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Neubauer C, Kantnerová K, Lamothe A, Savarino J, Hilkert A, Juchelka D, Hinrichs KU, Elvert M, Heuer V, Elsner M, Bakkour R, Julien M, Öztoprak M, Schouten S, Hattori S, Dittmar T. Discovering Nature's Fingerprints: Isotope Ratio Analysis on Bioanalytical Mass Spectrometers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:525-537. [PMID: 36971362 DOI: 10.1021/jasms.2c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
For a generation or more, the mass spectrometry that developed at the frontier of molecular biology was worlds apart from isotope ratio mass spectrometry, a label-free approach done on optimized gas-source magnetic sector instruments. Recent studies show that electrospray-ionization Orbitraps and other mass spectrometers widely used in the life sciences can be fine-tuned for high-precision isotope ratio analysis. Since isotope patterns form everywhere in nature based on well-understood principles, intramolecular isotope measurements allow unique insights into a fascinating range of research topics. This Perspective introduces a wider readership to current topics in stable isotope research with the aim of discussing how soft-ionization mass spectrometry coupled with ultrahigh mass resolution can enable long-envisioned progress. We highlight novel prospects of observing isotopes in intact polar compounds and speculate on future directions of this adventure into the overlapping realms of biology, chemistry, and geology.
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Affiliation(s)
- Cajetan Neubauer
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, Colorado 80303, United States
| | - Kristýna Kantnerová
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, Colorado 80303, United States
| | - Alexis Lamothe
- University Grenoble Alpes, CNRS, IRD, INRAE, Grenoble-INP, IGE, Grenoble 38400, France
| | - Joel Savarino
- University Grenoble Alpes, CNRS, IRD, INRAE, Grenoble-INP, IGE, Grenoble 38400, France
| | | | | | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Verena Heuer
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Martin Elsner
- Department of Chemistry, Technical University of Munich, D-85748 Garching, Germany
| | - Rani Bakkour
- Department of Chemistry, Technical University of Munich, D-85748 Garching, Germany
| | - Maxime Julien
- GFZ German Research Center for Geosciences, 14473 Potsdam, Germany
| | - Merve Öztoprak
- NIOZ Royal Netherlands Institute for Sea Research, Texel 1797 SZ, Netherlands
| | - Stefan Schouten
- NIOZ Royal Netherlands Institute for Sea Research, Texel 1797 SZ, Netherlands
| | - Shohei Hattori
- International Center for Isotope Effects Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210093, China
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, 26129 Oldenburg, Germany
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2
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Zhou X, Wang Z, Fan J, Ouyang Z. High-resolution separation of bioisomers using ion cloud profiling. Nat Commun 2023; 14:1535. [PMID: 36941278 PMCID: PMC10027677 DOI: 10.1038/s41467-023-37281-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
Elucidation of complex structures of biomolecules plays a key role in the field of chemistry and life sciences. In the past decade, ion mobility, by coupling with mass spectrometry, has become a unique tool for distinguishing isomers and isoforms of biomolecules. In this study, we develop a concept for performing ion mobility analysis using an ion trap, which enables isomer separation under ultra-high fields to achieve super high resolutions over 10,000. The potential of this technology has been demonstrated for analysis of isomers for biomolecules including disaccharides, phospholipids, and peptides with post-translational modifications.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China
| | - Zhuofan Wang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Jingjin Fan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China.
- Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China.
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3
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da Silva Borges L, Batista JHC, Bozzini L, Lourenço CD, Lopes NP, Clososki GC, Vessecchi R. Are benzoylium and nitrilium ions produced from substituted 2-arene-2-oxazolines during mass spectrometry? A study based on density functional theory calculations, quantum theory of atoms in molecules, and electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9449. [PMID: 36459945 DOI: 10.1002/rcm.9449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
RATIONALE Oxazolines are important compounds for drug development, synthesis, and pharmaceutical applications. Interest in analyzing and developing methods to characterize reaction products from these small heterocyclics has led us to study the gas-phase reactivity and fragmentation of seven 2-arene-2-oxazolines compounds using computational chemistry combined with mass spectrometry. METHOD Protonation sites were investigated using computed proton affinity, gas-phase basicity, and some quantum chemistry descriptors of reactivity; the B3LYP/6-31+G(d,p) computational model was used. Fragmentation mechanisms were suggested by employing data from collision-induced dissociation (CID), energy-resolved plots from MS/MS spectra, multiple-stage experiments, and survival-yield method. RESULTS Protonation studies based on quantum theory of atoms in molecules (QTAIM) and computational thermochemistry were useful to describe the reactivity of the investigated 2-arene-2-oxazolines, which can be protonated at the nitrogen atom. Three major fragmentation pathways were identified for the protonated molecules: formation of (a) benzoylium or (b) nitrilium ions through elimination of 71 and 72 u from the protonated molecules, respectively, and (c) elimination of 54 u from [M+H]+ . These pathways were exploited by the density functional theory calculations combined with QTAIM studies. CONCLUSIONS Our results can help in identifying 2-arene-2-oxazoline derivatives using electrospray ionization tandem mass spectrometry (ESI-MS/MS), which can be applied for monitoring reactions through the identified diagnostic ions (product ions). Also, we can suggest that benzoylium and nitrilium ions emerge during fragmentation under CID conditions.
