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Li S, Bohman B, Flematti GR, Jayatilaka D. Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph. J Cheminform 2023; 15:104. [PMID: 37936244 PMCID: PMC10631010 DOI: 10.1186/s13321-023-00776-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Identifying the molecular formula and fragmentation reactions of an unknown compound from its mass spectrum is crucial in areas such as natural product chemistry and metabolomics. We propose a method for identifying the correct candidate formula of an unidentified natural product from its mass spectrum. The method involves scoring the plausibility of parent candidate formulae based on a parent subformula graph (PSG), and two possible metrics relating to the number of edges in the PSG. This method is applicable to both electron-impact mass spectrometry (EI-MS) and tandem mass spectrometry (MS/MS) data. Additionally, this work introduces the two-dimensional fragmentation plot (2DFP) for visualizing PSGs. RESULTS Our results suggest that incorporating information regarding the edges of the PSG results in enhanced performance in correctly identifying parent formulae, in comparison to the more well-accepted "MS/MS score", on the 2016 Computational Assessment of Small Molecule Identification (CASMI 2016) data set (76.3 vs 58.9% correct formula identification) and the Research Centre for Toxic Compounds in the Environment (RECETOX) data set (66.2% vs 59.4% correct formula identification). In the extension of our method to identify the correct candidate formula from complex EI-MS data of semiochemicals, our method again performed better (correct formula appearing in the top 4 candidates in 20/23 vs 7/23 cases) than the MS/MS score, and enables the rapid identification of both the correct parent ion mass and the correct parent formula with minimal expert intervention. CONCLUSION Our method reliably identifies the correct parent formula even when the mass information is ambiguous. Furthermore, should parent formula identification be successful, the majority of associated fragment formulae can also be correctly identified. Our method can also identify the parent ion and its associated fragments in EI-MS spectra where the identity of the parent ion is unclear due to low quantities and overlapping compounds. Finally, our method does not inherently require empirical fitting of parameters or statistical learning, meaning it is easy to implement and extend upon. SCIENTIFIC CONTRIBUTION Developed, implemented and tested new metrics for assessing plausibility of candidate molecular formulae obtained from HR-MS data.
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Affiliation(s)
- Sean Li
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia.
| | - Björn Bohman
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Gavin R Flematti
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia
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2
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Sabri Bens M, Dassamiour S, Hambaba L, Akram Mela M, Sami R, M. Al-Mush AA, Benajiba N, Al Masoudi LM. In silico Investigation and BSA Denaturation Inhibitory Activity of Ethyl Acetate and N-butanol Extracts of Centaurea tougourensis Boiss. and Reut. INT J PHARMACOL 2022. [DOI: 10.3923/ijp.2022.1296.1308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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3
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Chambreau SD, Popolan-Vaida DM, Kostko O, Lee JK, Zhou Z, Brown TA, Jones P, Shao K, Zhang J, Vaghjiani GL, Zare RN, Leone SR. Thermal and Catalytic Decomposition of 2-Hydroxyethylhydrazine and 2-Hydroxyethylhydrazinium Nitrate Ionic Liquid. J Phys Chem A 2022; 126:373-394. [PMID: 35014846 DOI: 10.1021/acs.jpca.1c07408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
To develop chemical kinetics models for the combustion of ionic liquid-based monopropellants, identification of the elementary steps in the thermal and catalytic decomposition of components such as 2-hydroxyethylhydrazinium nitrate (HEHN) is needed but is currently not well understood. The first decomposition step in protic ionic liquids such as HEHN is typically the proton transfer from the cation to the anion, resulting in the formation of 2-hydroxyethylhydrazine (HEH) and HNO3. In the first part of this investigation, the high-temperature thermal decomposition of HEH is probed with flash pyrolysis (<1400 K) and vacuum ultraviolet (10.45 eV) photoionization time-of-flight mass spectrometry (VUV-PI-TOFMS). Next, the investigation into the thermal and catalytic decomposition of HEHN includes two mass spectrometric techniques: (1) tunable VUV-PI-TOFMS (7.4-15 eV) and (2) ambient ionization mass spectrometry utilizing both plasma and laser ionization techniques whereby HEHN is introduced onto a heated inert or iridium catalytic surface and the products are probed. The products can be identified by their masses, their ionization energies, and their collision-induced fragmentation patterns. Formation of product species indicates that catalytic surface recombination is an important reaction process in the decomposition mechanism of HEHN. The products and their possible elementary reaction mechanisms are discussed.
