1
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Biological studies with comprehensive 2D-GC-HRMS screening: Exploring the human sweat volatilome. Talanta 2023; 257:124333. [PMID: 36801554 DOI: 10.1016/j.talanta.2023.124333] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
A key issue in GCxGC-HRMS data analysis is how to approach large-sample studies in an efficient and comprehensive way. We have developed a semi-automated data-driven workflow from identification to suspect screening, which allows highly selective monitoring of each identified chemical in a large-sample dataset. The example dataset used to illustrate the potential of the approach consisted of human sweat samples from 40 participants, including field blanks (80 samples). These samples have been collected in a Horizon 2020 project to investigate the capacity of body odour to communicate emotion and influence social behaviour. We used dynamic headspace extraction, which allows comprehensive extraction with high preconcentration capability, and has to date only been used for a few biological applications. We were able to detect a set of 326 compounds from a diverse range of chemical classes (278 identified compounds, 39 class unknowns, and 9 true unknowns). Unlike partitioning-based extraction methods, the developed method detects semi-polar (log P < 2) nitrogen and oxygen-containing compounds. However, it is unable to detect certain acids due to the pH conditions of unmodified sweat samples. We believe that our framework will open up the possibility of efficiently using GCxGC-HRMS for large-sample studies in a wide range of applications such as biological and environmental studies.
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2
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Squara S, Manig F, Henle T, Hellwig M, Caratti A, Bicchi C, Reichenbach SE, Tao Q, Collino M, Cordero C. Extending the breadth of saliva metabolome fingerprinting by smart template strategies and effective pattern realignment on comprehensive two-dimensional gas chromatographic data. Anal Bioanal Chem 2023; 415:2493-2509. [PMID: 36631574 PMCID: PMC10149478 DOI: 10.1007/s00216-023-04516-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023]
Abstract
Comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-TOFMS) is one the most powerful analytical platforms for chemical investigations of complex biological samples. It produces large datasets that are rich in information, but highly complex, and its consistency may be affected by random systemic fluctuations and/or changes in the experimental parameters. This study details the optimization of a data processing strategy that compensates for severe 2D pattern misalignments and detector response fluctuations for saliva samples analyzed across 2 years. The strategy was trained on two batches: one with samples from healthy subjects who had undergone dietary intervention with high/low-Maillard reaction products (dataset A), and the second from healthy/unhealthy obese individuals (dataset B). The combined untargeted and targeted pattern recognition algorithm (i.e., UT fingerprinting) was tuned for key process parameters, the signal-to-noise ratio (S/N), and MS spectrum similarity thresholds, and then tested for the best transform function (global or local, affine or low-degree polynomial) for pattern realignment in the temporal domain. Reliable peak detection achieved its best performance, computed as % of false negative/positive matches, with a S/N threshold of 50 and spectral similarity direct match factor (DMF) of 700. Cross-alignment of bi-dimensional (2D) peaks in the temporal domain was fully effective with a supervised operation including multiple centroids (reference peaks) and a match-and-transform strategy using affine functions. Regarding the performance-derived response fluctuations, the most promising strategy for cross-comparative analysis and data fusion included the mass spectral total useful signal (MSTUS) approach followed by Z-score normalization on the resulting matrix.
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Affiliation(s)
- Simone Squara
- Dipartimento Di Scienza E Tecnologia del Farmaco, Università Degli Studi Di Torino, Via Pietro Giuria 9, 10125, Turin, Italy
| | - Friederike Manig
- Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Thomas Henle
- Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Michael Hellwig
- Special Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Andrea Caratti
- Dipartimento Di Scienza E Tecnologia del Farmaco, Università Degli Studi Di Torino, Via Pietro Giuria 9, 10125, Turin, Italy
| | - Carlo Bicchi
- Dipartimento Di Scienza E Tecnologia del Farmaco, Università Degli Studi Di Torino, Via Pietro Giuria 9, 10125, Turin, Italy
| | - Stephen E Reichenbach
- Computer Science and Engineering Department, University of Nebraska, Lincoln, NE, USA.,GC Image LLC, Lincoln, NE, USA
| | | | - Massimo Collino
- Dipartimento Di Neuroscienze "Rita Levi Montalcini", University of Turin, Turin, Italy.
| | - Chiara Cordero
- Dipartimento Di Scienza E Tecnologia del Farmaco, Università Degli Studi Di Torino, Via Pietro Giuria 9, 10125, Turin, Italy.
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3
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Fisher ratio feature selection by manual peak area calculations on comprehensive two-dimensional gas chromatography data using standard mixtures with variable composition, storage, and interferences. Anal Bioanal Chem 2022; 415:2575-2585. [PMID: 36520202 DOI: 10.1007/s00216-022-04484-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/19/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Comprehensive two-dimensional gas chromatography (GC×GC) is becoming increasingly more common for non-targeted characterization of complex volatile mixtures. The information gained with higher peak capacity and sensitivity provides additional sample composition information when one-dimensional GC is not adequate. GC×GC generates complex multivariate data sets when using non-targeted analysis to discover analytes. Fisher ratio (FR) analysis is applied to discern class markers, limiting complex GC×GC profiles to the most discriminating compounds between classes. While many approaches for feature selection using FR analysis exist, FR can be calculated relatively easily directly on peak areas after any native software has performed peak detection. This study evaluated the success rates of manual FR calculation and comparison to a critical F-value for samples analyzed by GC×GC with defined concentration differences. Long-term storage of samples and other spiked interferences were also investigated to examine their impact on analyzing mixtures using this FR feature selection strategy. Success rates were generally high with mostly 90-100% success rates and some instances of percentages between 80 and 90%. There were rare cases of false positives present and a low occurrence of false negatives. When errors were made in the selection of a compound, it was typically due to chromatographic artifacts present in chromatograms and not from the FR approach itself. This work provides foundational experimental data on the use of manual FR calculations for feature selection from GC×GC data.
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4
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Stilo F, Liberto E, Reichenbach SE, Tao Q, Bicchi C, Cordero C. Exploring the Extra-Virgin Olive Oil Volatilome by Adding Extra Dimensions to Comprehensive Two-Dimensional Gas Chromatography and Time-of-Flight Mass Spectrometry Featuring Tandem Ionization: Validation of Ripening Markers in Headspace Linearity Conditions. J AOAC Int 2021; 104:274-287. [PMID: 34020455 DOI: 10.1093/jaoacint/qsaa095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND Comprehensive two-dimensional gas chromatography (GC×GC) combined with time-of-flight (TOF) MS is the most informative analytical approach for chemical characterization of the complex food volatilome. Key analytical features include separation power and resolution enhancement, improved sensitivity, and structured separation patterns from chemically correlated analytes. OBJECTIVE In this study, we explore the complex extra-virgin olive oil volatilome by combining headspace (HS) solid-phase microextraction (SPME), applied under HS linearity conditions to GC×GC-TOF MS and featuring hard and soft ionization in tandem. METHOD Multiple analytical dimensions are combined in a single run and evaluated in terms of chemical dimensionality, method absolute and relative sensitivity, identification reliability provided by spectral signatures acquired at 70 and 12 eV, and dynamic and linear range of response provided by soft ionization. RESULTS Method effectiveness is validated on a sample set of oils from Picual olives at different ripening stages. Ripening markers [3,4-diethyl-1,5-hexadiene (RS/SR), 3,4-diethyl-1,5-hexadiene (meso), (5Z)-3-ethyl-1,5-octadiene, (5E)-3-ethyl-1,5-octadiene, (E, Z)-3,7-decadiene and (E, E)-3,7-decadiene, (Z)-2-hexenal, (Z)-3-hexenal and (Z)-3-hexenal, (E)-2-pentenal, (Z)-2-pentenal, 1-pentanol, 1-penten-3-ol, 3-pentanone, and 1-penten-3-one] and quality indexes [(Z)-3-hexenal/nonanal, (Z)-3-hexenal/octane, (E)-2-pentenal/nonanal, and (E)-2-pentenal/octane] are confirmed for their validity in HS linearity conditions. CONCLUSIONS For the complex olive oil volatilome, the proposed approach offers concrete advantages for the validation of the informative role of existing analytes while suggesting new potential markers to be studied in larger sample sets. HIGHLIGHTS The accurate fingerprinting of volatiles by HS-SPME operating in HS linearity conditions followed by GC×GC-TOF MS featuring tandem ionization gives the opportunity to improve the quality of analytical data and reliability of results.
