1
|
Kong F, Keshet U, Shen T, Rodriguez E, Fiehn O. LibGen: Generating High Quality Spectral Libraries of Natural Products for EAD-, UVPD-, and HCD-High Resolution Mass Spectrometers. Anal Chem 2023; 95:16810-16818. [PMID: 37939222 DOI: 10.1021/acs.analchem.3c02263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Compound annotation using spectral-matching algorithms is vital for (MS/MS)-based metabolomics research, but is hindered by the lack of high-quality reference MS/MS library spectra. Finding and removing errors from libraries, including noise ions, is mostly done manually. This process is both error-prone and time-consuming. To address these challenges, we have developed an automated library curation pipeline, LibGen, to universally build novel spectral libraries. This pipeline corrects mass errors, denoises spectra by subformula assignments, and performs quality control of the reference spectra by calculating explained intensity and spectral entropy. We employed LibGen to generate three high-quality libraries with chemical standards of 2241 natural products. To this end, we used an IQ-X orbital ion trap mass spectrometer to generate 1947 classic high-energy collision dissociation spectra (HCD) as well as 1093 ultraviolet-photodissociation (UVPD) mass spectra. The third library was generated by an electron-activated collision dissociation (EAD) 7600 ZenoTOF mass spectrometer yielding 3244 MS/MS spectra. The natural compounds covered 140 chemical classes from prenol lipids to benzypyrans with >97% of the compounds showing <0.2 Tanimoto-similarity, demonstrating a very high structural variance. Mass spectra showed much higher information content for both UVPD- and EAD-mass spectra compared to classic HCD spectra when using spectral entropy calculations. We validated the denoising algorithm by acquiring MS/MS spectra at high concentration and at 13-fold diluted chemical standards. At low concentrations, a higher proportion of spectra showed apparent fragment ions that could not be explained by subformula losses of the parent molecule. When more than 10% of the total intensity of MS/MS fragments was regarded as noise ions, spectra were considered as low quality and were not included in the libraries. As the overall process is fully automated, LibGen can be utilized by all researchers who create or curate mass spectral libraries. The libraries we created here are publicly available at MassBank.us.
Collapse
Affiliation(s)
- Fanzhou Kong
- Chemistry Department, One Shields Avenue, University of California-Davis, Davis, California 95616, United States
- West Coast Metabolomics Center, University of California-Davis, Davis, California 95616, United States
| | - Uri Keshet
- West Coast Metabolomics Center, University of California-Davis, Davis, California 95616, United States
| | - Tong Shen
- West Coast Metabolomics Center, University of California-Davis, Davis, California 95616, United States
| | - Elys Rodriguez
- Chemistry Department, One Shields Avenue, University of California-Davis, Davis, California 95616, United States
- West Coast Metabolomics Center, University of California-Davis, Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California-Davis, Davis, California 95616, United States
| |
Collapse
|
2
|
Cernuto A, Lopes A, Romanzin C, Cunha de Miranda B, Ascenzi D, Tosi P, Tonachini G, Maranzana A, Polášek M, Žabka J, Alcaraz C. Effects of collision energy and vibrational excitation of CH 3+ cations on its reactivity with hydrocarbons: But-2-yne CH 3CCCH 3 as reagent partner. J Chem Phys 2017; 147:154302. [PMID: 29055295 DOI: 10.1063/1.4990514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The methyl carbocation is ubiquitous in gaseous environments, such as planetary ionospheres, cometary comae, and the interstellar medium, as well as combustion systems and plasma setups for technological applications. Here we report on a joint experimental and theoretical study on the mechanism of the reaction CH3+ + CH3CCCH3 (but-2-yne, also known as dimethylacetylene), by combining guided ion beam mass spectrometry experiments with ab initio calculations of the potential energy hypersurface. Such a reaction is relevant in understanding the chemical evolution of Saturn's largest satellite, Titan. Two complementary setups have been used: in one case, methyl cations are generated via electron ionization, while in the other case, direct vacuum ultraviolet photoionization with synchrotron radiation of methyl radicals is used to study internal energy effects on the reactivity. Absolute reactive cross sections have been measured as a function of collision energy, and product branching ratios have been derived. The two most abundant products result from electron and hydride transfer, occurring via direct and barrierless mechanisms, while other channels are initiated by the electrophilic addition of the methyl cation to the triple bond of but-2-yne. Among the minor channels, special relevance is placed on the formation of C5H7+, stemming from H2 loss from the addition complex. This is the only observed condensation product with the formation of new C-C bonds, and it might represent a viable pathway for the synthesis of complex organic species in astronomical environments and laboratory plasmas.