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Affiliation(s)
- Steven D Chambreau
- Jacobs Technology, Inc., Edwards Air Force Base, California 93524, United States
| | - Denisia M Popolan-Vaida
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States.,Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Oleg Kostko
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jae Kyoo Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Zhenpeng Zhou
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Timothy A Brown
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Paul Jones
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Kuanliang Shao
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Jingsong Zhang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ghanshyam L Vaghjiani
- In-Space Propulsion Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRS, Edwards Air Force Base, California 93524, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen R Leone
- Departments of Chemistry and Physics, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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Porto NDA, Crucello J, Facanali R, Junior IM, Carvalho RM, Hantao LW. Profiling naphthenic acids in produced water using hollow fiber liquid-phase microextraction combined with gas chromatography coupled to Fourier transform Orbitrap mass spectrometry. J Chromatogr A 2021; 1655:462485. [PMID: 34474190 DOI: 10.1016/j.chroma.2021.462485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022]
Abstract
In this study, we describe the development of an analytical method to profile naphthenic acids (NAs) from produced water (PW). The NAs were isolated by hollow fiber liquid-phase microextraction (HF-LPME). A microwave-assisted methylation method was used to convert the free acids into its corresponding naphthenic methyl esters (NAMEs). The best reaction conditions were ascertained using central composite design. The optimized sample preparation method exhibited an improved analytical eco-scale value (80 vs. 61) compared to conventional liquid-liquid extraction. Although the primary goal was qualitative analysis of NAMEs (e.g., group-type separation) in produced water, the quantitative performance was also evaluated for future investigations. The instrumental detection and quantification limits were 0.10 ng mL-1 and 0.16 ng mL-1, respectively, using full spectrum data acquisition. The accuracy and precision of the proposed method ranged from 90.4 to 96.6 % and 3.3 to 13.1 %, respectively, using matrix-matched working solutions (0.1, 0.5, and 1.0 µg mL-1). The monoisotopic masses of the adduct ions ([M+H]+) and its corresponding fine isotopic patterns were used to determine the elemental composition of the NAMEs in the PW samples. Qualitative analysis indicated the O2 class as the predominant class in all samples with carbon numbers ranging from C5 to C19 and double bond equivalent (DBE) values of 1 to 8. Additional classes of polar compounds, i.e., O3, O4 and nitrogen-containing classes, are reported for the first time by gas chromatography coupled to Fourier transform Orbitrap mass spectrometry and chemical ionization.
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Affiliation(s)
- Nathália de Aguiar Porto
- Institute of Chemistry, University of Campinas, 270 Monteiro Lobato, Campinas, São Paulo 13083-862 Brazil
| | - Juliana Crucello
- Institute of Chemistry, University of Campinas, 270 Monteiro Lobato, Campinas, São Paulo 13083-862 Brazil
| | - Roselaine Facanali
- Institute of Chemistry, University of Campinas, 270 Monteiro Lobato, Campinas, São Paulo 13083-862 Brazil
| | - Iris Medeiros Junior
- Leopoldo Américo Miguez de Mello Research and Development Center, Petrobras, Rio de Janeiro 20031-912 Brazil
| | - Rogerio Mesquita Carvalho
- Leopoldo Américo Miguez de Mello Research and Development Center, Petrobras, Rio de Janeiro 20031-912 Brazil
| | - Leandro Wang Hantao
- Institute of Chemistry, University of Campinas, 270 Monteiro Lobato, Campinas, São Paulo 13083-862 Brazil.
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5
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Analytical challenges and recent advances in the identification and quantitation of extractables and leachables in pharmaceutical and medical products. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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6
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Development and validation of an LC-HRMS method for the determination of pyrrolizidine alkaloids and quinolones in honey employing a simple alkaline sample dilution. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2021. [DOI: 10.1007/s11694-021-01048-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Beck S. Fragmentation behavior of EDTA complexes under different activation conditions. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4775. [PMID: 34180100 DOI: 10.1002/jms.4775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Ethylenediaminetetraacetic acid (EDTA) is an aminopolycarboxylic acid and complexation agent that is able to bind a large variety of metals. The formation of highly stable metal-EDTA complexes is generally very quick. This has led to the use of EDTA in a variety of applications, including food, medical, and household applications. In the current study, we have investigated the fragmentation behavior of EDTA and various metal complexes under collision-induced dissociation (CID), infrared-multiphoton dissociation (IRMPD), and higher-energy collisional dissociation (HCD) activation conditions. Both, positive and negative mode electrospray ionization (ESI) were applied. The metals used to complex with EDTA ranged from alkaline earth metals, such as sodium and cesium, via calcium, nickel, zinc, aluminum, copper, iron, and indium to yttrium and several lanthanides. Furthermore, the protonated and deprotonated species of EDTA, as well as disodium and trisodium species, have been subjected to fragmentation. The results show that characteristic fragmentations were obtained for EDTA and the metal complexes under the investigated conditions. The use of an ion cyclotron resonance (ICR) and an Orbitrap mass spectrometer, as high resolution-accurate mass instruments, allowed the assignment of elemental compositions undoubtedly for the vast majority of fragments. Certain trends were observed that trend correlated with the size of the metal and the location within the periodic table.