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Affiliation(s)
- Federico Stilo
- Università degli Studi di Torino, Dipartimento di Scienza e Tecnologia del Farmaco, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Erica Liberto
- Università degli Studi di Torino, Dipartimento di Scienza e Tecnologia del Farmaco, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Stephen E Reichenbach
- GC Image LLC, 201 N 8th Street Unit 420, Lincoln, NE 68508, USA.,University of Nebraska-Lincoln, Computer Science and Engineering Department, 256 Avery Hall, Lincoln, NE 68588, USA
| | - Qingping Tao
- GC Image LLC, 201 N 8th Street Unit 420, Lincoln, NE 68508, USA
| | - Carlo Bicchi
- Università degli Studi di Torino, Dipartimento di Scienza e Tecnologia del Farmaco, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Chiara Cordero
- Università degli Studi di Torino, Dipartimento di Scienza e Tecnologia del Farmaco, Via Pietro Giuria 9, 10125, Torino, Italy
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5
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Stefanuto PH, Smolinska A, Focant JF. Advanced chemometric and data handling tools for GC×GC-TOF-MS. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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6
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Zanella D, Guiot J, Stefanuto PH, Giltay L, Henket M, Guissard F, André B, Malaise M, Potjewijd J, Schleich F, Louis R, Focant JF. Breathomics to diagnose systemic sclerosis using thermal desorption and comprehensive two-dimensional gas chromatography high-resolution time-of-flight mass spectrometry. Anal Bioanal Chem 2021; 413:3813-3822. [PMID: 33903944 DOI: 10.1007/s00216-021-03333-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/11/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022]
Abstract
Systemic sclerosis is a rare autoimmune disease associated with rapidly evolving interstitial lung disease, responsible for the disease severity and mortality. Specific biomarkers enabling the early diagnosis and prognosis associated with the disease progression are highly needed. Volatile organic compounds in exhaled breath are widely available and non-invasive and have the potential to reflect metabolic processes occurring within the body. Comprehensive two-dimensional gas chromatography coupled to high-resolution mass spectrometry was used to investigate the potential of exhaled breath to diagnose systemic sclerosis. The exhaled breath of 32 patients and 30 healthy subjects was analyzed. The high resolving power of this approach enabled the detection of 356 compounds in the breath of systemic sclerosis patients, which was characterized by an increase of mainly terpenoids and hydrocarbons. In addition, the use of 4 complementary statistical approaches (two-tailed equal variance t-test, fold change, partial least squares discriminant analysis, and random forest) resulted in the identification of 16 compounds that can be used to discriminate systemic sclerosis patients from healthy subjects. Receiver operating curves were generated that provided an accuracy of 90%, a sensitivity of 92%, and a specificity of 89%. The chemical identification of eight compounds predictive of systemic sclerosis was validated using commercially available standards. The analytical variations together with the volatile composition of room air were carefully monitored during the timeframe of the study to ensure the robustness of the technique. This study represents the first reported evaluation of exhaled breath analysis for systemic sclerosis diagnosis and provides surrogate markers for such disease.
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Affiliation(s)
- Delphine Zanella
- Molecular System, Organic & Biological Analytical Chemistry Group, University of Liege, 11 Allee du Six Aout, 4000, Liege, Belgium.
| | - Julien Guiot
- Respiratory Medicine, GIGA I3, CHU Liege, 4000, Liege, Belgium
| | - Pierre-Hugues Stefanuto
- Molecular System, Organic & Biological Analytical Chemistry Group, University of Liege, 11 Allee du Six Aout, 4000, Liege, Belgium
| | - Laurie Giltay
- Respiratory Medicine, GIGA I3, CHU Liege, 4000, Liege, Belgium
| | - Monique Henket
- Respiratory Medicine, GIGA I3, CHU Liege, 4000, Liege, Belgium
| | | | - Béatrice André
- Rheumatology Department, CHU Liege, 4000, Liege, Belgium
| | - Michel Malaise
- Rheumatology Department, CHU Liege, 4000, Liege, Belgium
| | - Judith Potjewijd
- Department of Internal Medicine, Division of Clinical and Experimental Immunology, Maastricht University Medical Center, 6229 HX, Maastricht, The Netherlands
| | | | - Renaud Louis
- Respiratory Medicine, GIGA I3, CHU Liege, 4000, Liege, Belgium
| | - Jean-François Focant
- Molecular System, Organic & Biological Analytical Chemistry Group, University of Liege, 11 Allee du Six Aout, 4000, Liege, Belgium
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7
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Gabetti E, Sgorbini B, Stilo F, Bicchi C, Rubiolo P, Chialva F, Reichenbach SE, Bongiovanni V, Cordero C, Cavallero A. Chemical fingerprinting strategies based on comprehensive two-dimensional gas chromatography combined with gas chromatography-olfactometry to capture the unique signature of Piemonte peppermint essential oil (Mentha x piperita var Italo-Mitcham). J Chromatogr A 2021; 1645:462101. [PMID: 33848659 DOI: 10.1016/j.chroma.2021.462101] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Accurate, reliable, and informative mapping of untargeted and targeted components across many samples is here performed by combining off-line GC-Olfactometry (GC-O) and comprehensive two-dimensional gas chromatography (GC×GC) coupled to time-of-flight mass spectrometry with variable ionization energy (TOF MS featuring Tandem Ionization™). In particular, untargeted and targeted (UT) features patterns are processed by chromatographic fingerprinting, giving differential priority to potent odorants' retention-times regions. Distinguishing peppermint essential oil (EO) from Piedmont (Italy - Mentha × piperita L. var. Italo-Mitcham - Menta di Pancalieri EO), with its unique sensory fingerprint (i.e., freshness and long-lasting sweetness), from high-quality peppermint EOs produced in other areas poses a great challenge. Chromatographic UT fingerprinting provided a great chemical dimensionality by mapping more than 350 peak-regions at 70 eV and 135 at 12 eV. From them, 95 components were identified and responses compared to available literature. Then, potent odorants, detected by GC-O using the aroma extraction dilution analysis (AEDA), were tracked over the chromatographic space and tentatively identified. With the highest flavor dilution (FD), 1,8-cineole (eucalyptus, fresh, camphoraceous); menthone (minty, herbaceous); and menthofuran (minty, musty, petroleum-like) were highlighted. Responsible for creamy and coumarinic notes were the diasteroisomers of (3,6)-dimethyl-4,5,6,7-tetrahydrobenzo[b]-furan-2(3H)-one (i.e., menthofurolactones), detected in higher relative abundance in Pancalieri EOs. By prioritizing the investigation of volatiles on higher LogFD retention regions, including 131 untargeted/targeted features, Pancalieri EOs were separately clustered from United States samples. Besides pre-targeted analytes, additional untargeted features were post-processed for identification within marker chemicals. Myrtenyl methyl ether, ethyl 3-methyl butanoate, propyl-2-methylbutanoate, and (E)-2-hexenal were putatively identified. Of the "unknown - knowns" with diagnostic roles, all metadata were collected including low energy spectra at 12 eV, which were found to be highly complementary to 70 eV spectra.
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Affiliation(s)
| | - Barbara Sgorbini
- University of Turin, Dipartimento di Scienza e Tecnologia del Farmaco Turin, Italy
| | - Federico Stilo
- University of Turin, Dipartimento di Scienza e Tecnologia del Farmaco Turin, Italy
| | - Carlo Bicchi
- University of Turin, Dipartimento di Scienza e Tecnologia del Farmaco Turin, Italy
| | - Patrizia Rubiolo
- University of Turin, Dipartimento di Scienza e Tecnologia del Farmaco Turin, Italy
| | | | - Stephen E Reichenbach
- Computer Science and Engineering Department, University of Nebraska - Lincoln, Lincoln, Nebraska, USA; GC Image, LLC, Lincoln, Nebraska, USA
| | | | - Chiara Cordero
- University of Turin, Dipartimento di Scienza e Tecnologia del Farmaco Turin, Italy.