Collapse
Affiliation(s)
- Andrea Cernuto
- Department of Physics, University of Trento, Via Sommarive 14, Trento I-38123, Italy
| | - Allan Lopes
- Laboratoire de Chimie Physique, Bât. 350, UMR 8000, CNRS-Univ. Paris-Sud 11 and Paris Saclay, Centre Universitaire Paris-Sud, 91405 Orsay Cedex, France
| | - Claire Romanzin
- Laboratoire de Chimie Physique, Bât. 350, UMR 8000, CNRS-Univ. Paris-Sud 11 and Paris Saclay, Centre Universitaire Paris-Sud, 91405 Orsay Cedex, France
| | | | - Daniela Ascenzi
- Department of Physics, University of Trento, Via Sommarive 14, Trento I-38123, Italy
| | - Paolo Tosi
- Department of Physics, University of Trento, Via Sommarive 14, Trento I-38123, Italy
| | - Glauco Tonachini
- Department of Chemistry, University of Torino, Via Pietro Giuria, 7, Torino I-10125, Italy
| | - Andrea Maranzana
- Department of Chemistry, University of Torino, Via Pietro Giuria, 7, Torino I-10125, Italy
| | - Miroslav Polášek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Jan Žabka
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Christian Alcaraz
- Laboratoire de Chimie Physique, Bât. 350, UMR 8000, CNRS-Univ. Paris-Sud 11 and Paris Saclay, Centre Universitaire Paris-Sud, 91405 Orsay Cedex, France
| |
Collapse
|
3
|
Polášek M, Zins EL, Alcaraz C, Žabka J, Křížová V, Giacomozzi L, Tosi P, Ascenzi D. Selective Generation of the Radical Cation Isomers [CH3CN](•+) and [CH2CNH](•+) via VUV Photoionization of Different Neutral Precursors and Their Reactivity with C2H4. J Phys Chem A 2016; 120:5041-52. [PMID: 26890990 DOI: 10.1021/acs.jpca.5b12757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental and theoretical studies have been carried out to demonstrate the selective generation of two different C2H3N(+) isomers, namely, the acetonitrile [CH3CN](•+) and the ketenimine [CH2CNH](•+) radical cations. Photoionization and dissociative photoionization experiments from different neutral precursors (acetonitrile and butanenitrile) have been performed using vacuum ultraviolet (VUV) synchrotron radiation in the 10-15 eV energy range, delivered by the DESIRS beamline at the SOLEIL storage ring. For butanenitrile (CH3CH2CH2CN) an experimental ionization threshold of 11.29 ± 0.05 eV is obtained, whereas the appearance energy for the formation of [CH2CNH](•+) fragments is 11.52 ± 0.05 eV. Experimental findings are fully supported by theoretical calculations at the G4 level of theory (ZPVE corrected energies at 0 K), giving a value of 11.33 eV for the adiabatic ionization energy of butanenitrile and an exothermicity of 0.49 for fragmentation into [CH2CNH](•+) plus C2H4, hampered by an energy barrier of 0.29 eV. The energy difference between [CH3CN](•+) and [CH2CNH](•+) is 2.28 eV (with the latter being the lowest energy isomer), and the isomerization barrier is 0.84 eV. Reactive monitoring experiments of the [CH3CN](•+) and [CH2CNH](•+) isomers with C2H4 have been performed using the CERISES guided ion beam tandem mass spectrometer and exploiting the selectivity of ethylene that gives exothermic charge exchange and proton transfer reactions with [CH3CN](•+) but not with [CH2CNH](•+) isomers. In addition, minor reactive channels are observed leading to the formation of new C-C bonds upon reaction of [CH3CN](•+) with C2H4, and their astrochemical implications are briefly discussed.