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Affiliation(s)
- Letícia da Silva Borges
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - João Henrique Carvalho Batista
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Leandro Bozzini
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Celso Donizete Lourenço
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Norberto Peporine Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Giuliano Cesar Clososki
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento Ciências Moleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
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Kong JY, Hilger RT, Jin C, Yerabolu R, Zimmerman JR, Replogle RW, Jarrell TM, Easterling L, Kumar R, Kenttämaa HI. Integration of a Multichannel Pulsed-Valve Inlet System to a Linear Quadrupole Ion Trap Mass Spectrometer for the Rapid Consecutive Introduction of Nine Reagents for Diagnostic Ion/Molecule Reactions. Anal Chem 2019; 91:15652-15660. [PMID: 31702133 DOI: 10.1021/acs.analchem.9b03768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gas-phase ion/molecule reactions have been used extensively for the structural elucidation of organic compounds in tandem mass spectrometry. Reagents for ion/molecule reactions can be introduced into a mass spectrometer via a continuous flow apparatus or through a pulsed inlet system. However, most of these approaches enable the use of only a single reagent at a time. In this work, a multichannel pulsed-valve inlet system was developed for the rapid consecutive introduction of up to nine different reagents or reagent systems into a linear quadrupole ion trap mass spectrometer for diagnostic gas-phase ion/molecule reactions. Automated triggering of the pulsed valves enabled these experiments to be performed on the high-performance liquid chromatography (HPLC) time scale. This enables high-throughput screening of several functionalities in analytes as they elute from an HPLC column.
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Affiliation(s)
- John Y Kong
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Ryan T Hilger
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Chunfen Jin
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Ravikiran Yerabolu
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - James R Zimmerman
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Randall W Replogle
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Tiffany M Jarrell
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Leah Easterling
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Rashmi Kumar
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Hilkka I Kenttämaa
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
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Tripodi GL, Correra TC, Angolini CFF, Ferreira BRV, Maître P, Eberlin MN, Roithová J. The Intermediates in Lewis Acid Catalysis with Lanthanide Triflates. European J Org Chem 2019; 2019:3560-3566. [PMID: 31680777 PMCID: PMC6813638 DOI: 10.1002/ejoc.201900171] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 01/27/2023]
Abstract
Lanthanide triflates are effective Lewis acid catalysts in reactions involving carbonyl compounds due to their high oxophilicity and water stability. Despite the growing interest, the identity of the catalytic species formed in lanthanide catalysed reactions is still unknown. We have therefore used mass spectrometry and ion spectroscopy to intercept and characterize the intermediates in a reaction catalysed by ytterbium and dysprosium triflates. We were able to identify a number of lanthanide intermediates formed in a simple condensation reaction between a C-acid and an aldehyde. Results show correlation between the reactivity of lanthanide complexes and their charge state and suggest that the triply charged complexes play a key role in lanthanide catalysed reactions. Spectroscopic data of the gaseous ions accompanied by theoretical calculations reveal that the difference between catalytic efficiencies of ytterbium and dysprosium ions can be explained by their different electrophilicity.
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Affiliation(s)
- Guilherme L. Tripodi
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJ NijmegenThe Netherlands
| | - Thiago C. Correra
- Departament of Organic ChemistryInstitute of ChemistryUniversity of São Paulo05508–000São Paulo‐SPBrazil
| | - Célio F. F. Angolini
- Center for Natural and Human SciencesFederal University of ABC (UFABC)09210–580Santo André ‐SPBrazil
| | - Bruno R. V. Ferreira
- Instituto Federal do Norte de Minas GeraisCampus Salinas39560–000Salinas‐MGBrazil
| | - Philippe Maître
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris‐SudUniversité Paris‐Saclay91405OrsayFrance
| | - Marcos N. Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of ChemistryState University of Campinas13084–971Campinas‐SPBrazil
- School of EngeneeringMackenzie Presbiterian University01302907São Paulo‐SPBrazil
| | - Jana Roithová
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJ NijmegenThe Netherlands
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Almeida Assis AC, Caetano J, Florêncio MH, Cordeiro C. Triacetone triperoxide characterization by FT-ICR mass spectrometry: Uncovering multiple forensic evidence. Forensic Sci Int 2019; 301:37-45. [PMID: 31128407 DOI: 10.1016/j.forsciint.2019.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 11/28/2022]
Abstract
Triacetone triperoxide is one of the most common used explosives by terrorist and criminal groups, being easily synthesized with over the counter reagents. Moreover, it's difficult to detect since it contains no nitrogen. Extreme resolution mass spectrometry, based on Fourier transform ion cyclotron resonance mass spectrometry provides a way to established its composition, being able to detect its presence in complex matrixes. In this work, we investigated the detailed chemical composition of triacetone triperoxide and analysed latent fingerprints for evidence of its handling. Our results allowed the characterization of the oligoperoxides formed in the synthesis of triacetone triperoxide: oligomers dihydroperoxy terminated [H(OOC(CH3)2)nOOH] and the oligomeric acetone carbonyl oxides terminated as hydroperoxides [H(O2C(CH3)2)nOOC(O)CH3]. The discrimination between the different synthetic routes using different acid catalysts is possible given the clear differences between the mass spectrum corresponding to each case. Moreover, we identified triacetone triperoxide in latent fingerprints following its manipulation. For criminal investigation, in addition to the unambiguous detection and identification of the explosive, it is of the highest interest to identify the reagents used, who produced it and who used it for criminal purposes.
