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Nam SL, Giebelhaus RT, Tarazona Carrillo KS, de la Mata AP, Harynuk JJ. Evaluation of normalization strategies for GC-based metabolomics. Metabolomics 2024; 20:22. [PMID: 38347235 DOI: 10.1007/s11306-023-02086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/21/2023] [Indexed: 02/15/2024]
Abstract
INTRODUCTION For many samples studied by GC-based metabolomics applications, extensive sample preparation involving extraction followed by a two-step derivatization procedure of methoximation and trimethylsilylation (TMS) is typically required to expand the metabolome coverage. Performing normalization is critical to correct for variations present in samples and any biases added during the sample preparation steps and analytical runs. Addressing the totality of variations with an adequate normalization method increases the reliability of the downstream data analysis and interpretation of the results. OBJECTIVES Normalizing to sample mass is one of the most commonly employed strategies, while the total peak area (TPA) as a normalization factor is also frequently used as a post-acquisition technique. Here, we present a new normalization approach, total derivatized peak area (TDPA), where data are normalized to the intensity of all derivatized compounds. TDPA relies on the benefits of silylation as a universal derivatization method for GC-based metabolomics studies. METHODS Two sample classes consisting of systematically incremented sample mass were simulated, with the only difference between the groups being the added amino acid concentrations. The samples were TMS derivatized and analyzed using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC-TOFMS). The performance of five normalization strategies (no normalization, normalized to sample mass, TPA, total useful peak area (TUPA), and TDPA) were evaluated on the acquired data. RESULTS Of the five normalization techniques compared, TUPA and TDPA were the most effective. On PCA score space, they offered a clear separation between the two classes. CONCLUSION TUPA and TDPA carry different strengths: TUPA requires peak alignment across all samples, which depends upon the completion of the study, while TDPA is free from the requirement of alignment. The findings of the study would enhance the convenient and effective use of data normalization strategies and contribute to overcoming the data normalization challenges that currently exist in the metabolomics community.
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Affiliation(s)
- Seo Lin Nam
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Ryland T Giebelhaus
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Kieran S Tarazona Carrillo
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - A Paulina de la Mata
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - James J Harynuk
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
- The Metabolomics Innovation Centre, Edmonton, AB, Canada.
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Thesnor V, Molinié R, Giebelhaus RT, de la Mata Espinosa AP, Harynuk JJ, Bénimélis D, Vanhoye B, Dunyach-Rémy C, Sylvestre M, Cheremond Y, Meffre P, Cebrián-Torrejón G, Benfodda Z. Antibacterial Activity and Untargeted Metabolomics Profiling of Acalypha arvensis Poepp. Molecules 2023; 28:7882. [PMID: 38067611 PMCID: PMC10708339 DOI: 10.3390/molecules28237882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The search for potent antimicrobial compounds is critical in the face of growing antibiotic resistance. This study explores Acalypha arvensis Poepp. (A. arvensis), a Caribbean plant traditionally used for disease treatment. The dried plant powder was subjected to successive extractions using different solvents: hexane (F1), dichloromethane (F2), methanol (F3), a 50:50 mixture of methanol and water (F4), and water (F5). Additionally, a parallel extraction was conducted using a 50:50 mixture of methanol and chloroform (F6). All the fractions were evaluated for their antimicrobial activity, and the F6 fraction was characterized using untargeted metabolomics using SPME-GC×GC-TOFMS. The extracts of A. arvensis F3, F4, and F5 showed antibacterial activity against Staphylococcus aureus ATCC 25923 (5 mg/mL), MRSA BA22038 (5 mg/mL), and Pseudomonas aeruginosa ATCC 27853 (10 mg/mL), and fraction F6 showed antibacterial activity against Staphylococcus aureus ATCC 29213 (2 mg/mL), Escherichia coli ATCC 25922 (20 mg/mL), Pseudomonas aeruginosa ATCC 27853 (10 mg/mL), Enterococcus faecalis ATCC 29212 (10 mg/mL), Staphylococcus aureus 024 (2 mg/mL), and Staphylococcus aureus 003 (2 mg/mL). Metabolomic analysis of F6 revealed 2861 peaks with 58 identified compounds through SPME and 3654 peaks with 29 identified compounds through derivatization. The compounds included methyl ester fatty acids, ethyl ester fatty acids, terpenes, ketones, sugars, amino acids, and fatty acids. This study represents the first exploration of A. arvensis metabolomics and its antimicrobial potential, providing valuable insights for plant classification, phytochemical research, and drug discovery.