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8
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Sudol PE, Ochoa GS, Synovec RE. Investigation of the limit of discovery using tile-based Fisher ratio analysis with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. J Chromatogr A 2021; 1644:462092. [PMID: 33823385 DOI: 10.1016/j.chroma.2021.462092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/26/2022]
Abstract
Comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS) is followed by tile-based Fisher ratio (F-ratio) analysis to investigate the "limit of discovery" for low concentration levels of sulfur-containing compounds in JP8 jet fuel. A mixture of 14 sulfur-containing compounds was spiked at 30 ppm, 15 ppm, 3 ppm and 1.5 ppm into the neat fuel prior to GC×GC-TOFMS analysis with a "reversed" column format (aka polar first dimension (1D) and non-polar second dimension (2D) column). Prior standard implementation of tile-based F-ratio analysis utilized an average F-ratio requiring a minimum of 3 mass channels (m/z) with the highest F-ratios. Herein, we explore the notion that use of the top F-ratio m/z for hitlist ranking is superior to the standard implementation for analytes near their limit-of-quantitation (LOQ), defined as an analyte concentration that produces a signal equal to ten times the standard deviation of the baseline noise (10σn). Hitlist ranking comparisons revealed that using only the top F-ratio m/z resulted in impressive improvements in discoverability for the low concentration comparisons. Specifically, for the 3 ppm versus neat hitlist, 1,4-oxathiane (LOQ = 2.5 ppm) improved from hit 114 via standard F-ratio analysis, to hit 25. For the 1.5 ppm versus neat hitlist, 2-propylthiophene (LOQ = 0.64 ppm) improved from hit 59 to 17, benzo[b]thiophene (LOQ = 1.1 ppm) from hit 98 to 28, and 2,5-dimethylthiophene (LOQ = 1.3 ppm) from hit 262 to 39. Additional hitlist ranking comparisons revealed the importance of proper tile size selection, as analyte discoverability deteriorated upon using either an inappropriately too small or too large of a tile.
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Affiliation(s)
- Paige E Sudol
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195, USA
| | - Grant S Ochoa
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195, USA
| | - Robert E Synovec
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195, USA.
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9
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Stilo F, Bicchi C, Robbat A, Reichenbach SE, Cordero C. Untargeted approaches in food-omics: The potential of comprehensive two-dimensional gas chromatography/mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116162] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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10
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Stilo F, Bicchi C, Jimenez-Carvelo AM, Cuadros-Rodriguez L, Reichenbach SE, Cordero C. Chromatographic fingerprinting by comprehensive two-dimensional chromatography: Fundamentals and tools. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116133] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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A unique data analysis framework and open source benchmark data set for the analysis of comprehensive two-dimensional gas chromatography software. J Chromatogr A 2020; 1635:461721. [PMID: 33246680 DOI: 10.1016/j.chroma.2020.461721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022]
Abstract
Comprehensive two-dimensional gas chromatography (GC × GC) is amongst the most powerful separation technologies currently existing. Since its advent in early 1990, it has become an established method which is readily available. However, one of its most challenging aspects, especially in hyphenation with mass spectrometry is the high amount of chemical information it provides for each measurement. The GC × GC community agrees that there, the highest demand for action is found. In response, the number of software packages allowing for in-depth data processing of GC × GC data has risen over the last couple of years. These packages provide sophisticated tools and algorithms allowing for more streamlined data evaluation. However, these tools/algorithms and their respective specific functionalities differ drastically within the available software packages and might result in various levels of findings if not appropriately implemented by the end users. This study focuses on two main objectives. First, to propose a data analysis framework and second to propose an open-source dataset for benchmarking software options and their specificities. Thus, allowing for an unanimous and comprehensive evaluation of GC × GC software. Thereby, the benchmark data includes a set of standard compound measurements and a set of chocolate aroma profiles. On this foundation, eight readily available GC × GC software packages were anonymously investigated for fundamental and advanced functionalities such as retention and detection device derived parameters, revealing differences in the determination of e.g. retention times and mass spectra.
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12
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Cialiè Rosso M, Stilo F, Squara S, Liberto E, Mai S, Mele C, Marzullo P, Aimaretti G, Reichenbach SE, Collino M, Bicchi C, Cordero C. Exploring extra dimensions to capture saliva metabolite fingerprints from metabolically healthy and unhealthy obese patients by comprehensive two-dimensional gas chromatography featuring Tandem Ionization mass spectrometry. Anal Bioanal Chem 2020; 413:403-418. [PMID: 33140127 PMCID: PMC7806578 DOI: 10.1007/s00216-020-03008-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
This study examines the information potential of comprehensive two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC×GC-TOF MS) and variable ionization energy (i.e., Tandem Ionization™) to study changes in saliva metabolic signatures from a small group of obese individuals. The study presents a proof of concept for an effective exploitation of the complementary nature of tandem ionization data. Samples are taken from two sub-populations of severely obese (BMI > 40 kg/m2) patients, named metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO). Untargeted fingerprinting, based on pattern recognition by template matching, is applied on single data streams and on fused data, obtained by combining raw signals from the two ionization energies (12 and 70 eV). Results indicate that at lower energy (i.e., 12 eV), the total signal intensity is one order of magnitude lower compared to the reference signal at 70 eV, but the ranges of variations for 2D peak responses is larger, extending the dynamic range. Fused data combine benefits from 70 eV and 12 eV resulting in more comprehensive coverage by sample fingerprints. Multivariate statistics, principal component analysis (PCA), and partial least squares discriminant analysis (PLS-DA) show quite good patient clustering, with total explained variance by the first two principal components (PCs) that increases from 54% at 70 eV to 59% at 12 eV and up to 71% for fused data. With PLS-DA, discriminant components are highlighted and putatively identified by comparing retention data and 70 eV spectral signatures. Within the most informative analytes, lactose is present in higher relative amount in saliva from MHO patients, whereas N-acetyl-D-glucosamine, urea, glucuronic acid γ-lactone, 2-deoxyribose, N-acetylneuraminic acid methyl ester, and 5-aminovaleric acid are more abundant in MUO patients. Visual feature fingerprinting is combined with pattern recognition algorithms to highlight metabolite variations between composite per-class images obtained by combining raw data from individuals belonging to different classes, i.e., MUO vs. MHO. Graphical abstract![]()
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Affiliation(s)
- Marta Cialiè Rosso
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Federico Stilo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Simone Squara
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Erica Liberto
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Stefania Mai
- Division of General Medicine, IRCCS Istituto Auxologico Italiano Ospedale S. Giuseppe, 28824, Piancavallo, Italy
| | - Chiara Mele
- Division of General Medicine, IRCCS Istituto Auxologico Italiano Ospedale S. Giuseppe, 28824, Piancavallo, Italy.,Department of Translational Medicine, University of Piemonte Orientale, 28100, Novara, Italy
| | - Paolo Marzullo
- Division of General Medicine, IRCCS Istituto Auxologico Italiano Ospedale S. Giuseppe, 28824, Piancavallo, Italy. .,Department of Translational Medicine, University of Piemonte Orientale, 28100, Novara, Italy.
| | - Gianluca Aimaretti
- Department of Translational Medicine, University of Piemonte Orientale, 28100, Novara, Italy
| | - Stephen E Reichenbach
- Computer Science and Engineering Department, University of Nebraska, Lincoln, NE, 68588, USA.,GC Image, LLC, Lincoln, NE, 68508, USA
| | - Massimo Collino
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, 10125, Torino, Italy
| | - Chiara Cordero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, 10125, Torino, Italy.
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13
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Stilo F, Liberto E, Spigolon N, Genova G, Rosso G, Fontana M, Reichenbach SE, Bicchi C, Cordero C. An effective chromatographic fingerprinting workflow based on comprehensive two-dimensional gas chromatography - Mass spectrometry to establish volatiles patterns discriminative of spoiled hazelnuts (Corylus avellana L.). Food Chem 2020; 340:128135. [PMID: 33011466 DOI: 10.1016/j.foodchem.2020.128135] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/28/2022]
Abstract
The volatile fraction of hazelnuts encrypts information about: cultivar/geographical origin, post-harvest treatments, oxidative stability and sensory quality. However, sensory features could be buried under other dominant chemical signatures posing challenges to an effective classification based on pleasant/unpleasant notes. Here a novel workflow that combines Untargeted and Targeted (UT) fingerprinting on comprehensive two-dimensional gas-chromatographic patterns is developed to discriminate spoiled hazelnuts from those of acceptable quality. By flash-profiling, six hazelnut classes are defined: Mould, Mould-rancid-solvent, Rancid, Rancid-stale, Rancid-solvent, and Uncoded KO. Chromatographic fingerprinting on composite 2D chromatograms from samples belonging to the same class (i.e., composite class-images) enabled effective selection of chemical markers: (a) octanoic acid that guides the sensory classification being positively correlated to mould; (b) ƴ-nonalactone, ƴ-hexalactone, acetone, and 1-nonanol that are decisive to classify OK and rancid samples; (c) heptanoic and hexanoic acids and ƴ-octalactone present in high relative abundance in rancid-solvent and rancid-stale samples.
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Affiliation(s)
- Federico Stilo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, I-10125 Torino, Italy.
| | - Erica Liberto
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, I-10125 Torino, Italy.
| | - Nicola Spigolon
- Soremartec Italia Srl, Piazzale Ferrero 1, Alba (Cuneo), Italy
| | - Giuseppe Genova
- Soremartec Italia Srl, Piazzale Ferrero 1, Alba (Cuneo), Italy
| | - Ginevra Rosso
- Soremartec Italia Srl, Piazzale Ferrero 1, Alba (Cuneo), Italy
| | - Mauro Fontana
- Soremartec Italia Srl, Piazzale Ferrero 1, Alba (Cuneo), Italy
| | - Stephen E Reichenbach
- University of Nebraska-Lincoln, MS 0115, Lincoln, NE, 68588-0115, USA; GC Image LLC, PO Box 57403, Lincoln, NE 68505-7403, USA.