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Affiliation(s)
- Ana Cristina Almeida Assis
- Laboratório de FT-ICR e Espectrometria de Massa Estrutural, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Portugal; Laboratório de Polícia Científica da Polícia Judiciária, Portugal.
| | - José Caetano
- EOD
- CBRN Unit/Police Special Unit - Polícia de Segurança Pública, Portugal.
| | - Maria Helena Florêncio
- Laboratório de FT-ICR e Espectrometria de Massa Estrutural, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Portugal.
| | - Carlos Cordeiro
- Laboratório de FT-ICR e Espectrometria de Massa Estrutural, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Portugal.
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Wu H, Yuan C, Zhang H, Yang G, Cui C, Yang M, Bian W, Fu H, Luo Z, Yao J. Ultrafast Deep-Ultraviolet Laser Ionization Mass Spectrometry Applicable To Identify Phenylenediamine Isomers. Anal Chem 2018; 90:10635-10640. [DOI: 10.1021/acs.analchem.8b03167] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Haiming Wu
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chengqian Yuan
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hanyu Zhang
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guanhua Yang
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chaonan Cui
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Mengzhou Yang
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wensheng Bian
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hongbing Fu
- Department of Chemistry, Capital Normal University, Beijing 100048, P. R. China
| | - Zhixun Luo
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiannian Yao
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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Xiu Y, Ma L, Zhao H, Sun X, Li X, Liu S. Differentiation and identification of ginsenoside structural isomers by two-dimensional mass spectrometry combined with statistical analysis. J Ginseng Res 2017; 43:368-376. [PMID: 31308808 PMCID: PMC6606828 DOI: 10.1016/j.jgr.2017.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/19/2017] [Accepted: 11/13/2017] [Indexed: 12/28/2022] Open
Abstract
Background In the current phytochemical research on ginseng, the differentiation and structural identification of ginsenosides isomers remain challenging. In this paper, a two-dimensional mass spectrometry (2D-MS) method was developed and combined with statistical analysis for the direct differentiation, identification, and relative quantification of protopanaxadiol (PPD)-type ginsenoside isomers. Methods Collision-induced dissociation was performed at successive collision energy values to produce distinct profiles of the intensity fraction (IF) and ratio of intensity (RI) of the fragment ions. To amplify the differences in tandem mass spectra between isomers, IF and RI were plotted against collision energy. The resulting data distributions were then used to obtain the parameters of the fitted curves, which were used to evaluate the statistical significance of the differences between these distributions via the unpaired t test. Results A triplet and two pairs of PPD-type ginsenoside isomers were differentiated and identified by their distinct IF and RI distributions. In addition, the fragmentation preference of PPD-type ginsenosides was determined on the basis of the activation energy. The developed 2D-MS method was also extended to quantitatively determine the molar composition of ginsenoside isomers in mixtures of biotransformation products. Conclusion In comparison with conventional mass spectrometry methods, 2D-MS provides more direct insights into the subtle structural differences between isomers and can be used as an alternative approach for the differentiation of isomeric ginsenosides and natural products.
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Affiliation(s)
- Yang Xiu
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Li Ma
- Institute of Mass Spectrometer and Atmospheric Environment, Jinan University, Guangzhou, China
| | - Huanxi Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Xiuli Sun
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Xue Li
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Shuying Liu
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
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Dziekonski ET, Johnson JT, Lee KW, McLuckey SA. Fourier-Transform MS and Closed-Path Multireflection Time-of-Flight MS Using an Electrostatic Linear Ion Trap. Anal Chem 2017; 89:10965-10972. [PMID: 28926221 DOI: 10.1021/acs.analchem.7b02797] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric T. Dziekonski
- Department of Chemistry Purdue University West Lafayette, Indiana 47907-2084, United States
| | - Joshua T. Johnson
- Department of Chemistry Purdue University West Lafayette, Indiana 47907-2084, United States
| | - Kenneth W. Lee
- Department of Chemistry Purdue University West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry Purdue University West Lafayette, Indiana 47907-2084, United States
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Andris E, Navrátil R, Jašík J, Terencio T, Srnec M, Costas M, Roithová J. Chasing the Evasive Fe═O Stretch and the Spin State of the Iron(IV)-Oxo Complexes by Photodissociation Spectroscopy. J Am Chem Soc 2017; 139:2757-2765. [PMID: 28125220 DOI: 10.1021/jacs.6b12291] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We demonstrate the application of infrared photodissocation spectroscopy for determination of the Fe═O stretching frequencies of high-valent iron(IV)-oxo complexes [(L)Fe(O)(X)]2+/+ (L = TMC, N4Py, PyTACN, and X = CH3CN, CF3SO3, ClO4, CF3COO, NO3, N3). We show that the values determined by resonance Raman spectroscopy in acetonitrile solutions are on average 9 cm-1 red-shifted with respect to unbiased gas-phase values. Furthermore, we show the assignment of the spin state of the complexes based on the vibrational modes of a coordinated anion and compare reactivities of various iron(IV)-oxo complexes generated as dications or monocations (bearing an anionic ligand). The coordinated anions can drastically affect the reactivity of the complex and should be taken into account when comparing reactivities of complexes bearing different ligands. Comparison of reactivities of [(PyTACN)Fe(O)(X)]+ generated in different spin states and bearing different anionic ligands X revealed that the nature of anion influences the reactivity more than the spin state. The triflate and perchlorate ligands tend to stabilize the quintet state of [(PyTACN)Fe(O)(X)]+, whereas trifluoroacetate and nitrate stabilize the triplet state of the complex.