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Affiliation(s)
- Valendy Thesnor
- UPR Chrome, University Nimes, CEDEX 1, 30021 Nîmes, France; (V.T.); (D.B.); (P.M.)
- COVACHIM-M2E Laboratory EA 3592, Department of Chemistry, UFR SEN, Fouillole Campus, University of Antilles, CEDEX, 97110 Pointe-à-Pitre, France;
- URE, Université d’État d’Haïti, Port-au-Prince HT6110, Haiti;
| | - Roland Molinié
- UMR INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UPJV, UFR de Pharmacie, 80037 Amiens, France; (R.M.); (B.V.)
| | - Ryland T. Giebelhaus
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2N4, Canada; (R.T.G.); (A.P.d.l.M.E.); (J.J.H.)
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2N4, Canada
| | - A. Paulina de la Mata Espinosa
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2N4, Canada; (R.T.G.); (A.P.d.l.M.E.); (J.J.H.)
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2N4, Canada
| | - James J. Harynuk
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2N4, Canada; (R.T.G.); (A.P.d.l.M.E.); (J.J.H.)
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2N4, Canada
| | - David Bénimélis
- UPR Chrome, University Nimes, CEDEX 1, 30021 Nîmes, France; (V.T.); (D.B.); (P.M.)
| | - Bérénice Vanhoye
- UMR INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UPJV, UFR de Pharmacie, 80037 Amiens, France; (R.M.); (B.V.)
| | | | - Muriel Sylvestre
- COVACHIM-M2E Laboratory EA 3592, Department of Chemistry, UFR SEN, Fouillole Campus, University of Antilles, CEDEX, 97110 Pointe-à-Pitre, France;
| | - Yvens Cheremond
- URE, Université d’État d’Haïti, Port-au-Prince HT6110, Haiti;
| | - Patrick Meffre
- UPR Chrome, University Nimes, CEDEX 1, 30021 Nîmes, France; (V.T.); (D.B.); (P.M.)
| | - Gerardo Cebrián-Torrejón
- COVACHIM-M2E Laboratory EA 3592, Department of Chemistry, UFR SEN, Fouillole Campus, University of Antilles, CEDEX, 97110 Pointe-à-Pitre, France;
| | - Zohra Benfodda
- UPR Chrome, University Nimes, CEDEX 1, 30021 Nîmes, France; (V.T.); (D.B.); (P.M.)
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Nam SL, Tarazona Carrillo K, de la Mata AP, Harynuk JJ. Untargeted Metabolomic Profiling of Aqueous and Lyophilized Pooled Human Feces from Two Diet Cohorts Using Two-Dimensional Gas Chromatography Coupled with Time-of-Flight Mass Spectrometry. Metabolites 2023; 13:828. [PMID: 37512535 PMCID: PMC10383202 DOI: 10.3390/metabo13070828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
The metabolic profiles of human feces are influenced by various genetic and environmental factors, which makes feces an attractive biosample for numerous applications, including the early detection of gut diseases. However, feces is complex, heterogeneous, and dynamic with a significant live bacterial biomass. With such challenges, stool metabolomics has been understudied compared to other biospecimens, and there is a current lack of consensus on methods to collect, prepare, and analyze feces. One of the critical steps required to accelerate the field is having a metabolomics stool reference material available. Fecal samples are generally presented in two major forms: fecal water and lyophilized feces. In this study, two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS) was used as an analytical platform to characterize pooled human feces, provided by the National Institute of Standards and Technology (NIST) as Research-Grade Test Materials. The collected fecal samples were derived from eight healthy individuals with two different diets: vegans and omnivores, matched by age, sex, and body mass index (BMI), and stored as fecal water and lyophilized feces. Various data analysis strategies were presented to determine the differences in the fecal metabolomic profiles. The results indicate that the sample storage condition has a major influence on the metabolic profiles of feces such that the impact from storage surpasses the metabolic differences from the diet types. The findings of the current study would contribute towards the development of a stool reference material.