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, I-10125 Torino, Italy.
| | - Chiara Cordero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via Pietro Giuria 9, I-10125 Torino, Italy.
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14
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Byrne JM, Dubois LM, Baker JD, Focant JF, Perrault KA. A non-targeted data processing workflow for volatile organic compound data acquired using comprehensive two-dimensional gas chromatography with dual channel detection. MethodsX 2020; 7:101009. [PMID: 32775230 PMCID: PMC7397399 DOI: 10.1016/j.mex.2020.101009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023] Open
Abstract
There has been an influx of technology for comprehensive two-dimensional gas chromatography analyses in recent years, calling for development of guided workflows and rigorous reporting of processes. This research focuses on the processing method for data collected on a dual channel detection system using flame ionization detection (FID) and quadrupole mass spectrometry (qMS) for the analysis of volatile organic compounds (VOCs). The samples analyzed were kava (Piper methysticum), which has a rich VOC profile that benefits substantially from a multidimensional approach due to enhanced peak capacity. The procedure which was customized here was the data processing workflow from a manual single-sample analysis to an integrated batch workflow that can be applied across studies.•Parameter choice for baseline correction and peak detection were defined when handling batch data.•Elution regions were defined using qMS data to automate compound identification.•Stencils were transformed onto FID data and sequenced for quantitative information.This dataset can be used as a training tool, as all details, methods and results for the workflow have been provided for users to compare with. The focus on data workflow reproducibility in the field of multidimensional chromatography will assist in adoption by users in new application areas.
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Affiliation(s)
- Julianne M Byrne
- Laboratory of Forensic and Bioanalytical Chemistry, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Lena M Dubois
- Organic and Biological Analytical Chemistry Laboratory, MolSys, University of Liège, Liège, Belgium
| | - Jonathan D Baker
- School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Jean-François Focant
- Organic and Biological Analytical Chemistry Laboratory, MolSys, University of Liège, Liège, Belgium
| | - Katelynn A Perrault
- Laboratory of Forensic and Bioanalytical Chemistry, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, HI, USA
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15
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Zanella D, Henket M, Schleich F, Dejong T, Louis R, Focant JF, Stefanuto PH. Comparison of the effect of chemically and biologically induced inflammation on the volatile metabolite production of lung epithelial cells by GC×GC-TOFMS. Analyst 2020; 145:5148-5157. [PMID: 32633741 DOI: 10.1039/d0an00720j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Exhaled breath analysis has a high potential for early non-invasive diagnosis of lung inflammatory diseases, such as asthma. The characterization and understanding of the inflammatory metabolic pathways involved into volatile organic compounds (VOCs) production could bring exhaled breath analysis into clinical practice and thus open new therapeutic routes for inflammatory diseases. In this study, lung inflammation was simulated in vitro using A549 epithelial cells. We compared the VOC production from A549 epithelial cells after a chemically induced oxidative stress in vitro, exposing the cells to H2O2, and a biological stress, exposing the cells to an inflammatory pool of sputum supernatants. Special attention was devoted to define proper negative and positive controls (8 different types) for our in vitro models, including healthy sputum co-culture. Sputum from 25 asthmatic and 8 healthy patients were collected to create each pool of supernatants. Each sample type was analyzed in 4 replicates using solid-phase microextraction (SPME) comprehensive two-dimensional gas chromatography hyphenated to time-of-flight mass spectrometry (GC×GC-TOFMS). This approach offers high resolving power for complex VOC mixtures. According to the type of inflammation induced, significantly different VOCs were produced by the epithelial cells compared to all controls. For both chemical and biological challenges, an increase of carbonyl compounds (54%) and hydrocarbons (31%) was observed. Interestingly, only the biological inflammation model showed a significant cell proliferation together with an increased VOC production linked to asthma airway inflammation. This study presents a complete GC×GC-TOFMS workflow for in vitro VOC analysis, and its potential to characterize complex lung inflammatory mechanisms.
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Affiliation(s)
- Delphine Zanella
- University of Liege, Molecular System, Organic & Biological Analytical Chemistry Group, 11 Allee du Six Aout, 4000 Liege, Belgium.
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16
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Climate and Processing Effects on Tea ( Camellia sinensis L. Kuntze) Metabolome: Accurate Profiling and Fingerprinting by Comprehensive Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry. Molecules 2020; 25:molecules25102447. [PMID: 32456315 PMCID: PMC7288030 DOI: 10.3390/molecules25102447] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 11/18/2022] Open
Abstract
This study applied an untargeted–targeted (UT) fingerprinting approach, based on comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOF MS), to assess the effects of rainfall and temperature (both seasonal and elevational) on the tea metabolome. By this strategy, the same compound found in multiple samples need only to be identified once, since chromatograms and mass spectral features are aligned in the data analysis process. Primary and specialized metabolites of leaves from two Chinese provinces, Yunnan (pu′erh) and Fujian (oolong), and a farm in South Carolina (USA, black tea) were studied. UT fingerprinting provided insight into plant metabolism activation/inhibition, taste and trigeminal sensations, and antioxidant properties, not easily attained by other analytical approaches. For example, pu′erh and oolong contained higher relative amounts of amino acids, organic acids, and sugars. Conversely, black tea contained less of all targeted compounds except fructose and glucose, which were more similar to oolong tea. Findings revealed compounds statistically different between spring (pre-monsoon) and summer (monsoon) in pu′erh and oolong teas as well as compounds that exhibited the greatest variability due to seasonal and elevational differences. The UT fingerprinting approach offered unique insights into how differences in growing conditions and commercial processing affect the nutritional benefits and sensory characteristics of tea beverages.
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Sedentariness and Urinary Metabolite Profile in Type 2 Diabetic Patients, a Cross-Sectional Study. Metabolites 2020; 10:metabo10050205. [PMID: 32443532 PMCID: PMC7281751 DOI: 10.3390/metabo10050205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 11/17/2022] Open
Abstract
Recent findings indicate a significant association between sedentary (SED)-time and type 2 diabetes mellitus (T2DM). The aim of this study was to investigate whether different levels of SED-time could impact on biochemical and physiological processes occurring in sedentary and physically inactive T2DM patients. In particular, patients from the “Italian Diabetes and Exercise Study (IDES)_2 trial belonging to the first and fourth quartile of SED-time were compared. Urine samples were analyzed by comprehensive two-dimensional gas chromatography (GC × GC) with parallel detection by mass spectrometry and flame ionization detection (GC × 2GC-MS/FID). This platform enables accurate profiling and fingerprinting of urinary metabolites while maximizing the overall information capacity, quantitation reliability, and response linearity. Moreover, using advanced pattern recognition, the fingerprinting process was extended to untargeted and targeted features, revealing diagnostic urinary fingerprints between groups. Quantitative metabolomics was then applied to analytes of relevance for robust comparisons. Increased levels of glycine, L-valine, L-threonine, L-phenylalanine, L-leucine, L-alanine, succinic acid, 2-ketoglutaric acid, xylitol, and ribitol were revealed in samples from less sedentary women. In conclusion, SED-time is associated with changes in urine metabolome signatures. These preliminary results suggest that reducing SED-time could be a strategy to improve the health status of a large proportion of diabetic patients.
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Hung NV, Mohabeer C, Vaccaro M, Marcotte S, Agasse-Peulon V, Abdelouahed L, Taouk B, Cardinael P. Development of two-dimensional gas chromatography (GC×GC) coupled with Orbitrap-technology-based mass spectrometry: Interest in the identification of biofuel composition. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4495. [PMID: 31903666 DOI: 10.1002/jms.4495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/17/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
Comprehensive gas chromatography (GC) has emerged in recent years as the technique of choice for the analysis of volatile and semivolatile compounds in complex matrices. Coupling it with high-resolution mass spectrometry (MS) makes a powerful tool for identification and quantification of organic compounds. The results obtained in this study showed a significant improvement by using GC×GC-EI-MS in comparison with GC-EI-MS; the separation of chromatogram peaks was highly improved, which facilitated detection and identification. However, the limitation of Orbitrap mass analyzer compared with time-of-flight analyzer is the data acquisition rate; the frequency average was about 25 Hz at a mass resolving power of 15.000, which is barely sufficient for the proper reconstruction of the narrowest chromatographic peaks. On the other hand, the different spectra obtained in this study showed an average mass accuracy of about 1 ppm. Within this average mass accuracy, some reasonable elemental compositions can be proposed and combined with characteristic fragment ions, and the molecules can be identified with precision. At a mass resolving power of 7.500, the scan rate reaches 43 Hz and the GC×GC-MS peaks can be represented by more than 10 data points, which should be sufficient for quantification. The GC×GC-MS was also applied to analyze a cellulose bio-oil sample. Following this, a highly resolved chromatogram was obtained, allowing EI mass spectra containing molecular and fragment ions of many distinct molecules present in the sample to be identified.