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Affiliation(s)
- Sebastian Beck
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
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8
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Banerjee S, Joshi U, Singh A, Saharan VA. Lipids for Taste masking and Taste assessment in pharmaceutical formulations. Chem Phys Lipids 2020; 235:105031. [PMID: 33352198 DOI: 10.1016/j.chemphyslip.2020.105031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/30/2020] [Accepted: 12/16/2020] [Indexed: 12/15/2022]
Abstract
Pharmaceutical products often have drawbacks of unacceptable taste and palatability which makes it quite difficult for oral administration to some special populations like pediatrics and geriatrics. To curb this issue different approaches like coating, granulation, extrusion, inclusion complexation, ion-exchange resins, etc for taste masking are employed and among them use of lipids have drawn special attention of researchers. Lipids have a lower melting point which is ideal for incorporating drugs in some of these methods like hot-melt extrusion, melt granulation, spray drying/congealing and emulsification. Lipids play a significant role as a barrier to sustain the release of drugs and biocompatible nature of lipids increases their acceptability by the human body. Further, lipids provide vast opportunities of altering pharmacokinetics of the active ingredients by modulating release profiles. In taste sensors, also known as electronic tongue or e-tongue, lipids are used in preparing taste sensing membranes which are subsequently used in preparing taste sensors. Lipid membrane taste sensors have been widely used in assessing taste and palatability of pharmaceutical and food formulations. This review explores applications of lipids in masking the bitter taste in pharmaceutical formulations and significant role of lipids in evaluation of taste and palatability.
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Affiliation(s)
- Surojit Banerjee
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, Uttarakhand, 248001, India
| | - Ujjwal Joshi
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, Uttarakhand, 248001, India
| | - Anupama Singh
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, Uttarakhand, 248001, India
| | - Vikas Anand Saharan
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, Uttarakhand, 248001, India.
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9
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Yang Y, Wang Y, Yao D, Zhao S, Yang S, Ji D, Sun J, Wang Y, Liu Z, Hu B, Zhang R, Wang Y. Significant decreases in the volatile organic compound concentration, atmospheric oxidation capacity and photochemical reactivity during the National Day holiday over a suburban site in the North China Plain. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114657. [PMID: 33618483 DOI: 10.1016/j.envpol.2020.114657] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/25/2020] [Accepted: 04/22/2020] [Indexed: 05/13/2023]
Abstract
To what extent anthropogenic emissions could influence volatile organic compound (VOCs) concentrations and related atmospheric reactivity is still poorly understood. China's 70th National Day holidays, during which anthropogenic emissions were significantly reduced to ensure good air quality on Anniversary Day, provides a unique opportunity to investigate these processes. Atmospheric oxidation capacity (AOC), OH reactivity, secondary transformation, O3 formation and VOCs-PM2.5 sensitivity are evaluated based on parameterization methods and simultaneous measurements of VOCs, O3, NOx, CO, SO2, PM2.5, JO1D, JNO2, JNO3 carried out at a suburban site between Beijing and Tianjin before, during, and after the National Day holiday 2019. During the National Day holidays, the AOC, OH reactivity, O3 formation potential (OFP) and secondary organic aerosol formation potential (SOAP) were 1.6 × 107 molecules cm-3 s-1, 41.8 s-1, 299.2 μg cm-3 and 1471.8 μg cm-3, respectively, which were 42%, 29%, 47% and 42% lower than pre-National Day values and -12%, 42%, 36% and 42% lower than post-National Day values, respectively. Reactions involving OH radicals dominated the AOC during the day, but OH radicals and O3 reactions at night. Alkanes (the degree of unsaturation = 0, (D, Equation (1)) accounted for the largest contributions to the total VOCs concentration, oxygenated VOCs (OVOCs; D ≤ 1) to OH reactivity and OFP, and aromatics (D = 4) to the SOAP. O3 production was identified as VOCs-limited by VOCs (ppbC)/NOx (ppbv) ratios during the sampling campaign, with greater VOCs limitation during post- National Day and more-aged air masses during the National Day. The VOCs-sensitivity coefficient (VOCs-S) suggested that VOCs were more sensitive to PM2.5 in low-pollution domains and during the National Day holiday. This study emphasizes the importance of not only the abundance, reactivity, and secondary transformation of VOCs but also the effects of VOCs on PM2.5 for the development of effective control strategies to minimize O3 and PM2.5 pollution.
