be457288824cc79c094c3d5af5642f schema:name doi
    178 schema:value 10.1038/nprot.2011.335
    179 rdf:type schema:PropertyValue
    180 Nc02941be1dfe462ba123acb39f093bd4 rdf:first sg:person.010010573072.33
    181 rdf:rest N3023a43f63f54ae3bebed9c7ad315401
    182 Ncaee9624cc8c42cdb3d0127c3e427dbd rdf:first N5a9cbc19057e4a788207e44c0b0d149d
    183 rdf:rest Nac00d2c3c1ae49a980ed91c88106b304
    184 Nd51959fb74124aada4305c95f327ffed schema:affiliation grid-institutes:grid.5379.8
    185 schema:familyName Knowles
    186 schema:givenName Joshau D
    187 rdf:type schema:Person
    188 Nd7aa9e59b8034037ae243dee378e5a47 schema:issueNumber 7
    189 rdf:type schema:PublicationIssue
    190 Ndf2f4dadc3324f24b3eeda5618ff7c7d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    191 schema:name Metabolomics
    192 rdf:type schema:DefinedTerm
    193 Ne4c1d4ff46514598aec98fdbb2352bf1 schema:name pubmed_id
    194 schema:value 21720319
    195 rdf:type schema:PropertyValue
    196 Ne6f725c3ff8547f38225c29f0b894461 rdf:first sg:person.0671021450.18
    197 rdf:rest Ncaee9624cc8c42cdb3d0127c3e427dbd
    198 Nf231f5bdb1814df8b938ece0dcd2c99b rdf:first sg:person.01007611374.40
    199 rdf:rest N50da15b489d34722a429b6f49d663e82
    200 Nf4db881e0ef34bef937692d069a9ca76 rdf:first sg:person.01140423003.13
    201 rdf:rest Nb007eef629224453a479097711ce22b9
    202 Nf6c80f9c812e40d2a8300f1b8b849c3c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    203 schema:name Humans
    204 rdf:type schema:DefinedTerm
    205 anzsrc-for:03 schema:inDefinedTermSet anzsrc-for:
    206 schema:name Chemical Sciences
    207 rdf:type schema:DefinedTerm
    208 anzsrc-for:0301 schema:inDefinedTermSet anzsrc-for:
    209 schema:name Analytical Chemistry
    210 rdf:type schema:DefinedTerm
    211 sg:grant.2758011 http://pending.schema.org/fundedItem sg:pub.10.1038/nprot.2011.335
    212 rdf:type schema:MonetaryGrant
    213 sg:journal.1037502 schema:issn 1750-2799
    214 1754-2189
    215 schema:name Nature Protocols
    216 schema:publisher Springer Nature
    217 rdf:type schema:Periodical
    218 sg:person.010010573072.33 schema:affiliation grid-institutes:grid.417815.e
    219 schema:familyName Wilson
    220 schema:givenName Ian D
    221 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010010573072.33
    222 rdf:type schema:Person
    223 sg:person.01007611374.40 schema:affiliation grid-institutes:grid.5379.8
    224 schema:familyName Goodacre
    225 schema:givenName Royston
    226 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007611374.40
    227 rdf:type schema:Person
    228 sg:person.01016430011.14 schema:affiliation grid-institutes:grid.5379.8
    229 schema:familyName Brown
    230 schema:givenName Marie
    231 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01016430011.14
    232 rdf:type schema:Person
    233 sg:person.01032405132.18 schema:affiliation grid-institutes:grid.5379.8
    234 schema:familyName Kell
    235 schema:givenName Douglas B
    236 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032405132.18
    237 rdf:type schema:Person
    238 sg:person.01042634342.49 schema:affiliation grid-institutes:grid.454377.6
    239 schema:familyName Dunn
    240 schema:givenName Warwick B
    241 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042634342.49
    242 rdf:type schema:Person
    243 sg:person.01140423003.13 schema:affiliation grid-institutes:grid.17089.37
    244 schema:familyName Broadhurst
    245 schema:givenName David
    246 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01140423003.13
    247 rdf:type schema:Person
    248 sg:person.01157062742.50 schema:affiliation grid-institutes:grid.5379.8
    249 schema:familyName Halsall
    250 schema:givenName Antony
    251 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157062742.50
    252 rdf:type schema:Person
    253 sg:person.01247330464.11 schema:affiliation grid-institutes:grid.418236.a
    254 schema:familyName Haselden
    255 schema:givenName John N
    256 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247330464.11
    257 rdf:type schema:Person
    258 sg:person.01300177150.05 schema:affiliation grid-institutes:grid.5379.8
    259 schema:familyName Zelena
    260 schema:givenName Eva
    261 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300177150.05
    262 rdf:type schema:Person
    263 sg:person.0671021450.18 schema:affiliation grid-institutes:grid.5379.8
    264 schema:familyName Francis-McIntyre
    265 schema:givenName Sue
    266 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0671021450.18
    267 rdf:type schema:Person
    268 sg:person.0747502723.50 schema:affiliation grid-institutes:grid.5379.8
    269 schema:familyName Begley
    270 schema:givenName Paul
    271 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0747502723.50
    272 rdf:type schema:Person
    273 sg:person.0762101646.16 schema:affiliation grid-institutes:grid.418236.a
    274 schema:familyName Nicholls
    275 schema:givenName Andrew W
    276 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0762101646.16
    277 rdf:type schema:Person