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Affiliation(s)
- Erik Andris
- Department of Organic Chemistry, Faculty of Science, Charles University , Hlavova 2030/8, 12843 Prague 2, Czech Republic
| | - Rafael Navrátil
- Department of Organic Chemistry, Faculty of Science, Charles University , Hlavova 2030/8, 12843 Prague 2, Czech Republic
| | - Juraj Jašík
- Department of Organic Chemistry, Faculty of Science, Charles University , Hlavova 2030/8, 12843 Prague 2, Czech Republic
| | - Thibault Terencio
- Department of Organic Chemistry, Faculty of Science, Charles University , Hlavova 2030/8, 12843 Prague 2, Czech Republic
| | - Martin Srnec
- J. Heyrovsky Institute of Physical Chemistry of the CAS , v.v i., Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Miquel Costas
- Departament de Quimica and Institute of Computational Chemistry and Catalysis (IQCC), University of Girona , Campus Montilivi, Girona 17071, Spain
| | - Jana Roithová
- Department of Organic Chemistry, Faculty of Science, Charles University , Hlavova 2030/8, 12843 Prague 2, Czech Republic
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Trefely S, Ashwell P, Snyder NW. FluxFix: automatic isotopologue normalization for metabolic tracer analysis. BMC Bioinformatics 2016; 17:485. [PMID: 27887574 PMCID: PMC5123363 DOI: 10.1186/s12859-016-1360-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/19/2016] [Indexed: 11/24/2022] Open
Abstract
Background Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [13C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for the detection and differentiation of the isotopologues of each metabolite of interest. For meaningful interpretation, mass spectrometry data from metabolic tracer experiments must be corrected to account for the naturally occurring isotopologue distribution. The calculations required for this correction are time consuming and error prone and existing programs are often platform specific, non-intuitive, commercially licensed and/or limited in accuracy by using theoretical isotopologue distributions, which are prone to artifacts from noise or unresolved interfering signals. Results Here we present FluxFix (http://fluxfix.science), an application freely available on the internet that quickly and reliably transforms signal intensity values into percent mole enrichment for each isotopologue measured. ‘Unlabeled’ data, representing the measured natural isotopologue distribution for a chosen analyte, is entered by the user. This data is used to generate a correction matrix according to a well-established algorithm. The correction matrix is applied to labeled data, also entered by the user, thus generating the corrected output data. FluxFix is compatible with direct copy and paste from spreadsheet applications including Excel (Microsoft) and Google sheets and automatically adjusts to account for input data dimensions. The program is simple, easy to use, agnostic to the mass spectrometry platform, generalizable to known or unknown metabolites, and can take input data from either a theoretical natural isotopologue distribution or an experimentally measured one. Conclusions Our freely available web-based calculator, FluxFix (http://fluxfix.science), quickly and reliably corrects metabolic tracer data for natural isotopologue abundance enabling faster, more robust and easily accessible data analysis.
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Affiliation(s)
- Sophie Trefely
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, 19104, USA. .,Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Peter Ashwell
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, 19104, USA
| | - Nathaniel W Snyder
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, 19104, USA
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Dennis EA, Gundlach-Graham AW, Ray SJ, Enke CG, Hieftje GM. Distance-of-Flight Mass Spectrometry: What, Why, and How? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1772-1786. [PMID: 27562501 DOI: 10.1007/s13361-016-1458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
Distance-of-flight mass spectrometry (DOFMS) separates ions of different mass-to-charge (m/z) by the distance they travel in a given time after acceleration. Like time-of-flight mass spectrometry (TOFMS), separation and mass assignment are based on ion velocity. However, DOFMS is not a variant of TOFMS; different methods of ion focusing and detection are used. In DOFMS, ions are driven orthogonally, at the detection time, onto an array of detectors parallel to the flight path. Through the independent detection of each m/z, DOFMS can provide both wider dynamic range and increased throughput for m/z of interest compared with conventional TOFMS. The iso-mass focusing and detection of ions is achieved by constant-momentum acceleration (CMA) and a linear-field ion mirror. Improved energy focus (including turn-around) is achieved in DOFMS, but the initial spatial dispersion of ions remains unchanged upon detection. Therefore, the point-source nature of surface ionization techniques could put them at an advantage for DOFMS. To date, three types of position-sensitive detectors have been used for DOFMS: a microchannel plate with a phosphorescent screen, a focal plane camera, and an IonCCD array; advances in detector technology will likely improve DOFMS figures-of-merit. In addition, the combination of CMA with TOF detection has provided improved resolution and duty factor over a narrow m/z range (compared with conventional, single-pass TOFMS). The unique characteristics of DOFMS can enable the intact collection of large biomolecules, clusters, and organisms. DOFMS might also play a key role in achieving the long-sought goal of simultaneous MS/MS. Graphical Abstract ᅟ.