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Affiliation(s)
- Yuan Yang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yonghong Wang
- Institute for Atmospheric and Earth System Research / Physics, Faculty of Science, P.O.Box 64, 00014, University of Helsinki, Helsinki, Finland.
| | - Dan Yao
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Shuman Zhao
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuanghong Yang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China; Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Dongsheng Ji
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Jie Sun
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yinghong Wang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Zirui Liu
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Bo Hu
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Renjian Zhang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yuesi Wang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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10
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Prothmann J, Spégel P, Sandahl M, Turner C. Identification of lignin oligomers in Kraft lignin using ultra-high-performance liquid chromatography/high-resolution multiple-stage tandem mass spectrometry (UHPLC/HRMS n). Anal Bioanal Chem 2018; 410:7803-7814. [PMID: 30306235 PMCID: PMC6244760 DOI: 10.1007/s00216-018-1400-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/13/2018] [Accepted: 09/24/2018] [Indexed: 11/29/2022]
Abstract
Kraft lignin is the main source of technically produced lignin. For the development of valuable products based on Kraft lignin, its molecular structure is important. However, the chemical composition of Kraft lignin is still not well known. So far, the analysis of Kraft lignin by mass spectrometry (MS) has been mainly focused on monomeric compounds. Previous MS studies on lignin oligomers (LOs) considered only synthesised LO standards and/or lignins produced by processes other than the Kraft process. Furthermore, published MS methods suffer from using high resolution only in the MS1 stage in multiple-stage tandem MS methods. A high resolution in all MSn stages would provide more detailed information about LO fragmentation pathways. Since lignin samples are complex mixtures of a large number of similar phenolic compounds, the selection of tentative LOs in the MS data is challenging. In this study, we present a method for non-targeted analysis of LOs in Kraft lignin using ultra-high-performance liquid chromatography/high-resolution multiple-stage tandem mass spectrometry (UHPLC/HRMSn). A pre-selection strategy for LOs has been established based on a data-dependent neutral loss MS3 method in combination with a principal component analysis-quadratic discriminant analysis classification model (PCA-QDA). The method was optimised using a design of experiments (DOE) approach. The developed approach improved the pre-selection of tentative LOs in complex mixtures. From 587 detected peaks, 36 peaks were identified as LOs. ᅟ ![]()
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Affiliation(s)
- Jens Prothmann
- Department of Chemistry, Centre for Analysis and Synthesis, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Peter Spégel
- Department of Chemistry, Centre for Analysis and Synthesis, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Margareta Sandahl
- Department of Chemistry, Centre for Analysis and Synthesis, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Charlotta Turner
- Department of Chemistry, Centre for Analysis and Synthesis, Lund University, P.O. Box 124, 22100, Lund, Sweden.
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11
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Ma X, Coleman ML, Waldbauer JR. Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria. Environ Microbiol 2018; 20:3001-3011. [PMID: 30047191 DOI: 10.1111/1462-2920.14338] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 11/29/2022]
Abstract
Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.
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Affiliation(s)
- Xiufeng Ma
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
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12
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Azad I, Nasibullah M, Khan T, Hassan F, Akhter Y. Exploring the novel heterocyclic derivatives as lead molecules for design and development of potent anticancer agents. J Mol Graph Model 2018; 81:211-228. [PMID: 29609141 DOI: 10.1016/j.jmgm.2018.02.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/22/2018] [Accepted: 02/19/2018] [Indexed: 12/22/2022]
Abstract
This paper deals with in silico evaluation of newly proposed heterocyclic derivatives in search of potential anticancer activity. Best possible drug candidates have been proposed using a rational approach employing a pipeline of computational techniques namely MetaPrint2D prediction, molinspiration, cheminformatics, Osiris Data warrior, AutoDock and iGEMDOCK. Lazar toxicity prediction, AdmetSAR predictions, and targeted docking studies were also performed. 27 heterocyclic derivatives were selected for bioactivity prediction and drug likeness score on the basis of Lipinski's rule, Viber rule, Ghose filter, leadlikeness and Pan Assay Interference Compounds (PAINS) rule. Bufuralol, Sunitinib, and Doxorubicin were selected as reference standard drug for the comparison of molecular descriptors and docking. Bufuralol is a known non-selective adreno-receptor blocking agent. Studies showed that beta blockers are also used against different types of cancers. Sunitinib is well known Food and Drug administration (FDA) approved pyrrole containing tyrosine kinase inhibitor and our proposed molecules possess similarities with both drug and doxorubicin is another moiety having anticancer activity. All heterocyclic derivatives were found to obey the drug filters except standard drug Doxorubicin. Bioactivity score of the compounds was predicted for drug targets including enzymes, nuclear receptors, kinase inhibitors, G protein-coupled receptor (GPCR) ligands and ion channel modulators. Absorption, distribution, metabolism and toxicity (ADMET) prediction of all proposed compound showed good Blood-brain barrier (BBB) penetration, Human intestinal absorption (HIA), Caco-2 cell permeability except compound-11 and was found to have no AdmetSAR toxicity as well as carcinogenic effect. Compounds 1-9 were slightly mutagenic while compound 2, 11, 20 and 21 showed carcinogenic effect according to Lazar toxicity prediction. Rests of the compounds were predicted to have no side effect. Molecular docking was performed with vascular endothelial growth factor receptor-2(VEGFR2) and glutathione S-transferase-1 (GSTP1) because both are common cancer causing proteins. Sunitinib and Doxorubicin possess great affinity to inhibit these cancers causing protein. Self-organizing map (SOM) was used to depict data in a simple 2D presentation. Our studies justify that good oral bioavailability and therapeutic efficacy of 10, 12-19 and 22-27 compounds can be considered as potential anticancer agents.