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Affiliation(s)
- Nguyen Viet Hung
- Laboratoire SMS-EA3233, UNIROUEN, Normandie Université, Place Emile Blondel, F-76821, Mont-Saint-Aignan Cedex, France
| | - Chetna Mohabeer
- Laboratoire de Sécurité des Procédés Chimiques, LSPC EA-4704, Normandie Univ, INSA Rouen Normandie, UNIROUEN, 76000, Rouen, France
| | - Marie Vaccaro
- Laboratoire SMS-EA3233, UNIROUEN, Normandie Université, Place Emile Blondel, F-76821, Mont-Saint-Aignan Cedex, France
| | - Stéphane Marcotte
- Normandie Université, INSA de Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), Avenue del'Université, 76800, Saint-Etienne-du-Rouvray, France
| | - Valérie Agasse-Peulon
- Laboratoire SMS-EA3233, UNIROUEN, Normandie Université, Place Emile Blondel, F-76821, Mont-Saint-Aignan Cedex, France
| | - Lokmane Abdelouahed
- Laboratoire de Sécurité des Procédés Chimiques, LSPC EA-4704, Normandie Univ, INSA Rouen Normandie, UNIROUEN, 76000, Rouen, France
| | - Bechara Taouk
- Laboratoire de Sécurité des Procédés Chimiques, LSPC EA-4704, Normandie Univ, INSA Rouen Normandie, UNIROUEN, 76000, Rouen, France
| | - Pascal Cardinael
- Laboratoire SMS-EA3233, UNIROUEN, Normandie Université, Place Emile Blondel, F-76821, Mont-Saint-Aignan Cedex, France
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19
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Mommers J, van der Wal S. Column Selection and Optimization for Comprehensive Two-Dimensional Gas Chromatography: A Review. Crit Rev Anal Chem 2020; 51:183-202. [DOI: 10.1080/10408347.2019.1707643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- John Mommers
- DSM Material Science Center, Geleen, The Netherlands
| | - Sjoerd van der Wal
- Polymer-Analysis Group, University of Amsterdam, Amsterdam, The Netherlands
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20
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Li X, Luo Y, Jiang X, Zhang H, Zhu F, Hu S, Hou H, Hu Q, Pang Y. Chemical Analysis and Simulated Pyrolysis of Tobacco Heating System 2.2 Compared to Conventional Cigarettes. Nicotine Tob Res 2020; 21:111-118. [PMID: 29319815 DOI: 10.1093/ntr/nty005] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 01/06/2018] [Indexed: 01/13/2023]
Abstract
Introduction Tobacco Heating System 2.2 (THS 2.2, marketed as iQOS) is a heat-not-burn (HNB) tobacco product that has been successfully introduced to global markets. Despite its expanding market, few independent and systematic researches into THS 2.2 have been carried out to date. Methods We tested a comprehensive list of total particulate matter (TPM), water, tar, nicotine, propylene glycol, glycerin, carbon monoxide, volatile organic compounds, aromatic amines, hydrogen cyanide, ammonia, N-nitrosamines, phenol, and polycyclic aromatic hydrocarbon under both ISO and HCI regimes. We also simulated pyrolysis of THS 2.2 heating sticks and made comparisons with conventional cigarette tobacco fillers using comprehensive gas chromatography-mass spectrometry (GC × GC-MS) to determine whether the specially designed ingredients help reduce harmful constituents. Results Other than some carbonyls, ammonia, and N-nitrosoanabasine (NAB), the delivered releases from THS 2.2 were at least 80% lower than those from 3R4F. Tar and nicotine remained almost the same as 3R4F. Interestingly, the normalized yield of THS 2.2 to 3R4F under the HCI regime was lower than that under the ISO regime. Conclusions THS 2.2 delivered fewer harmful constituents than the conventional cigarette 3R4F. Simulated pyrolysis results showed that the lower temperature instead of specially designed ingredients contributed to the distinct shift. In particular, if smoking machines are involved to evaluate the HNB products, smoking regimes of heat-not-burn tobacco products should be carefully chosen. Implications To our knowledge, few independent studies of HNB products have been published. In this paper, a comprehensive list of chemical releases was tested systematically and compared to those from 3R4F. Although THS 2.2 generates lower levels of harmful constituents, the nicotine and tar levels were almost identical to 3R4F.The results should be discussed carefully in the future when assessing the dual-use with other conventional cigarettes, nicotine dependence of HNB products, etc. This study also suggests that regulatory agencies should pay attention to the smoking regimes that are adopted to evaluate HNB tobacco products.
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Affiliation(s)
- Xiangyu Li
- Department of Environmental Science and Technology, School of Environment, Tsinghua University, Beijing, China
| | - Yanbo Luo
- Department of Analytical Chemistry, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xingyi Jiang
- Department of Biotechnology, School of International Education, Henan University of Technology, Zhengzhou, Henan, China
| | - Hongfei Zhang
- Department of Tobacco Chemistry, School Of Food Science and Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, China
| | - Fengpeng Zhu
- Department of Tobacco Chemistry, School Of Food Science and Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, China
| | - Shaodong Hu
- Department of polymer science and engineer, Sichuan University, Chengdu, Sichuan, China
| | - Hongwei Hou
- Department of Inorganic Chemistry, Chemistry, University of Science and Technology of China, Hefei, Anhui, China
| | - Qingyuan Hu
- Department of Optics, Anhui Institute of Optics and Fine Mechanics, The Chinese Academy of Sciences, Hefei, Anhui, China
| | - Yongqiang Pang
- Department of Analytical Chemistry, Chemistry, University of Science and Technology of China, Hefei, Anhui, China
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21
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Gas chromatography in combination with fast high-resolution time-of-flight mass spectrometry: Technical overview and perspectives for data visualization. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115677] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Untargeted Serum Metabolic Profiling by Comprehensive Two-Dimensional Gas Chromatography–High-Resolution Time-of-Flight Mass Spectrometry. J Proteome Res 2019; 19:1013-1028. [DOI: 10.1021/acs.jproteome.9b00535] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
| | - Marie-Alice Meuwis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Edouard Louis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
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23
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Comparison of Pre-Processing and Variable Selection Strategies in Group-Based GC×GC-TOFMS Analysis. SEPARATIONS 2019. [DOI: 10.3390/separations6030041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chemometric analysis of comprehensive two-dimensional chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS) data has been reported with various workflows, yet little effort has been devoted to evaluating the impacts of workflow variation on study conclusions. The report presented herein aims to investigate the effects of different pre-processing and variable selection strategies on the scores’ plot outputs from GC×GC-TOFMS data acquired from lavender and tea tree essential oils. Our results suggest that pre-processing, such as applying log transformation to the data set, can result in significant differentiation of sample clustering when compared to only mean centering. Additionally, exploring differences between analysis of variance, Fisher-ratio, and partial least squares-discriminant analysis feature selection resulted in little variation in scores plots. This work highlights the effects different chemometric workflows can have on results to help facilitate harmonization efforts.
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Liu J, Zhang X, Yang J, Zhou J, Yuan Y, Jiang C, Chi X, Huang L. Agarwood wound locations provide insight into the association between fungal diversity and volatile compounds in Aquilaria sinensis. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190211. [PMID: 31417726 PMCID: PMC6689645 DOI: 10.1098/rsos.190211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
The aim of the present study was to investigate the effect of wound location on the fungal communities and volatile distribution of agarwood in Aquilaria sinensis. Two-dimensional gas chromatography with high-resolution time-of-flight mass spectrometry revealed 60 compounds from the NIST library, including 25 sesquiterpenes, seven monoterpenes, two diterpenes, nine aromatics, nine alkanes and eight others. Of five agarwood types, Types IV and II contained the greatest number and concentration of sesquiterpenes, respectively. The fungal communities of the agarwood were dominated by the phylum Ascomycota and were significantly affected by the type of wound tissue. Community richness indices (observed species, Chao1, PD whole tree, ACE indices) indicated that Types I and IV harboured the most and least species-rich fungal communities, and the fungal communities of Types V, I, III and IV/II were dominated by Lasiodiplodia, Hydnellum, Phaeoisaria and Ophiocordyceps species, respectively. Correlations between fungal species and agarwood components revealed that the chemical properties of A. sinensis were associated with fungal diversity. More specifically, the dominant fungal genera of Types V, I and III (Lasiodiplodia, Hydnellum and Phaeoisaria, respectively) were strongly correlated with specific terpenoid compounds. The finding that wound location affects the fungal communities and volatile distribution of agarwood provides insight into the formation of distinct agarwood types.