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Affiliation(s)
- Elise A Dennis
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
- Perkin Elmer, Shelton, CT, 06484, USA
| | - Alexander W Gundlach-Graham
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Steven J Ray
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Christie G Enke
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Gary M Hieftje
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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Kuchař L, Asfaw B, Rybová J, Ledvinová J. Tandem Mass Spectrometry of Sphingolipids: Applications for Diagnosis of Sphingolipidoses. Adv Clin Chem 2016; 77:177-219. [PMID: 27717417 DOI: 10.1016/bs.acc.2016.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In recent years, mass spectrometry (MS) has become the dominant technology in lipidomic analysis. It is widely used in diagnosis and research of lipid metabolism disorders including those characterized by impairment of lysosomal functions and storage of nondegraded-degraded substrates. These rare diseases, which include sphingolipidoses, have severe and often fatal clinical consequences. Modern MS methods have contributed significantly to achieve a definitive diagnosis, which is essential in clinical practice to begin properly targeted patient care. Here we summarize MS and tandem MS methods used for qualitative and quantitative analysis of sphingolipids (SL) relative to the diagnostic process for sphingolipidoses and studies focusing on alterations in cell functions due to these disorders. This review covers the following topics: Tandem MS is sensitive and robust in determining the composition of sphingolipid classes in various biological materials. Its ability to establish SL metabolomic profiles using MS bench-top analyzers, significantly benefits the first stages of a diagnosis as well as metabolic studies of these disorders. It can thus contribute to a better understanding of the biological significance of SL.
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Affiliation(s)
- L Kuchař
- Charles University in Prague and General University Hospital, Prague, Czech Republic.
| | - B Asfaw
- Charles University in Prague and General University Hospital, Prague, Czech Republic
| | - J Rybová
- Charles University in Prague and General University Hospital, Prague, Czech Republic
| | - J Ledvinová
- Charles University in Prague and General University Hospital, Prague, Czech Republic.
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14
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Tang W, Sheng H, Kong JY, Yerabolu R, Zhu H, Max J, Zhang M, Kenttämaa HI. Gas-phase ion-molecule reactions for the identification of the sulfone functionality in protonated analytes in a linear quadrupole ion trap mass spectrometer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1435-1441. [PMID: 27197036 DOI: 10.1002/rcm.7569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE The oxidation of sulfur atoms is an important biotransformation pathway for many sulfur-containing drugs. In order to rapidly identify the sulfone functionality in drug metabolites, a tandem mass spectrometric method based on ion-molecule reactions was developed. METHODS A phosphorus-containing reagent, trimethyl phosphite (TMP), was allowed to react with protonated analytes with various functionalities in a linear quadrupole ion trap mass spectrometer. The reaction products and reaction efficiencies were measured. RESULTS Only protonated sulfone model compounds were found to react with TMP to form a characteristic [TMP adduct-MeOH] product ion. All other protonated compounds investigated, with functionalities such as sulfoxide, N-oxide, hydroxylamino, keto, carboxylic acid, and aliphatic and aromatic amino, only react with TMP via proton transfer and/or addition. The specificity of the reaction was further demonstrated by using a sulfoxide-containing anti-inflammatory drug, sulindac, as well as its metabolite sulindac sulfone. CONCLUSIONS A method based on functional group-selective ion-molecule reactions in a linear quadrupole ion trap mass spectrometer has been demonstrated for the identification of the sulfone functionality in protonated analytes. A characteristic [TMP adduct-MeOH] product ion was only formed for the protonated sulfone analytes. The applicability of the TMP reagent in identifying sulfone functionalities in drug metabolites was also demonstrated. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Weijuan Tang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- DuPont, 200 Powder Mill Rd., Wilmington, DE, 19843, USA
| | - Huaming Sheng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Merck, 125 E Lincoln Ave, Rahway, NJ, 07065, USA
| | - John Y Kong
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ravikiran Yerabolu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Hanyu Zhu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Joann Max
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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15
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Declerck S, Vander Heyden Y, Mangelings D. Enantioseparations of pharmaceuticals with capillary electrochromatography: A review. J Pharm Biomed Anal 2016; 130:81-99. [PMID: 27156645 DOI: 10.1016/j.jpba.2016.04.024] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/13/2016] [Accepted: 04/17/2016] [Indexed: 11/19/2022]
Abstract
The chiral separation of pharmaceuticals is one of the major research topics in the pharmaceutical industry. Chromatographic techniques are most frequently used in this context. Separations in capillary electrochromatography (CEC) are an alternative and achieved by chromatographic retention and electrophoretic mobility principles. As a result, CEC is characterized by a high selectivity and efficiency. The limited number of stationary phases specifically developed for CEC, the low number of commercially available CEC columns, the frits to maintain the stationary phase, which forms fragile spots in the columns, and the limited column robustness and reproducibility, make CEC not very attractive for industrial application. However, CEC is still applied and studied in the academic field. This review discusses the enantioseparation of drugs in CEC published during the last four years, with a critical view on the reproducibility and the practical utility of these applications.
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Affiliation(s)
- Sven Declerck
- Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, B-1090 Brussels, Belgium.
| | - Yvan Vander Heyden
- Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, B-1090 Brussels, Belgium.
| | - Debby Mangelings
- Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, B-1090 Brussels, Belgium.