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Affiliation(s)
- Seo Lin Nam
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | | | - James J Harynuk
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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Nolvachai Y, Amaral MSS, Marriott PJ. Foods and Contaminants Analysis Using Multidimensional Gas Chromatography: An Update of Recent Studies, Technology, and Applications. Anal Chem 2023; 95:238-263. [PMID: 36625115 DOI: 10.1021/acs.analchem.2c04680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yada Nolvachai
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Michelle S S Amaral
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Philip J Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
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The Metabolomic Profile of the Essential Oil from Zanthoxylum caribaeum (syn. chiloperone) Growing in Guadeloupe FWI using GC × GC-TOFMS. Metabolites 2022; 12:metabo12121293. [PMID: 36557331 PMCID: PMC9782392 DOI: 10.3390/metabo12121293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The essential oil (EO) from the leaves of Zanthoxylum caribaeum (syn. Chiloperone) (Rutaceae) was studied previously for its acaricidal, antimicrobial, antioxidant, and insecticidal properties. In prior studies, the most abundant compound class found in leaf oils from Brazil, Costa Rica, and Paraguay was terpenoids. Herein, essential oil from the leaves of Zanthoxylum caribaeum (prickly yellow, bois chandelle blanc (FWI), peñas Blancas (Costa Rica), and tembetary hu (Paraguay)) growing in Guadeloupe was analyzed with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC-TOFMS), and thirty molecules were identified. A comparison with previously published leaf EO compositions of the same species growing in Brazil, Costa Rica, and Paraguay revealed a number of molecules in common such as β-myrcene, limonene, β-caryophyllene, α-humulene, and spathulenol. Some molecules identified in Zanthoxylum caribaeum from Guadeloupe showed some antimetabolic effects on enzymes; the in-depth study of this plant and its essential oil with regard to metabolic diseases merits further exploration.
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Dias RP, Nam SL, Schmidt SA, de la Mata AP, Harynuk J. Multivariate Optimization Procedure for Dynamic Headspace Extractions Coupled to GC(×GC). LCGC EUROPE 2022. [DOI: 10.56530/lcgc.eu.gi5670v6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Volatile organic compounds (VOCs) are ubiquitous chemicals of great interest in the study of aromas and flavours of foods. Many recent studies present optimized headspace (HS) and dynamic headspace (DHS) methods for specific sample types; however, the literature does not present (to the best of our knowledge) a generalized procedure for the thorough optimization of a DHS extraction. This article presents an approach using design of experiments (DoE) for the optimization of DHS extraction parameters. The approach is demonstrated for two different food sample types with diverse populations of VOCs: active sourdough colony as an example with a high moisture content, and sourdough bread as an example with a lower moisture content. Optimized methods are assessed for VOC extraction reproducibility and exhaustiveness; guidelines for DHS optimization are presented.