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Affiliation(s)
- Iqbal Azad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow 226026, UP, India
| | - Malik Nasibullah
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow 226026, UP, India.
| | - Tahmeena Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow 226026, UP, India; Department of Chemistry, Isabella Thoburn College, University of Lucknow, Lucknow 226007, UP, India
| | - Firoj Hassan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow 226026, UP, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, VidyaVihar, Raebareli Road, Lucknow, UP 2260025, India
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Achinivu EC. Protic Ionic Liquids for Lignin Extraction-A Lignin Characterization Study. Int J Mol Sci 2018; 19:E428. [PMID: 29385108 PMCID: PMC5855650 DOI: 10.3390/ijms19020428] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 11/17/2022] Open
Abstract
Protic ionic liquids (PILs) have been established as effective solvents for the selective extraction and recovery of lignin from lignocellulosic biomass. In this study, we utilize extensive analytical techniques to characterize the PIL-extracted lignins to (1) expand on the physical/chemical structure, and to (2) develop a better understanding of the mechanism behind the lignin dissolution process. The PIL-lignins were characterized using elemental and FT-IR analyses, alongside molecular weight distribution and chemical modeling via MM2. For the more ionic pyrrolidinium acetate ([Pyrr][Ac]), there is an increase in the fragmentation of lignin, resulting in lignin with a smaller average molecular weight and a more uniform dispersity. This lends better understanding to previous findings indicating that higher ionicity in a PIL leads to increased lignin extraction.
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Affiliation(s)
- Ezinne C Achinivu
- Ionic Liquids & Electrolytes for Energy Technologies (ILEET) Laboratory, Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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14
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Pardakhti M, Moharreri E, Wanik D, Suib SL, Srivastava R. Machine Learning Using Combined Structural and Chemical Descriptors for Prediction of Methane Adsorption Performance of Metal Organic Frameworks (MOFs). ACS COMBINATORIAL SCIENCE 2017; 19:640-645. [PMID: 28800219 DOI: 10.1021/acscombsci.7b00056] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using molecular simulation for adsorbent screening is computationally expensive and thus prohibitive to materials discovery. Machine learning (ML) algorithms trained on fundamental material properties can potentially provide quick and accurate methods for screening purposes. Prior efforts have focused on structural descriptors for use with ML. In this work, the use of chemical descriptors, in addition to structural descriptors, was introduced for adsorption analysis. Evaluation of structural and chemical descriptors coupled with various ML algorithms, including decision tree, Poisson regression, support vector machine and random forest, were carried out to predict methane uptake on hypothetical metal organic frameworks. To highlight their predictive capabilities, ML models were trained on 8% of a data set consisting of 130,398 MOFs and then tested on the remaining 92% to predict methane adsorption capacities. When structural and chemical descriptors were jointly used as ML input, the random forest model with 10-fold cross validation proved to be superior to the other ML approaches, with an R2 of 0.98 and a mean absolute percent error of about 7%. The training and prediction using the random forest algorithm for adsorption capacity estimation of all 130,398 MOFs took approximately 2 h on a single personal computer, several orders of magnitude faster than actual molecular simulations on high-performance computing clusters.