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16
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Russell ZE, DiDona ST, Amsden JJ, Parker CB, Kibelka G, Gehm ME, Glass JT. Compatibility of Spatially Coded Apertures with a Miniature Mattauch-Herzog Mass Spectrograph. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:578-584. [PMID: 26744293 DOI: 10.1007/s13361-015-1323-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/06/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
In order to minimize losses in signal intensity often present in mass spectrometry miniaturization efforts, we recently applied the principles of spatially coded apertures to magnetic sector mass spectrometry, thereby achieving increases in signal intensity of greater than 10× with no loss in mass resolution Chen et al. (J. Am. Soc. Mass Spectrom. 26, 1633-1640, 2015), Russell et al. (J. Am. Soc. Mass Spectrom. 26, 248-256, 2015). In this work, we simulate theoretical compatibility and demonstrate preliminary experimental compatibility of the Mattauch-Herzog mass spectrograph geometry with spatial coding. For the simulation-based theoretical assessment, COMSOL Multiphysics finite element solvers were used to simulate electric and magnetic fields, and a custom particle tracing routine was written in C# that allowed for calculations of more than 15 million particle trajectory time steps per second. Preliminary experimental results demonstrating compatibility of spatial coding with the Mattauch-Herzog geometry were obtained using a commercial miniature mass spectrograph from OI Analytical/Xylem.
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Affiliation(s)
- Zachary E Russell
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Shane T DiDona
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Jason J Amsden
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Charles B Parker
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Gottfried Kibelka
- CMS Field Products, OI Analytical, a Xylem brand, College Station, TX, 77842-9010, USA
| | - Michael E Gehm
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Jeffrey T Glass
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA.
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17
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Chen EX, Russell ZE, Amsden JJ, Wolter SD, Danell RM, Parker CB, Stoner BR, Gehm ME, Glass JT, Brady DJ. Order of Magnitude Signal Gain in Magnetic Sector Mass Spectrometry Via Aperture Coding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1633-1640. [PMID: 26111517 DOI: 10.1007/s13361-015-1178-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/03/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Miniaturizing instruments for spectroscopic applications requires the designer to confront a tradeoff between instrument resolution and instrument throughput [and associated signal-to-background-ratio (SBR)]. This work demonstrates a solution to this tradeoff in sector mass spectrometry by the first application of one-dimensional (1D) spatially coded apertures, similar to those previously demonstrated in optics. This was accomplished by replacing the input slit of a simple 90° magnetic sector mass spectrometer with a specifically designed coded aperture, deriving the corresponding forward mathematical model and spectral reconstruction algorithm, and then utilizing the resulting system to measure and reconstruct the mass spectra of argon, acetone, and ethanol. We expect the application of coded apertures to sector instrument designs will lead to miniature mass spectrometers that maintain the high performance of larger instruments, enabling field detection of trace chemicals and point-of-use mass spectrometry.
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Affiliation(s)
- Evan X Chen
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
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18
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Abdoul-Carime H, Farizon B, Farizon M, Mulatier JC, Dutasta JP, Chermette H. Solution vs. gas phase relative stability of the choline/acetylcholine cavitand complexes. Phys Chem Chem Phys 2015; 17:4448-57. [PMID: 25579781 DOI: 10.1039/c4cp05354k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
How the information obtained from the gas phase experiments can reflect the processes in solution is a crucial question for analytical chemistry, and particularly the selective host-guest recognition mechanisms which are fundamental in biology. Here we combine ElectroSpray Ionization mass spectrometry (ESI-MS) and the Collision Induced Dissociation (CID) experiments to the density functional theory to investigate the interaction of acetylcholine and the choline cation with a triphosphonate cavitand. While the relative abundance of the cation complexes in the ESI mass spectrum reflects the preferential capture of the acetylcholine ion over the choline ion by the cavitand in the solution, the gas phase CID measurements indicate that after desolvation the choline cation is the most strongly bound to the host. The experimental results are interpreted by theory that underlines the role of the counterion in the stabilization of the complexes in solution and therefore in the selective recognition of substrates of biological interest.
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Affiliation(s)
- Hassan Abdoul-Carime
- Université de Lyon, Université Claude Bernard Lyon1, Institut de Physique Nucléaire de Lyon, CNRS/IN2P3 UMR 5822, 43 Bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France.
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19
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Tripković T, Charvy C, Alves S, Lolić AĐ, Baošić RM, Nikolić-Mandić SD, Tabet JC. Electrospray ionization linear trap quadrupole Orbitrap in analysis of old tempera paintings: application to nineteenth-century Orthodox icons. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:679-692. [PMID: 26353990 DOI: 10.1255/ejms.1346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteomic approach in combination with mass spectrometry demonstrates a great potential for identification of proteinaceous materials in works of art. In this study we used a linear trap quadrupole Orbitrap (LTQ-Orbitrap), a state-of-the-art mass spectrometer for parts per million accuracy analyses of peptides behind tryptic hydrolysis. After the efficiency of the proteomic method was confirmed for reference and model samples, micro-samples from historical paintings were for the first time analysed using this technique. Superior performances of the liquid chromatography-mass spectrometry approach using a LTQ-Orbitrap mass spectrometer allowed identification of egg yolk peptides in two samples from nineteenth-century Orthodox icons, indicating egg tempera as the painting technique. Accurate precursor ion masses, in the range of ±2 ppm, and retention times of tryptic peptides strengthen protein identification. Additionally, in all historical samples the presence of animal glues suggested that the ground layer was likely bound using bovine collagen. Comparing to results acquired using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry in our previous study, here we achieved higher ion scores and protein scores, better sequence coverage and more identified proteins. In fact, a combination of the two mass spectrometric techniques provided overlapping and complementary data, related to the detection of peptides with different physicochemical properties.