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Affiliation(s)
- Juan Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Xiang Zhang
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, People's Republic of China
| | - Jian Yang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Junhui Zhou
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Xiulian Chi
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, People's Republic of China
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25
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Breast Cancer Metabolomics: From Analytical Platforms to Multivariate Data Analysis. A Review. Metabolites 2019; 9:metabo9050102. [PMID: 31121909 PMCID: PMC6572290 DOI: 10.3390/metabo9050102] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/24/2022] Open
Abstract
Cancer is a major health issue worldwide for many years and has been increasing significantly. Among the different types of cancer, breast cancer (BC) remains the leading cause of cancer-related deaths in women being a disease caused by a combination of genetic and environmental factors. Nowadays, the available diagnostic tools have aided in the early detection of BC leading to the improvement of survival rates. However, better detection tools for diagnosis and disease monitoring are still required. In this sense, metabolomic NMR, LC-MS and GC-MS-based approaches have gained attention in this field constituting powerful tools for the identification of potential biomarkers in a variety of clinical fields. In this review we will present the current analytical platforms and their applications to identify metabolites with potential for BC biomarkers based on the main advantages and advances in metabolomics research. Additionally, chemometric methods used in metabolomics will be highlighted.
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26
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Stilo F, Liberto E, Reichenbach SE, Tao Q, Bicchi C, Cordero C. Untargeted and Targeted Fingerprinting of Extra Virgin Olive Oil Volatiles by Comprehensive Two-Dimensional Gas Chromatography with Mass Spectrometry: Challenges in Long-Term Studies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5289-5302. [PMID: 30994349 DOI: 10.1021/acs.jafc.9b01661] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Comprehensive two-dimensional gas chromatography coupled with mass spectrometric detection (GC × GC-MS) offers an information-rich basis for effective chemical fingerprinting of food. However, GC × GC-MS yields 2D-peak patterns (i.e., sample 2D fingerprints) whose consistency may be affected by variables related to either the analytical platform or to the experimental parameters adopted for the analysis. This study focuses on the complex volatile fraction of extra-virgin olive oil and addresses 2D-peak patterns variations, including MS signal fluctuations, as they may occur in long-term studies where pedo-climatic, harvest year, or shelf life changes are studied. The 2D-pattern misalignments are forced by changing chromatographic settings and MS acquisition. All procedural steps, preceding pattern recognition by template matching, are analyzed and a rational workflow defined to accurately realign patterns and analytes metadata. Signal-to-noise ratio (SNR) detection threshold, reference spectra extraction, and similarity match factor threshold are critical to avoid false-negative matches. Distance thresholds and polynomial transform parameters are key for effective template matching. In targeted analysis (supervised workflow) with optimized parameters, method accuracy reaches 92.5% (i.e., % of true-positive matches) while for combined untargeted and targeted ( UT) fingerprinting (unsupervised workflow), accuracy reaches 97.9%. Response normalization also is examined, evidencing good performance of multiple internal standard normalization that effectively compensates for discriminations occurring during injection of highly volatile compounds. The resulting workflow is simple, effective, and time efficient.
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Affiliation(s)
- Federico Stilo
- Dipartimento di Scienza e Tecnologia del Farmaco , Università degli Studi di Torino , Turin I-10125 , Italy
| | - Erica Liberto
- Dipartimento di Scienza e Tecnologia del Farmaco , Università degli Studi di Torino , Turin I-10125 , Italy
| | - Stephen E Reichenbach
- Computer Science and Engineering Department , University of Nebraska , Lincoln , Nebraska 68588 , United States
- GC Image, LLC , Lincoln , Nebraska 68508 , United States
| | - Qingping Tao
- GC Image, LLC , Lincoln , Nebraska 68508 , United States
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco , Università degli Studi di Torino , Turin I-10125 , Italy
| | - Chiara Cordero
- Dipartimento di Scienza e Tecnologia del Farmaco , Università degli Studi di Torino , Turin I-10125 , Italy
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Cordero C, Kiefl J, Reichenbach SE, Bicchi C. Characterization of odorant patterns by comprehensive two-dimensional gas chromatography: A challenge in omic studies. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Jones OAH. Illuminating the dark metabolome to advance the molecular characterisation of biological systems. Metabolomics 2018; 14:101. [PMID: 30830382 DOI: 10.1007/s11306-018-1396-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/07/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND The latest version of the Human Metabolome Database (v4.0) lists 114,100 individual entries. Typically, however, metabolomics studies identify only around 100 compounds and many features identified in mass spectra are listed only as 'unknown compounds'. The lack of ability to detect all metabolites present, and fully identify all metabolites detected (the dark metabolome) means that, despite the great contribution of metabolomics to a range of areas in the last decade, a significant amount of useful information from publically funded studies is being lost or unused each year. This loss of data limits our potential gain in knowledge and understanding of important research areas such as cell biology, environmental pollution, plant science, food chemistry and health and biomedical research. Metabolomics therefore needs to develop new tools and methods for metabolite identification to advance as a field. AIM OF REVIEW In this critical review, some potential issues with metabolite identification are identified and discussed. New and novel emerging technologies and tools which may contribute to expanding the number of compounds identified in metabolomics studies (thus illuminating the dark metabolome) are reviewed. The aim is to stimulate debate and research in the molecular characterisation of biological systems to drive forward metabolomic research. KEY SCIENTIFIC CONCEPTS OF REVIEW The work specifically discusses dynamic nuclear polarisation nuclear magnetic resonance spectroscopy (DNP-NMR), non-proton NMR active nuclei, two-dimensional liquid chromatography (2DLC) and Raman spectroscopy (RS). It is suggested that developing new methods for metabolomics with these techniques could lead to advances in the field and better characterisation of biological systems.
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Affiliation(s)
- Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3001, Australia.
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29
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Bressanello D, Liberto E, Collino M, Chiazza F, Mastrocola R, Reichenbach SE, Bicchi C, Cordero C. Combined untargeted and targeted fingerprinting by comprehensive two-dimensional gas chromatography: revealing fructose-induced changes in mice urinary metabolic signatures. Anal Bioanal Chem 2018. [DOI: 10.1007/s00216-018-0950-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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30
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Zushi Y, Hashimoto S. Direct Classification of GC × GC-Analyzed Complex Mixtures Using Non-Negative Matrix Factorization-Based Feature Extraction. Anal Chem 2018; 90:3819-3825. [DOI: 10.1021/acs.analchem.7b04313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yasuyuki Zushi
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Shunji Hashimoto
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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31
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A four dimensional separation method based on continuous heart-cutting gas chromatography with ion mobility and high resolution mass spectrometry. J Chromatogr A 2018; 1536:50-57. [DOI: 10.1016/j.chroma.2017.07.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/02/2017] [Accepted: 07/04/2017] [Indexed: 01/03/2023]
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32
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Magagna F, Liberto E, Reichenbach SE, Tao Q, Carretta A, Cobelli L, Giardina M, Bicchi C, Cordero C. Advanced fingerprinting of high-quality cocoa: Challenges in transferring methods from thermal to differential-flow modulated comprehensive two dimensional gas chromatography. J Chromatogr A 2018; 1536:122-136. [DOI: 10.1016/j.chroma.2017.07.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 05/02/2017] [Accepted: 07/04/2017] [Indexed: 11/30/2022]
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Savareear B, Brokl M, Wright C, Focant JF. Thermal desorption comprehensive two-dimensional gas chromatography coupled to time of flight mass spectrometry for vapour phase mainstream tobacco smoke analysis. J Chromatogr A 2017; 1525:126-137. [PMID: 29030031 DOI: 10.1016/j.chroma.2017.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/02/2017] [Accepted: 10/05/2017] [Indexed: 01/26/2023]
Abstract
A thermal desorption comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (TD-GC×GC-TOFMS) method has been developed for the analysis of mainstream tobacco smoke (MTS) vapour phase (VP). The selection process of the sample introduction approach involved comparing the results obtained from three different approaches: a) use of gas sampling bag followed by SPME (Tedlar®-SPME), b) gas sampling bag followed by TD (Tedlar®-TD), and c) sampling directly on TD sorbents (Direct-TD). Six different SPME fibers and six different TD sorbent beds were evaluated for the extraction capacities in terms of total number of peaks and related intensities or peak areas. The best results were obtained for the Direct-TD approach using Tenax TA/Carbograph1TD/Carboxen1003 sorbent tubes. The optimisation of TD tube desorption parameters was carried out using a face-centered central composite experimental design and resulted in the use of the Tenax TA/Carbograph 1TD/Carboxen 1003 sorbent with a 7.5min desorption time, a 60mL/min tube desorption flow, and a 250°C tube desorption temperature. The optimised method was applied to the separation of MTS-VP constituents, with 665 analytes detected. The method precision ranged from 1% to 15% for over 99% of identified peak areas and from 0% to 3% and 0% to 1% for both first (1tR) and second (2tR) dimension retention times, respectively. The method was applied to the analyses of two cigarette types differing in their filter construction. Principal component analysis (PCA) allowed a clear differentiation of the studied cigarette types (PC1 describing 94% of the explained variance). Supervised Fisher ratio analysis permitted the identification of compounds responsible for the chemical differences between the two sample types. A set of 91 most relevant compounds was selected by applying a Fisher ratio cut-off approach and most of them were selectively removed by one of the cigarette filter types.
