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

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; Human Serum Metabolome (HUSERMET) Consortium

doi:10.1038/nprot.2011.335

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

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, Human Serum Metabolome (HUSERMET) Consortium

Research output: Contribution to journal › Article › peer-review

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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.

Original language	English
Pages (from-to)	1060-83
Number of pages	24
Journal	Nature protocols
Volume	6
Issue number	7
DOIs	https://doi.org/10.1038/nprot.2011.335
Publication status	Published - Jul 2011

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Dunn, W. B., Broadhurst, D., Begley, P., Zelena, E., Francis-McIntyre, S., Anderson, N., Brown, M., Knowles, J. D., Halsall, A., Haselden, J. N., Nicholls, A. W., Wilson, I. D., Kell, D. B., Goodacre, R., & Human Serum Metabolome (HUSERMET) Consortium (2011). Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature protocols, 6(7), 1060-83. https://doi.org/10.1038/nprot.2011.335

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title = "Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry",

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.",

author = "Dunn, {Warwick B} and David Broadhurst and Paul Begley and Eva Zelena and Sue Francis-McIntyre and Nadine Anderson and Marie Brown and Knowles, {Joshau D} and Antony Halsall and Haselden, {John N} and Nicholls, {Andrew W} and Wilson, {Ian D} and Kell, {Douglas B} and Royston Goodacre and {Human Serum Metabolome (HUSERMET) Consortium}",

year = "2011",

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doi = "10.1038/nprot.2011.335",

language = "English",

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Dunn, WB, Broadhurst, D, Begley, P, Zelena, E, Francis-McIntyre, S, Anderson, N, Brown, M, Knowles, JD, Halsall, A, Haselden, JN, Nicholls, AW, Wilson, ID, Kell, DB, Goodacre, R & Human Serum Metabolome (HUSERMET) Consortium 2011, 'Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry', Nature protocols, vol. 6, no. 7, pp. 1060-83. https://doi.org/10.1038/nprot.2011.335

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T1 - Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

AU - Dunn, Warwick B

AU - Broadhurst, David

AU - Begley, Paul

AU - Zelena, Eva

AU - Francis-McIntyre, Sue

AU - Anderson, Nadine

AU - Brown, Marie

AU - Knowles, Joshau D

AU - Halsall, Antony

AU - Haselden, John N

AU - Nicholls, Andrew W

AU - Wilson, Ian D

AU - Kell, Douglas B

AU - Goodacre, Royston

AU - Human Serum Metabolome (HUSERMET) Consortium

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AB - 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.

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EP - 1083

JO - Nature protocols

JF - Nature protocols

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ER -

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

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