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Affiliation(s)
- T Tripković
- Institute for the Protection of Cultural Monuments of Serbia, Radoslava Grujića 11, 11000 Belgrade, Serbia.
| | - C Charvy
- Universite Pierre et Marie Curie-Paris 6, Institut Parisien de Chimie Moleculaire, UMR 7201, 4 place Jussieu, 75252 Paris Cedex 05, France.
| | - S Alves
- Universite Pierre et Marie Curie-Paris 6, Institut Parisien de Chimie Moleculaire, UMR 7201, 4 place Jussieu, 75252 Paris Cedex 05, France.
| | - A Đ Lolić
- University of Belgrade, Faculty of Chemistry, Studentski trg 12, 11000 Belgrade, Serbia.
| | - R M Baošić
- University of Belgrade, Faculty of Chemistry, Studentski trg 12, 11000 Belgrade, Serbia.
| | - S D Nikolić-Mandić
- University of Belgrade, Faculty of Chemistry, Studentski trg 12, 11000 Belgrade, Serbia.
| | - J C Tabet
- Universite Pierre et Marie Curie-Paris 6, Institut Parisien de Chimie Moleculaire, UMR 7201, 4 place Jussieu, 75252 Paris Cedex 05, France.
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20
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Lin L, Lin H, Zhang M, Dong X, Yin X, Qu C, Ni J. Types, principle, and characteristics of tandem high-resolution mass spectrometry and its applications. RSC Adv 2015. [DOI: 10.1039/c5ra22856e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We review the principle and functional characteristics of different types or models for THRMS and provide a brief description of its applications in medical research, food safety, and environmental protection fields.
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Affiliation(s)
- Longfei Lin
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Hongmei Lin
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Miao Zhang
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Xiaoxv Dong
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Xingbin Yin
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Changhai Qu
- Modern Research Center for TCM
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Jian Ni
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
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21
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Tanase IG, Popa DE, Udriştioiu GE, Bunaciu AA, Aboul‐Enein HY. Validation and Quality Control of an ICP‐MS Method for the Quantification and Discrimination of Trace Metals and Application in Paper Analysis: An Overview. Crit Rev Anal Chem 2014; 44:311-27. [DOI: 10.1080/10408347.2013.863141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
ABSTRACT
Lipidomics is a distinct subspecialty of metabolomics concerned with hydrophobic molecules that organize into membranes. Most of the lipid classes present in
Mycobacterium tuberculosis
are found only in
Actinobacteria
and show extreme structural diversity. This article highlights the conceptual basis and the practical challenges associated with the mass spectrometry–based lipidomic study of
M. tuberculosis
to solve basic questions about the virulence of this lipid-laden organism.
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23
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Bull JN, Lee JWL, Gardiner SH, Vallance C. An introduction to velocity-map imaging mass spectrometry (VMImMS). EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:117-129. [PMID: 24895772 DOI: 10.1255/ejms.1264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This account introduces a new variant of time-of-flight mass spectrometry, termed velocity-map imaging mass spectrometry (VMImMS). While the ion abundances recorded in conventional ToF-MS measurements are highly useful for molecular quantification and structure determination, the final parent and fragment ion yields are Largely blind to the dynamics of the processes in which the ions were formed inside the mass spectrometer. By recording the velocity distribution of each ion in tandem with the mass spectrum, not only can the details of the dissociative ionisation dynamics be unravelled, but the extra dimensions of information can be used for enhanced molecular fingerprinting, separating contributions from ions with identical mass-to-charge ratio and resolving components within mixtures, to name but a few examples. Measuring ion-velocity distributions within a mass spectrometry measurement is not new, but incorporating imaging techniques developed within the reaction dynamics community provides vastly improved velocity resolution for all ions simultaneously in a single-stage instrument. This account provides an introduction to VMImMS, outlines the fundamental instrumentation and detector requirements and the challenges associated with developing the method further, and details proof-of-concept work from our Laboratory on a number of potential applications of the technique.
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24
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Gas-Phase Ion Chemistry of Rare Earths and Actinides. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-63256-2.00263-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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25
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Xuereb A, Ulbricht H, Paternostro M. Optomechanical interface for probing matter-wave coherence. Sci Rep 2013; 3:3378. [PMID: 24287490 PMCID: PMC3843315 DOI: 10.1038/srep03378] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/08/2013] [Indexed: 11/23/2022] Open
Abstract
We combine matter-wave interferometry and cavity optomechanics to propose a coherent matter–light interface based on mechanical motion at the quantum level. We demonstrate a mechanism that is able to transfer non-classical features imprinted on the state of a matter-wave system to an optomechanical device, transducing them into distinctive interference fringes. This provides a reliable tool for the inference of quantum coherence in the particle beam. Moreover, we discuss how our system allows for intriguing perspectives, paving the way to the construction of a device for the encoding of quantum information in matter-wave systems. Our proposal, which highlights previously unforeseen possibilities for the synergistic exploitation of these two experimental platforms, is explicitly based on existing technology, available and widely used in current cutting-edge experiments.