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Affiliation(s)
- Maryam Pardakhti
- Department
of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ehsan Moharreri
- Institute
of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - David Wanik
- Department
of Civil and Environmental Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Steven L. Suib
- Institute
of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ranjan Srivastava
- Department
of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
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15
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Farenc M, Witt M, Craven K, Barrère-Mangote C, Afonso C, Giusti P. Characterization of Polyolefin Pyrolysis Species Produced Under Ambient Conditions by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Ion Mobility-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:507-514. [PMID: 28050872 DOI: 10.1007/s13361-016-1572-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/25/2016] [Accepted: 12/03/2016] [Indexed: 06/06/2023]
Abstract
Polyolefins such as polyethylene (PE) and polypropylene (PP) are often characterized from their pyrolysis products by Py-MS. Nowadays the development of plasma-based direct probe atmospheric pressure sources allow the direct analysis of these polymers. These sources operate at atmospheric pressure, which implies a limited control of the ionization conditions. It was shown that side reactions could occur with species present in air, such as O2, which may lead to the formation of oxidized compounds. In this work, ion mobility-mass spectrometry (IM-MS) and Fourier transform ion cyclotron resonance mass spectrometry (FTICR) were used for the exhaustive characterization of the PP and PE pyrolysis ions produced using plasma-based atmospheric pressure ion sources. Both PP and PE yielded distributions of pyrolysis products presenting different amounts of unsaturation but also different numbers of oxygen atoms. In addition, the ions produced from PP presented a lower collision cross-section (CCS) than those produced from PE. In the same way, both PP and PE present repeated patterns separated by 14 m/z in the bidimensional drift time versus m/z plots. Within these plots, several trend lines can be evidenced, which are specific of each polymer investigated. Differences were observed between isotactic and atactic samples concerning the pyrolysis profile relative abundance and collision cross-section. Graphical Abstract ᅟ.
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Affiliation(s)
- Mathilde Farenc
- TOTAL Refining and Chemicals, TRTG, Gonfreville l'Orcher, France
- INSA Rouen, UNIROUEN, CNRS, COBRA, Normandie University, 76000, Rouen, France
- TOTAL RC - CNRS Joint Laboratory C2MC: Complex Matrices Molecular Characterization, Pau, France
| | - Matthias Witt
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359, Bremen, Germany
| | - Kirsten Craven
- Waters Corporation, Stamford Avenue, Wilmslow, SK9 4AX, UK
| | - Caroline Barrère-Mangote
- TOTAL Refining and Chemicals, TRTG, Gonfreville l'Orcher, France
- TOTAL RC - CNRS Joint Laboratory C2MC: Complex Matrices Molecular Characterization, Pau, France
| | - Carlos Afonso
- INSA Rouen, UNIROUEN, CNRS, COBRA, Normandie University, 76000, Rouen, France.
- TOTAL RC - CNRS Joint Laboratory C2MC: Complex Matrices Molecular Characterization, Pau, France.
| | - Pierre Giusti
- TOTAL Refining and Chemicals, TRTG, Gonfreville l'Orcher, France
- TOTAL RC - CNRS Joint Laboratory C2MC: Complex Matrices Molecular Characterization, Pau, France
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16
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Wisnewski AV, Liu J, Nassar AF. In vitro cleavage of diisocyanate-glutathione conjugates by human gamma-glutamyl transpeptidase-1. Xenobiotica 2015; 46:726-32. [PMID: 26678254 DOI: 10.3109/00498254.2015.1118576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Isocyanates differ from many other xenobiotics in their ability to form S-linked conjugates with glutathione (GSH) through direct nucleophilic addition reactions (e.g. without enzymatic "preactivation" and/or transferase activity), potentially predisposing them to metabolism via the mercapturic acid pathway. In vivo, mono-isocyanates are metabolized via the mercapturic acid pathway and excreted as N-acetylated cysteine conjugates, however, the metabolism of di-isocyanates remains unclear. We assessed the ability of purified human gamma-glutamyl transpeptidase-1 (GGT-1), a primary enzyme of the mercapturic acid pathway, to cleave S-linked GSH conjugates of 4,4'-methylene diphenyl diisocyanate (MDI) and 1,6-hexamethylene diisocyanate (HDI), two widely used industrial chemicals. A combination of liquid chromatography (LC), tandem mass spectrometry (MS/MS) and hydrogen-deuterium exchange studies confirmed GGT-1 mediated formation of the 607.2 and 525.2 m/z (M + H)(+) ions corresponding to bis(cys-gly)-MDI and bis(cys-gly)-HDI, respectively, the cleavage products expected from the corresponding bis(GSH)-diisocyanate conjugates. Additional intermediate metabolites and mono(cys-gly)-conjugates with partially hydrolyzed diisocyanate were also observed. Consistent with GGT enzyme kinetics, metabolism proceeded more rapidly under conditions that favored transpeptidation versus hydrolytic mechanisms of cleavage. Together the data demonstrate the capacity of human GGT-1 to cleave GSH conjugates of both aromatic and aliphatic diisocyanates, suggesting a potential role in their metabolism.