    278 sg:pub.10.1007/s00216-008-2220-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050870590
    279 https://doi.org/10.1007/s00216-008-2220-8
    280 rdf:type schema:CreativeWork
    281 sg:pub.10.1007/s11306-005-1108-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037718367
    282 https://doi.org/10.1007/s11306-005-1108-2
    283 rdf:type schema:CreativeWork
    284 sg:pub.10.1007/s11306-006-0028-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046195559
    285 https://doi.org/10.1007/s11306-006-0028-0
    286 rdf:type schema:CreativeWork
    287 sg:pub.10.1007/s11306-006-0037-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1014281361
    288 https://doi.org/10.1007/s11306-006-0037-z
    289 rdf:type schema:CreativeWork
    290 sg:pub.10.1007/s11306-007-0063-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043894656
    291 https://doi.org/10.1007/s11306-007-0063-5
    292 rdf:type schema:CreativeWork
    293 sg:pub.10.1007/s11306-007-0082-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023480149
    294 https://doi.org/10.1007/s11306-007-0082-2
    295 rdf:type schema:CreativeWork
    296 sg:pub.10.1007/s11306-008-0152-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003660520
    297 https://doi.org/10.1007/s11306-008-0152-0
    298 rdf:type schema:CreativeWork
    299 sg:pub.10.1023/a:1013713905833 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027843923
    300 https://doi.org/10.1023/a:1013713905833
    301 rdf:type schema:CreativeWork
    302 sg:pub.10.1038/81137 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045090002
    303 https://doi.org/10.1038/81137
    304 rdf:type schema:CreativeWork
    305 sg:pub.10.1038/nature06882 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002778922
    306 https://doi.org/10.1038/nature06882
    307 rdf:type schema:CreativeWork
    308 sg:pub.10.1038/nbt.1500 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033238111
    309 https://doi.org/10.1038/nbt.1500
    310 rdf:type schema:CreativeWork
    311 sg:pub.10.1038/nbt823 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051888256
    312 https://doi.org/10.1038/nbt823
    313 rdf:type schema:CreativeWork
    314 sg:pub.10.1038/nchembio.364 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020884064
    315 https://doi.org/10.1038/nchembio.364
    316 rdf:type schema:CreativeWork
    317 sg:pub.10.1038/nprot.2010.50 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036792816
    318 https://doi.org/10.1038/nprot.2010.50
    319 rdf:type schema:CreativeWork
    320 sg:pub.10.1038/nrmicro1177 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044547329
    321 https://doi.org/10.1038/nrmicro1177
    322 rdf:type schema:CreativeWork
    323 sg:pub.10.1186/1471-2105-10-227 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010131855
    324 https://doi.org/10.1186/1471-2105-10-227
    325 rdf:type schema:CreativeWork
    326 sg:pub.10.1186/1471-2105-7-530 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017234046
    327 https://doi.org/10.1186/1471-2105-7-530
    328 rdf:type schema:CreativeWork
    329 grid-institutes:grid.17089.37 schema:alternateName Department of Medicine, Katz Group Centre for Pharmacy & Health, University of Alberta, Edmonton, Alberta, Canada
    330 schema:name Department of Medicine, Katz Group Centre for Pharmacy & Health, University of Alberta, Edmonton, Alberta, Canada
    331 School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    332 rdf:type schema:Organization
    333 grid-institutes:grid.417815.e schema:alternateName Department of Clinical Pharmacology, Drug Metabolism and Pharmacokinetics, AstraZeneca, Cheshire, UK
    334 schema:name Department of Clinical Pharmacology, Drug Metabolism and Pharmacokinetics, AstraZeneca, Cheshire, UK
    335 rdf:type schema:Organization
    336 grid-institutes:grid.418236.a schema:alternateName Department of Investigative Preclinical Toxicology, GlaxoSmithKline, Hertfordshire, UK
    337 schema:name Department of Investigative Preclinical Toxicology, GlaxoSmithKline, Hertfordshire, UK
    338 rdf:type schema:Organization
    339 grid-institutes:grid.454377.6 schema:alternateName Centre for Advanced Discoveries and Experimental Therapeutics, Manchester Biomedical Research Centre and School of Biomedicine, Manchester, UK
    340 schema:name Centre for Advanced Discoveries and Experimental Therapeutics, Manchester Biomedical Research Centre and School of Biomedicine, Manchester, UK
    341 Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    342 School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    343 rdf:type schema:Organization
    344 grid-institutes:grid.5379.8 schema:alternateName School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    345 School of Computer Science, The University of Manchester, Manchester, UK
    346 schema:name Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    347 School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    348 School of Computer Science, The University of Manchester, Manchester, UK
    349 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...