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Affiliation(s)
- Benjamin Savareear
- Centre for Analytical Research and Technologies (CART), University of Liege, Belgium
| | - Michał Brokl
- Group Research and Development, British American Tobacco, Southampton, UK
| | - Chris Wright
- Group Research and Development, British American Tobacco, Southampton, UK
| | - Jean-Francois Focant
- Centre for Analytical Research and Technologies (CART), University of Liege, Belgium.
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Savareear B, Lizak R, Brokl M, Wright C, Liu C, Focant JF. Headspace solid-phase microextraction coupled to comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry for the analysis of aerosol from tobacco heating product. J Chromatogr A 2017; 1520:135-142. [PMID: 28911941 DOI: 10.1016/j.chroma.2017.09.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 02/08/2023]
Abstract
A method involving headspace solid-phase microextraction (HS-SPME) and comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS) was developed and optimised to elucidate the volatile composition of the particulate phase fraction of aerosol produced by tobacco heating products (THPs). Three SPME fiber types were studied in terms of extraction capacity and precision measurements. Divinylbenzene polydimethylsiloxane appeared as the most efficient coating for these measurements. A central composite design of experiment was utilised for the optimization of the extraction conditions. Qualitative and semi-quantitative analysis of the headspace above THP aerosol condensate was carried out using optimised extraction conditions. Semi-quantitative analyses of detected constituents were performed by assuming that their relative response factors to the closest internal standard (itR) were equal to 1. Using deconvoluted mass spectral data (library similarity and reverse match >750) and linear retention indices (match window of ±15 index units), 205 peaks were assigned to individual compounds, 82 of which (including 43 substances previously reported to be present in tobacco) have not been reported previously in tobacco aerosol. The major volatile fraction of the headspace contained ketones, alcohols, aldehydes, alicyclic hydrocarbons alkenes, and alkanes. The method was further applied to compare the volatiles from the particulate phase of aerosol composition of THP with that of reference cigarette smoke and showed that the THP produced a less complex chemical mixture. This new method showed good efficiency and precision for the peak areas and peak numbers from the volatile fraction of aerosol particulate phase for both THP and reference cigarettes.
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Affiliation(s)
- Benjamin Savareear
- Centre for Analytical Research and Technologies (CART), University of Liege, Belgium
| | - Radoslaw Lizak
- Centre for Analytical Research and Technologies (CART), University of Liege, Belgium
| | - Michał Brokl
- Group Research and Development, British American Tobacco, Southampton, UK
| | - Chris Wright
- Group Research and Development, British American Tobacco, Southampton, UK
| | - Chuan Liu
- Group Research and Development, British American Tobacco, Southampton, UK
| | - Jean-Francois Focant
- Centre for Analytical Research and Technologies (CART), University of Liege, Belgium.
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35
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Magagna F, Guglielmetti A, Liberto E, Reichenbach SE, Allegrucci E, Gobino G, Bicchi C, Cordero C. Comprehensive Chemical Fingerprinting of High-Quality Cocoa at Early Stages of Processing: Effectiveness of Combined Untargeted and Targeted Approaches for Classification and Discrimination. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:6329-6341. [PMID: 28682071 DOI: 10.1021/acs.jafc.7b02167] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This study investigates chemical information of volatile fractions of high-quality cocoa (Theobroma cacao L. Malvaceae) from different origins (Mexico, Ecuador, Venezuela, Columbia, Java, Trinidad, and Sao Tomè) produced for fine chocolate. This study explores the evolution of the entire pattern of volatiles in relation to cocoa processing (raw, roasted, steamed, and ground beans). Advanced chemical fingerprinting (e.g., combined untargeted and targeted fingerprinting) with comprehensive two-dimensional gas chromatography coupled with mass spectrometry allows advanced pattern recognition for classification, discrimination, and sensory-quality characterization. The entire data set is analyzed for 595 reliable two-dimensional peak regions, including 130 known analytes and 13 potent odorants. Multivariate analysis with unsupervised exploration (principal component analysis) and simple supervised discrimination methods (Fisher ratios and linear regression trees) reveal informative patterns of similarities and differences and identify characteristic compounds related to sample origin and manufacturing step.
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Affiliation(s)
- Federico Magagna
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino , I-10125 Turin, Italy
| | - Alessandro Guglielmetti
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino , I-10125 Turin, Italy
| | - Erica Liberto
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino , I-10125 Turin, Italy
| | - Stephen E Reichenbach
- Department of Computer Science and Engineering, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0115, United States
| | | | | | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino , I-10125 Turin, Italy
| | - Chiara Cordero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino , I-10125 Turin, Italy
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36
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Pixel-by-pixel correction of retention time shifts in chromatograms from comprehensive two-dimensional gas chromatography coupled to high resolution time-of-flight mass spectrometry. J Chromatogr A 2017. [DOI: 10.1016/j.chroma.2017.05.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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37
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A minimally-invasive method for profiling volatile organic compounds within postmortem internal gas reservoirs. Int J Legal Med 2017; 131:1271-1281. [DOI: 10.1007/s00414-017-1621-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/31/2017] [Indexed: 10/19/2022]
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38
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Pizzolante G, Cordero C, Tredici SM, Vergara D, Pontieri P, Del Giudice L, Capuzzo A, Rubiolo P, Kanchiswamy CN, Zebelo SA, Bicchi C, Maffei ME, Alifano P. Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles. BMC PLANT BIOLOGY 2017; 17:30. [PMID: 28249605 PMCID: PMC5333409 DOI: 10.1186/s12870-017-0986-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND A chemical cross-talk between plants and insects is required in order to achieve a successful co-adaptation. In response to herbivory, plants produce specific compounds, and feeding insects respond adequately7 to molecules produced by plants. Here we show the role of the gut microbial community of the mint beetle Chrysolina herbacea in the chemical cross-talk with Mentha aquatica (or watermint). RESULTS By using two-dimensional gas chromatography-mass spectrometry we first evaluated the chemical patterns of both M. aquatica leaf and frass volatiles extracted by C. herbacea males and females feeding on plants, and observed marked differences between males and females volatiles. The sex-specific chemical pattern of the frass paralleled with sex-specific distribution of cultivable gut bacteria. Indeed, all isolated gut bacteria from females belonged to either α- or γ-Proteobacteria, whilst those from males were γ-Proteobacteria or Firmicutes. We then demonstrated that five Serratia marcescens strains from females possessed antibacterial activity against bacteria from males belonging to Firmicutes suggesting competition by production of antimicrobial compounds. By in vitro experiments, we lastly showed that the microbial communities from the two sexes were associated to specific metabolic patterns with respect to their ability to biotransform M. aquatica terpenoids, and metabolize them into an array of compounds with possible pheromone activity. CONCLUSIONS Our data suggest that cultivable gut bacteria of Chrysolina herbacea males and females influence the volatile blend of herbivory induced Mentha aquatica volatiles in a sex-specific way.