Collapse
Affiliation(s)
- Miroslav Polášek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 2155/3, 18223 Prague 8, Czech Republic
| | - Emilie-Laure Zins
- Sorbonne Universités, UPMC Univ. Paris 06, MONARIS, UMR 8233, Université Pierre et Marie Curie , 4 Place Jussieu, case courrier 49, F-75252 Paris Cedex 05, France
| | - Christian Alcaraz
- Laboratoire de Chimie Physique, Bât. 350, UMR 8000, CNRS-Univ. Paris-Sud & Paris-Saclay , Centre Universitaire Paris-Sud, 91405 Orsay Cedex, France.,Synchrotron SOLEIL , L'Orme des Merisiers, Saint-Aubin - BP 48, 91192 Gif-sur-Yvette, France
| | - Ján Žabka
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 2155/3, 18223 Prague 8, Czech Republic
| | - Věra Křížová
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 2155/3, 18223 Prague 8, Czech Republic
| | - Linda Giacomozzi
- Department of Physics, University of Trento , Via Sommarive 14, 38123 Povo, Italy
| | - Paolo Tosi
- Department of Physics, University of Trento , Via Sommarive 14, 38123 Povo, Italy
| | - Daniela Ascenzi
- Department of Physics, University of Trento , Via Sommarive 14, 38123 Povo, Italy
| |
Collapse
|
4
|
Jašík J, Gerlich D, Roithová J. Two-Color Infrared Predissociation Spectroscopy of C6H62+ Isomers Using Helium Tagging. J Phys Chem A 2014; 119:2532-42. [DOI: 10.1021/jp5088064] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juraj Jašík
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
| | - Dieter Gerlich
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
- Department
of Physics, University of Technology, 09107 Chemnitz, Germany
| | - Jana Roithová
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
| |
Collapse
|
5
|
Heift D, Benkő Z, Grützmacher H. Redox-Triggered Reversible Interconversion of a Monocyclic and a Bicyclic Phosphorus Heterocycle. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
6
|
Redox-Triggered Reversible Interconversion of a Monocyclic and a Bicyclic Phosphorus Heterocycle. Angew Chem Int Ed Engl 2014; 53:6757-61. [DOI: 10.1002/anie.201402884] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/18/2014] [Indexed: 11/07/2022]
|
7
|
Schymanski EL, Neumann S. The Critical Assessment of Small Molecule Identification (CASMI): Challenges and Solutions. Metabolites 2013; 3:517-38. [PMID: 24958137 PMCID: PMC3901296 DOI: 10.3390/metabo3030517] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/25/2013] [Accepted: 06/07/2013] [Indexed: 12/28/2022] Open
Abstract
The Critical Assessment of Small Molecule Identification, or CASMI, contest was founded in 2012 to provide scientists with a common open dataset to evaluate their identification methods. In this article, the challenges and solutions for the inaugural CASMI 2012 are presented. The contest was split into four categories corresponding with tasks to determine molecular formula and molecular structure, each from two measurement types, liquid chromatography-high resolution mass spectrometry (LC-HRMS), where preference was given to high mass accuracy data, and gas chromatography-electron impact-mass spectrometry (GC-MS), i.e., unit accuracy data. These challenges were obtained from plant material, environmental samples and reference standards. It was surprisingly difficult to obtain data suitable for a contest, especially for GC-MS data where existing databases are very large. The level of difficulty of the challenges is thus quite varied. In this article, the challenges and the answers are discussed, and recommendations for challenge selection in subsequent CASMI contests are given.
Collapse
Affiliation(s)
- Emma L Schymanski
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf CH-8600, Switzerland.
| | - Steffen Neumann
- IPB: Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Weinberg 3, Halle (Saale) DE-06120, Germany.
| |
Collapse
|
8
|
Stravs MA, Schymanski EL, Singer HP, Hollender J. Automatic recalibration and processing of tandem mass spectra using formula annotation. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:89-99. [PMID: 23303751 DOI: 10.1002/jms.3131] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 09/28/2012] [Accepted: 10/19/2012] [Indexed: 05/22/2023]
Abstract
High accuracy, high resolution tandem mass spectrometry (MS/MS) is becoming more common in analytical applications, yet databases of these spectra remain limited. Databases require good quality spectra with sufficient compound information, but processing, calibration, noise reduction and retrieval of compound information are time-consuming tasks that prevent many contributions. We present a comprehensive workflow for the automatic processing of MS/MS using formula annotation for recalibration and cleanup to generate high quality spectra of standard compounds for upload to MassBank (www.massbank.jp). Compound information is retrieved via Internet services. Reference standards of 70 pesticides were measured at various collision energies on an LTQ-Orbitrap XL to develop and evaluate the workflow. A total of 944 resulting spectra are now available on MassBank. Evidence of nitrogen adduct formation during MS/MS fragmentation processes was found, highlighting the benefits high accuracy MS/MS offers for spectral interpretation. A database of recalibrated, cleaned-up spectra resulted in the most correct spectra ranked in first place, regardless of whether the search spectra were recalibrated or not, whereas the average rank of the correct molecular formula was improved from 2.55 (uncalibrated) to 1.53 when using recalibrated MS/MS data. The workflow is available as an R package RMassBank capable of generating MassBank records from raw MS and MS/MS data and can be adjusted to process data acquired with different settings and instruments. This workflow is a vital step towards addressing the need for more high quality, high accuracy MS/MS spectra in spectral databases and provides important information for spectral interpretation.
Collapse
Affiliation(s)
- Michael A Stravs
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | | | | | | |
Collapse
|