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Affiliation(s)
- Adam V Wisnewski
- a Department of Medicine , Yale University School of Medicine , New Haven , CT , USA
| | - Jian Liu
- a Department of Medicine , Yale University School of Medicine , New Haven , CT , USA
| | - Ala F Nassar
- a Department of Medicine , Yale University School of Medicine , New Haven , CT , USA
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17
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Junza A, Barbosa S, Codony MR, Jubert A, Barbosa J, Barrón D. Identification of metabolites and thermal transformation products of quinolones in raw cow's milk by liquid chromatography coupled to high-resolution mass spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:2008-2021. [PMID: 24499328 DOI: 10.1021/jf405554z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The presence of residues of antibiotics, metabolites, and thermal transformation products (TPs), produced during thermal treatment to eliminate pathogenic microorganisms in milk, could represent a risk for people. Cow's milk samples spiked with enrofloxacin (ENR), ciprofloxacin (CIP), difloxacin (DIF), and sarafloxacin (SAR) and milk samples from cows medicated with ENR were submitted to several thermal treatments. The milk samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to find and identify TPs and metabolites. In this work, 27 TPs of 4 quinolones and 24 metabolites of ENR were found. Some of these compounds had been reported previously, but others were characterized for the first time, including lactose-conjugated CIP, the formamidation reaction for CIP and SAR, and hydroxylation or ketone formation to produce three different isomers for all quinolones studied.
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Affiliation(s)
- Alexandra Junza
- Departament de Quı́mica Analı́tica, Universitat de Barcelona , Campus de l'Alimentació de Torribera, Avinguda Prat de la Riba 171, 08921 Sta. Coloma de Gramanet, Barcelona, Spain
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18
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Critical practical aspects in the application of liquid chromatography–mass spectrometric studies for the characterization of impurities and degradation products. J Pharm Biomed Anal 2014; 87:191-217. [DOI: 10.1016/j.jpba.2013.04.027] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 04/18/2013] [Indexed: 11/18/2022]
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19
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Lobodin VV, Marshall AG, Hsu CS. Compositional Space Boundaries for Organic Compounds. Anal Chem 2012; 84:3410-6. [DOI: 10.1021/ac300244f] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Vladislav V. Lobodin
- Ion Cyclotron Resonance Program,
National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive,
Tallahassee, Florida 32310-4005, United States
| | - Alan G. Marshall
- Ion Cyclotron Resonance Program,
National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive,
Tallahassee, Florida 32310-4005, United States
- Department of Chemistry and
Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee,
Florida 32306, United States
| | - Chang Samuel Hsu
- Future Fuels Institute, Florida
State University, Tallahassee, Florida 32310, United States
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20
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Eckert PA, Roach PJ, Laskin A, Laskin J. Chemical Characterization of Crude Petroleum Using Nanospray Desorption Electrospray Ionization Coupled with High-Resolution Mass Spectrometry. Anal Chem 2012; 84:1517-25. [DOI: 10.1021/ac202801g] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Peter A. Eckert
- William R. Wiley Environmental and Molecular Sciences Laboratory
| | - Patrick J. Roach
- Chemical and Materials Sciences
Division, Pacific Northwest National Laboratory, P.O. Box 999, K8-88, Richland, Washington 99352, United States
| | - Alexander Laskin
- William R. Wiley Environmental and Molecular Sciences Laboratory
| | - Julia Laskin
- Chemical and Materials Sciences
Division, Pacific Northwest National Laboratory, P.O. Box 999, K8-88, Richland, Washington 99352, United States
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21
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Kind T, Fiehn O. Advances in structure elucidation of small molecules using mass spectrometry. BIOANALYTICAL REVIEWS 2010; 2:23-60. [PMID: 21289855 PMCID: PMC3015162 DOI: 10.1007/s12566-010-0015-9] [Citation(s) in RCA: 298] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 08/03/2010] [Indexed: 12/22/2022]
Abstract
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Kind
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
| | - Oliver Fiehn
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
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22
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Marcaurelle LA, Comer E, Dandapani S, Duvall JR, Gerard B, Kesavan S, Lee MD, Liu H, Lowe JT, Marie JC, Mulrooney CA, Pandya BA, Rowley A, Ryba TD, Suh BC, Wei J, Young DW, Akella LB, Ross NT, Zhang YL, Fass DM, Reis SA, Zhao WN, Haggarty SJ, Palmer M, Foley MA. An aldol-based build/couple/pair strategy for the synthesis of medium- and large-sized rings: discovery of macrocyclic histone deacetylase inhibitors. J Am Chem Soc 2010; 132:16962-76. [PMID: 21067169 DOI: 10.1021/ja105119r] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An aldol-based build/couple/pair (B/C/P) strategy was applied to generate a collection of stereochemically and skeletally diverse small molecules. In the build phase, a series of asymmetric syn- and anti-aldol reactions were performed to produce four stereoisomers of a Boc-protected γ-amino acid. In addition, both stereoisomers of O-PMB-protected alaninol were generated to provide a chiral amine coupling partner. In the couple step, eight stereoisomeric amides were synthesized by coupling the chiral acid and amine building blocks. The amides were subsequently reduced to generate the corresponding secondary amines. In the pair phase, three different reactions were employed to enable intramolecular ring-forming processes: nucleophilic aromatic substitution (S(N)Ar), Huisgen [3+2] cycloaddition, and ring-closing metathesis (RCM). Despite some stereochemical dependencies, the ring-forming reactions were optimized to proceed with good to excellent yields, providing a variety of skeletons ranging in size from 8- to 14-membered rings. Scaffolds resulting from the RCM pairing reaction were diversified on the solid phase to yield a 14 400-membered library of macrolactams. Screening of this library led to the discovery of a novel class of histone deacetylase inhibitors, which display mixed enzyme inhibition, and led to increased levels of acetylation in a primary mouse neuron culture. The development of stereo-structure/activity relationships was made possible by screening all 16 stereoisomers of the macrolactams produced through the aldol-based B/C/P strategy.