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Moreira de Oliveira A, Teixeira CA, Hantao LW. Advanced tuning of the ion management parameters in GC × GC-HRMS using a Fourier transform Orbitrap mass analyzer for pixel-based data handling and multivariate analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1646-1654. [PMID: 35383813 DOI: 10.1039/d2ay00314g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
GC × GC investigations are well known to generate a substantial amount of information-rich and structurally complex data, requiring advanced data processing strategies like chemometrics. Many workflows are available for data handling and processing, such as the peak-table and pixel-based approaches. The goal of this work is to present a solution based on method development to solve the missing pixel problem that may be encountered in experiments performed with GC and GC × GC coupled to the Fourier transform orbital ion trap (FT-Orbitrap) mass analyzer. Data input is vital for pixel-based chemometric analyses, as some post-processing solutions may lead to significant loss of chemical information in the data set. Hence, a key requisite is that the chemical information is consistently indexed in the data arrays for proper pixel-based data handling and analysis. In this study, we carefully evaluated the ion management parameters to preserve the intrinsic structure and information of the data arrays of the GC × GC-FT-Orbitrap for future pixel-oriented chemometric analysis. The most acceptable conditions yielded acquisition rates up to 42.6 spectra per s, while a routine setting of 24.7 Hz was successfully employed in analyses of different petroleum fractions, producing both consistent tensor sizes and acceptable peak reconstructions. A data acquisition rate of 24.7 spectra per s and a mass resolving power of 15 000 allowed the resolution of a mass split of only 0.004 Da - which is an interesting configuration for challenging applications in petroleomics. Using such advanced settings, the missing pixel problem was reduced from up to 30% to much less than 0.04% of the data array dimension. Thus, the proposed configuration can be employed in studies that require pixel-oriented multivariate data analysis.
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Affiliation(s)
| | - Carlos Alberto Teixeira
- Institute of Chemistry, University of Campinas, Rua Monteiro Lobato 270, 13083-862 Campinas, SP, Brazil.
| | - Leandro Wang Hantao
- Institute of Chemistry, University of Campinas, Rua Monteiro Lobato 270, 13083-862 Campinas, SP, Brazil.
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Schöneich S, Ochoa GS, Monzón CM, Synovec RE. Minimum variance optimized Fisher ratio analysis of comprehensive two-dimensional gas chromatography / mass spectrometry data: Study of the pacu fish metabolome. J Chromatogr A 2022; 1667:462868. [DOI: 10.1016/j.chroma.2022.462868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 11/25/2022]
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Gould O, Drabińska N, Ratcliffe N, de Lacy Costello B. Hyphenated Mass Spectrometry versus Real-Time Mass Spectrometry Techniques for the Detection of Volatile Compounds from the Human Body. Molecules 2021; 26:molecules26237185. [PMID: 34885767 PMCID: PMC8659178 DOI: 10.3390/molecules26237185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023] Open
Abstract
Mass spectrometry (MS) is an analytical technique that can be used for various applications in a number of scientific areas including environmental, security, forensic science, space exploration, agri-food, and numerous others. MS is also continuing to offer new insights into the proteomic and metabolomic fields. MS techniques are frequently used for the analysis of volatile compounds (VCs). The detection of VCs from human samples has the potential to aid in the diagnosis of diseases, in monitoring drug metabolites, and in providing insight into metabolic processes. The broad usage of MS has resulted in numerous variations of the technique being developed over the years, which can be divided into hyphenated and real-time MS techniques. Hyphenated chromatographic techniques coupled with MS offer unparalleled qualitative analysis and high accuracy and sensitivity, even when analysing complex matrices (breath, urine, stool, etc.). However, these benefits are traded for a significantly longer analysis time and a greater need for sample preparation and method development. On the other hand, real-time MS techniques offer highly sensitive quantitative data. Additionally, real-time techniques can provide results in a matter of minutes or even seconds, without altering the sample in any way. However, real-time MS can only offer tentative qualitative data and suffers from molecular weight overlap in complex matrices. This review compares hyphenated and real-time MS methods and provides examples of applications for each technique for the detection of VCs from humans.
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Affiliation(s)
- Oliver Gould
- Centre for Research in Biosciences, Frenchay Campus, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK; (N.R.); (B.d.L.C.)
- Correspondence: (O.G.); (N.D.)
| | - Natalia Drabińska
- Department of Chemistry and Biodynamics of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland
- Food Volatilomics and Sensomics Group, Faculty of Food Science and Nutrition, Poznan University of Life Sciences, 60-637 Poznan, Poland
- Correspondence: (O.G.); (N.D.)
| | - Norman Ratcliffe
- Centre for Research in Biosciences, Frenchay Campus, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK; (N.R.); (B.d.L.C.)
| | - Ben de Lacy Costello
- Centre for Research in Biosciences, Frenchay Campus, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK; (N.R.); (B.d.L.C.)
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