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Affiliation(s)
- Graziano Pizzolante
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
| | - Chiara Cordero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Pietro Giuria n°9, 10125 Torino, Italy
| | - Salvatore M. Tredici
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
| | - Davide Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
| | - Paola Pontieri
- Dipartimento di Biologia, Sezione di Igiene, Institute of Biosciences and Bioresources-UOS Portici (IBBR-UOS Portici), CNR, Portici (NA) c/o, 80134 Naples, Italy
| | - Luigi Del Giudice
- Dipartimento di Biologia, Sezione di Igiene, Institute of Biosciences and Bioresources-UOS Portici (IBBR-UOS Portici), CNR, Portici (NA) c/o, 80134 Naples, Italy
| | - Andrea Capuzzo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Quarello 15/A, 10135 Torino, Italy
| | - Patrizia Rubiolo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Pietro Giuria n°9, 10125 Torino, Italy
| | - Chidananda N. Kanchiswamy
- Research and Innovation Centre Genomics and Biology of Fruit Crop Department, Fondazione Edmund Mach (FEM), Istituto Agrario San Michele (IASMA), Via Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Simon A. Zebelo
- Department of Natural Sciences, University of Maryland Eastern Shore, 1117 Trigg Hall, Princess Anne, 21853 MD USA
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Pietro Giuria n°9, 10125 Torino, Italy
| | - Massimo E. Maffei
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Quarello 15/A, 10135 Torino, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
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Lengger SK, Fromont J, Grice K. Tapping the archives: the sterol composition of marine sponge species, as determined non-invasively from museum-preserved specimens, reveals biogeographical features. GEOBIOLOGY 2017; 15:184-194. [PMID: 27686333 DOI: 10.1111/gbi.12206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
Over 8600 species are currently recorded in the phylum Porifera (sponges). They produce a large diversity of biochemical compounds including sterols, with more than 250 different sterols identified. Some of these sterols are of great interest, due to their use for fingerprinting in ecological and biomarker (molecular fossil) studies. As a large number of identified extant species from biodiversity surveys are housed in museum collections, preserved in ethanol, these present a potentially rich source of identified specimens for comparative lipid analyses. Here, we show that, in at least one species, sterol distributions obtained from the ethanol used to preserve specimens of sponges were representative, and comparable to the sterol distribution obtained from wet-frozen and from freeze-dried tissue from the same species. We employed both GC-MS and two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOFMS), with an improved signal-to-noise ratio for even minor constituents. Analysis of two additional specimens of the same species, but of different provenance, resulted in detection of marked differences in sterol composition, which could be attributed to variations in geography, environmental conditions, microbial communities, diet or cryptic speciation. The possibility of using ethanol from identified, preserved museum sponges could drastically increase the number of available samples. This could enable the study of their sterol complements, and the detailed investigation of differences due to geographical and oceanographic, phylogenetic, and other factors in unprecedented detail.
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Affiliation(s)
- S K Lengger
- Department of Chemistry, WA Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin University, Perth, WA, Australia
| | - J Fromont
- Western Australian Museum, Welshpool DC, WA, Australia
| | - K Grice
- Department of Chemistry, WA Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin University, Perth, WA, Australia
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40
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Combined untargeted and targeted fingerprinting with comprehensive two-dimensional chromatography for volatiles and ripening indicators in olive oil. Anal Chim Acta 2016; 936:245-58. [DOI: 10.1016/j.aca.2016.07.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/27/2016] [Accepted: 07/01/2016] [Indexed: 11/20/2022]
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42
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Potential of the reversed-inject differential flow modulator for comprehensive two-dimensional gas chromatography in the quantitative profiling and fingerprinting of essential oils of different complexity. J Chromatogr A 2015; 1417:79-95. [DOI: 10.1016/j.chroma.2015.09.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 12/16/2022]
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43
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Egert B, Weinert CH, Kulling SE. A peaklet-based generic strategy for the untargeted analysis of comprehensive two-dimensional gas chromatography mass spectrometry data sets. J Chromatogr A 2015; 1405:168-77. [PMID: 26074098 DOI: 10.1016/j.chroma.2015.05.056] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 12/17/2022]
Abstract
Comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) is a well-established key technology in analytical chemistry and increasingly used in the field of untargeted metabolomics. However, automated processing of large GC×GC-MS data sets is still a major bottleneck in untargeted, large-scale metabolomics. For this reason we introduce a novel peaklet-based alignment strategy. The algorithm is capable of an untargeted deterministic alignment exploiting a density based clustering procedure within a time constrained similarity matrix. Exploiting minimal (1)D and (2)D retention time shifts between peak modulations, the alignment is done without the need for peak merging which also eliminates the need for linear or nonlinear retention time correction procedures. The approach is validated in detail using data of urine samples from a large human metabolomics study. The data was acquired by a Shimadzu GCMS-QP2010 Ultra GC×GC-qMS system and consists of 512 runs, including 312 study samples and 178 quality control sample injections, measured within a time period of 22 days. The final result table consisted of 313 analytes, each of these being detectable in at least 75% of the study samples. In summary, we present an automated, reliable and fully transparent workflow for the analysis of large GC×GC-qMS metabolomics data sets.
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Affiliation(s)
- Björn Egert
- Max Rubner-Institut, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany.
| | - Christoph H Weinert
- Max Rubner-Institut, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Sabine E Kulling
- Max Rubner-Institut, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
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Zushi Y, Hashimoto S, Tanabe K. Global spectral deconvolution based on non-negative matrix factorization in GC × GC-HRTOFMS. Anal Chem 2015; 87:1829-38. [PMID: 25572711 DOI: 10.1021/ac5038544] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A global spectral deconvolution, based on non-negative matrix factorization (NMF) in comprehensive two-dimensional gas chromatography high-resolution time-of-flight mass spectrometry, was developed. We evaluated the ability of various instrumental parameters and NMF settings to derive high-performance detection in nontarget screening using a sediment sample. To evaluate the performance of the process, a NIST library search was used to identify the deconvoluted spectra. Differences of the instrumental scan rates (25 and 50 Hz) in deconvolution were evaluated and results show that a high scan rate enhanced the number of compounds detected in the sediment sample. A higher mass resolution in the range of 1,000 to 10,000 and a higher m/z precision in the deconvolution were needed to obtain an accurate mass database. After removal of multiple duplicate hits, which occurred in batch processes of NIST library search on the deconvolution result, 62 unique assignable spectra with a match factor ≥900 were obtained in the deconvoluted chromatogram from the sediment sample, including 54 spectra that were refined by the deconvolution. This method will help to detect and build up well-resolved reference spectra from various complex mixtures and will accelerate nontarget screening.
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Affiliation(s)
- Yasuyuki Zushi
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies , 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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Abstract
Multidimensional gas chromatography (MDGC) methods are high-resolution volatile chemical separation techniques, and comprise classical heart-cutting MDGC and its more recent incarnation, comprehensive 2D GC. Although available for a long period, MDGC approaches are still not widely practiced in the field of bioanalysis, possibly reflecting the general preference for regular GC versus MDGC approaches. With the recent introduction of ‘-omic’ techniques that emphasize global nontargeted profiling of metabolites within living systems, it is evident that MDGC is gaining momentum as a separation tool, since it offers very high resolution. By untangling metabolites within highly complex biological matrices, and expanding the metabolic coverage, MDGC plays a frontline role in ‘-omics’ based studies. This review highlights state-of-the-art MDGC approaches, and summarizes the recent developments in bioanalytics.
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Urinary metabolic fingerprinting of mice with diet-induced metabolic derangements by parallel dual secondary column-dual detection two-dimensional comprehensive gas chromatography. J Chromatogr A 2014; 1361:265-76. [DOI: 10.1016/j.chroma.2014.08.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 07/31/2014] [Accepted: 08/04/2014] [Indexed: 12/19/2022]
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47
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Chin ST, Marriott PJ. Multidimensional gas chromatography beyond simple volatiles separation. Chem Commun (Camb) 2014; 50:8819-33. [DOI: 10.1039/c4cc02018a] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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48
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Resolution of co-eluting compounds of Cannabis Sativa in comprehensive two-dimensional gas chromatography/mass spectrometry detection with Multivariate Curve Resolution-Alternating Least Squares. Talanta 2014; 121:273-80. [DOI: 10.1016/j.talanta.2013.12.044] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 12/17/2013] [Accepted: 12/22/2013] [Indexed: 01/07/2023]
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49
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Zushi Y, Hashimoto S, Tamada M, Masunaga S, Kanai Y, Tanabe K. Retrospective analysis by data processing tools for comprehensive two-dimensional gas chromatography coupled to high resolution time-of-flight mass spectrometry: A challenge for matrix-rich sediment core sample from Tokyo Bay. J Chromatogr A 2014; 1338:117-26. [DOI: 10.1016/j.chroma.2014.02.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/04/2014] [Accepted: 02/04/2014] [Indexed: 12/31/2022]
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Current practice of liquid chromatography–mass spectrometry in metabolomics and metabonomics. J Pharm Biomed Anal 2014; 87:12-25. [DOI: 10.1016/j.jpba.2013.06.032] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/26/2013] [Accepted: 06/29/2013] [Indexed: 02/06/2023]
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