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Affiliation(s)
- Lisa A Marcaurelle
- Chemical Biology Platform, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States.
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23
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Lovering F, Bikker J, Humblet C. Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success. J Med Chem 2009; 52:6752-6. [PMID: 19827778 DOI: 10.1021/jm901241e] [Citation(s) in RCA: 2419] [Impact Index Per Article: 161.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Jack Bikker
- 401 North Middletown Road, Pearl River, New York 10965
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24
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Kwan EE, Huang SG. Structural Elucidation with NMR Spectroscopy: Practical Strategies for Organic Chemists. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700966] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Eugene E. Kwan
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, Fax: +1‐617‐495‐1460
| | - Shaw G. Huang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, Fax: +1‐617‐495‐1460
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25
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Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 2007; 8:105. [PMID: 17389044 PMCID: PMC1851972 DOI: 10.1186/1471-2105-8-105] [Citation(s) in RCA: 700] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2006] [Accepted: 03/27/2007] [Indexed: 11/25/2022] Open
Abstract
Background Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas. Results An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries. Conclusion The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65–81%. Corresponding software and supplemental data are available for downloads from the authors' website.
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26
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Meija J. Mathematical tools in analytical mass spectrometry. Anal Bioanal Chem 2006; 385:486-99. [PMID: 16514517 DOI: 10.1007/s00216-006-0298-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 12/14/2005] [Accepted: 01/05/2006] [Indexed: 10/25/2022]
Abstract
Over the last few decades, mass spectrometry has become a powerful tool for exploring various aspects of molecular processes occurring in biological systems. Such exploration is leading to a greater understanding of various complex life processes; unraveling these processes poses the greatest challenge to contemporary bioscience. With due respect to sample preparation, data analysis is rapidly becoming a major obstacle to the conversion of experimental knowledge into valid conclusions. It is interesting to note that many problems related to mass spectrometry can be solved using techniques from computer science, graph theory and discrete mathematics. The aim of this manuscript is to recollect several essays that demonstrate the power and the need to apply such skills to mass spectrometry data interpretation. Special attention is paid to situations where traditional chemical analysis reaches its limits but mathematical reasoning can still allow us to reach valid conclusions.
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Affiliation(s)
- Juris Meija
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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27
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Feher M, Schmidt JM. Property distributions: differences between drugs, natural products, and molecules from combinatorial chemistry. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2003; 43:218-27. [PMID: 12546556 DOI: 10.1021/ci0200467] [Citation(s) in RCA: 574] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The differences between three different compound classes, natural products, molecules from combinatorial synthesis, and drug molecules, were investigated. The major structural differences between natural and combinatorial compounds originate mainly from properties introduced to make combinatorial synthesis more efficient. These include the number of chiral centers, the prevalence of aromatic rings, the introduction of complex ring systems, and the degree of the saturation of the molecule as well as the number and ratios of different heteroatoms. As drug molecules derive from both natural and synthetic sources, they cover a joint area in property space of natural and combinatorial compounds. A PCA-based scheme is presented that differentiates the three classes of compounds. It is suggested that by mimicking certain distribution properties of natural compounds, combinatorial products might be made that are substantially more diverse and have greater biological relevance.
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Affiliation(s)
- Miklos Feher
- SignalGene Inc., 335 Laird Road, Unit 2, Guelph, Ontario, N1G 4P7, Canada.
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