Mass spectrometry for the identification of the discriminating signals from metabolomics: Current status and future trends

Werner, Erwan; Heilier, Jean-François; Ducruix, Céline; Ezan, Éric; Junot, Christophe; Tabet, Jean‐Claude

doi:10.1016/j.jchromb.2008.07.004

Cited by 188 publications

(151 citation statements)

References 190 publications

(211 reference statements)

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“…Thus LC-MS or GC-MS are more suitable for qualitative and quantitative measurement of individual metabolites [4][5][6] and have been widely used in metabolite profiling studies of human urine for biomarker discovery. [7][8][9][10][11][12] Pasikanti et al 13 reported a method for GC-MS profiling of human urine where 150 putative metabolites were detected and 144 of them were assigned a name by using retention indices and mass spectral matching scores with the NIST library.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Coupling Reversed Phase, Aqueous Normal Phase, and Hydrophilic Interaction Liquid Chromatography with Orbitrap Mass Spectrometry for Metabolomic Studies of Human Urine

et al. 2012

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In this study, we assessed three liquid chromatographic platforms: reversed phase (RP), aqueous normal phase (ANP) and hydrophilic interaction (HILIC) for the analysis of polar metabolite standard mixtures and for their coverage of urinary metabolites. The two zwitterionic HILIC columns showed high-quality chromatographic performance for metabolite standards, improved separation for isomers and the greatest coverage of polar metabolites in urine. In contrast, on the reversed phase column most metabolites eluted very rapidly with little or no separation. Using an Exactive Orbitrap mass spectrometer with a HILIC liquid chromatographic platform approximately 800 metabolites with repeatable peak areas (RSD ≤ 25%) could be putatively identified in human urine, by elemental composition assignment within a 3 ppm mass error.The ability of the methodology for the verification of non-molecular ions, which arise from adduct formation, and the possibility of distinguishing isomers could also be demonstrated. Careful examination of the raw data and the use of masses for predicted metabolites produced an extension of the metabolite list for human urine.

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Section: Introductionmentioning

confidence: 99%

Evaluation of Coupling Reversed Phase, Aqueous Normal Phase, and Hydrophilic Interaction Liquid Chromatography with Orbitrap Mass Spectrometry for Metabolomic Studies of Human Urine

et al. 2012

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“…The latter parameter is thought to be less important in MS n . 19,20 This dependence on several parameters has severely impeded the creation of MS/MS or MS n libraries. Furthermore, although pseudomolecular cations obey even-electron fragmentation rules, the dissociation of pseudomolecular anions can occur either via heterolytic or via homolytic cleavages and might involve ion-neutral complexes.…”

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confidence: 99%

Mass Spectrometry-Based Fragmentation as an Identification Tool in Lignomics

et al. 2010

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The ensemble of all phenolics for which the biosynthesis is coregulated with lignin biosynthesis, i.e., metabolites from the general phenylpropanoid, monolignol, and (neo)-lignan biosynthetic pathways and their derivatives, as well as the lignin oligomers, is coined the lignome. In lignifying tissues, the lignome comprises a significant portion of the metabolome. However, as is true for metabolomics in general, the structural elucidation of unknowns represents the biggest challenge in characterizing the lignome. To minimize the necessity to purify unknowns for NMR analysis, it would be desirable to be able to extract structural information from liquid chromatography-mass spectrometry data directly. However, mass spectral libraries for metabolomics are scarce, and no libraries exist for the lignome. Therefore, elucidating the gas-phase fragmentation behavior of the major bonding types encountered in lignome-associated molecules would considerably advance the systematic characterization of the lignome. By comparative MS n analysis of a series of molecules belonging to the -aryl ether, benzodioxane, phenylcoumaran, and resinol groups, we succeeded in annotating typical fragmentations for each of these bonding structures as well as fragmentations that enabled the identification of the aromatic units involved in each bonding structure. Consequently, this work lays the foundation for a detailed characterization of the lignome in different plant species, mutants, and transgenics and for the MS-based sequencing of lignin oligomers and (neo)lignans.Lignin is an aromatic heteropolymer that is mainly present in secondary-thickened plant cell walls where it provides the necessary strength and hydrophobicity for plants to grow in an upward direction and to enable the transport of water, nutrients, and photoassimilates. Lignin is mainly composed of p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units derived from the combinatorial coupling of p-coumaryl, coniferyl, and sinapyl alcohols ( Figure 1A), 1 the so-called monolignols that are produced by the general phenylpropanoid and monolignol biosynthetic pathways. [2][3][4][5] Following oxidation by peroxidase and/or laccase, the resulting electron-delocalized monolignol radical has unpaired electron density at its 1-, 3-, O-4-, 5-, and 8-positions ( Figure 1B). As radical coupling at the 8-position is favored, coupling with another monolignol radical results in, after rearomatization, a mixture of dehydrodimers with 8-8′, 8-5′, and 8-O-4′ linkages ( Figure 1C).In addition to these major monomers, several other monomers have been identified in particular species or in plants with modified lignin biosynthesis, 1,3 such as 5-hydroxyconiferyl alcohol in caffeic acid O-methyltransferase (COMT) downregulated transgenic plants, 6,7 dihydroconiferyl alcohol in cinnamyl alcohol dehydrogenase (CAD) deficient loblolly pine, 8 acylated monolignols, such as sinapyl p-hydroxybenzoate in poplar, 9 and hydroxycinnamic acid or hydroxycinnamate esters, such as feruloyl tyramine in tobacco....

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“…Ion features, defined here as a chromatographic peak with a given retention time and m/z value, are analyzed using a statistical package such as SAS or S-plus to determine which features vary statistically significantly and are related to a test hypothesis (Tolstikov and Fiehn 2002;Katajamaa and Oresic 2007;Werner, Heilier et al 2008) . The significant ion feature changes are then used to prioritize metabolite identification.…”

Section: Approachmentioning

confidence: 99%

Software Techniques for Enabling High-Throughput Analysis of Metabolomic Datasets

DeHaven¹,

Evans²,

Dai³

et al. 2012

Metabolomics

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Mass spectrometry for the identification of the discriminating signals from metabolomics: Current status and future trends

Cited by 188 publications

References 190 publications

Evaluation of Coupling Reversed Phase, Aqueous Normal Phase, and Hydrophilic Interaction Liquid Chromatography with Orbitrap Mass Spectrometry for Metabolomic Studies of Human Urine

Evaluation of Coupling Reversed Phase, Aqueous Normal Phase, and Hydrophilic Interaction Liquid Chromatography with Orbitrap Mass Spectrometry for Metabolomic Studies of Human Urine

Mass Spectrometry-Based Fragmentation as an Identification Tool in Lignomics

Software Techniques for Enabling High-Throughput Analysis of Metabolomic Datasets

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