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Affiliation(s)
- André Xuereb
- 1] Centre for Theoretical Atomic, Molecular and Optical Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom [2] Department of Physics, University of Malta, Msida MSD 2080, Malta
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26
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Owen BC, Jarrell TM, Schwartz JC, Oglesbee R, Carlsen M, Archibold EF, Kenttämaa HI. A Differentially Pumped Dual Linear Quadrupole Ion Trap (DLQIT) Mass Spectrometer: A Mass Spectrometer Capable of MSn Experiments Free From Interfering Reactions. Anal Chem 2013; 85:11284-90. [PMID: 24171553 DOI: 10.1021/ac401956f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Benjamin C. Owen
- Center for Direct
Catalytic Conversion of Biomass to Biofuels, Bindley Bioscience Center, Purdue University, 1203
W. State Street, West Lafayette, Indiana 47907, United States
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Tiffany M. Jarrell
- Center for Direct
Catalytic Conversion of Biomass to Biofuels, Bindley Bioscience Center, Purdue University, 1203
W. State Street, West Lafayette, Indiana 47907, United States
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jae C. Schwartz
- Thermo Fisher Scientific, 355 River Oak Parkway, San
Jose, California 95134, United States
| | - Rob Oglesbee
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Mark Carlsen
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Enada F. Archibold
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hilkka I. Kenttämaa
- Center for Direct
Catalytic Conversion of Biomass to Biofuels, Bindley Bioscience Center, Purdue University, 1203
W. State Street, West Lafayette, Indiana 47907, United States
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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Negri G, Tabach R. Saponins, tannins and flavonols found in hydroethanolic extract from Periandra dulcis roots. REVISTA BRASILEIRA DE FARMACOGNOSIA-BRAZILIAN JOURNAL OF PHARMACOGNOSY 2013. [DOI: 10.1590/s0102-695x2013000600001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Vessecchi R, Emery FS, Lopes NP, Galembeck SE. Electronic structure and gas-phase chemistry of protonated α- and β-quinonoid compounds: a mass spectrometry and computational study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:816-824. [PMID: 23495028 DOI: 10.1002/rcm.6519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/18/2013] [Accepted: 01/18/2013] [Indexed: 06/01/2023]
Abstract
RATIONALE The use of quinonoid compounds against tropical diseases and as antitumor agents has prompted the search for new naturally occurring and synthetic derivatives. Among these quinonoid compounds, lapachol and its isomers (α- and β-lapachone) serve as models for the synthesis of new compounds with biological activity, and the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis as a tool to elucidate and characterize these products has furnished important information about these compounds. METHODS ESI-MS/MS analysis under collision-induced dissociation conditions was used to describe the fragmentation mechanisms for protonated 1,4-naphthoquinone, 1,2-naphthoquinone, α-lapachone, and β-lapachone. The B3LYP/6-31+G(d,p) model was used to obtain proton affinities, gas-phase basicities, and molecular electrostatic potential maps, thus indicating the probable protonation sites. Fragmentation pathways were suggested on the basis of the relative enthalpies of the product ions. RESULTS The ESI-MS signals of the cationized molecules of ortho quinonoid compounds were more intense than those of the protonated molecule. Formation of the major product ions with m/z 187 from protonated α- and β-lapachone has been attributed to a retro-Diels-Alder (RDA) reaction. CONCLUSIONS MS/MS studies on lapachol isomers (α- and β-lapachone) will facilitate the interpretation of the liquid chromatography (LC)-MS/MS analysis of new metabolites. MS/MS data on the 1,4-naphthoquinone, 1,2-naphthoquinone, α-lapachone and β-lapachone core will help characterize new derivatives from in vitro/in vivo metabolism studies in complex matrices. The product ions revealed the major fragmentation mechanisms and these ions will serve as diagnostic ions to identify each studied compound.
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Affiliation(s)
- Ricardo Vessecchi
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brasil.
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Lipidomic profiling of model organisms and the world's major pathogens. Biochimie 2012; 95:109-15. [PMID: 22971440 DOI: 10.1016/j.biochi.2012.08.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 08/14/2012] [Indexed: 01/15/2023]
Abstract
Lipidomics is a subspecialty of metabolomics that focuses on water insoluble metabolites that form membrane barriers. Most lipidomic databases catalog lipids from common model organisms, like humans or Escherichia coli. However, model organisms' lipid profiles show surprisingly little overlap with those of specialized pathogens, creating the need for organism-specific lipidomic databases. Here we review rapid progress in lipidomic platform development with regard to chromatography, detection and bioinformatics. We emphasize new methods of comparative lipidomics, which use aligned datasets to identify lipids changed after introducing a biological variable. These new methods provide an unprecedented ability to broadly and quantitatively describe lipidic change during biological processes and identify changed lipids with low error rates.
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Mass spectrometric and theoretical studies on dissociation of the SS bond in the allicin: Homolytic cleavage vs heterolytic cleavage. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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31
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A review of recent advances in mass spectrometric methods for gas-phase chiral analysis of pharmaceutical and biological compounds. J Pharm Biomed Anal 2012; 69:133-47. [PMID: 22579598 DOI: 10.1016/j.jpba.2012.04.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 11/22/2022]
Abstract
Chirality has been of great interest in pharmaceutical and biological sciences. The capabilities of mass spectrometry (MS) for rapid analysis of complex mixtures have encouraged its exploration for gas-phase chiral differentiation. Although particular instances of successful discrimination between enantiomers have been reported over the past three decades, a general method of quantitative chiral analysis by MS has only been demonstrated recently. This review describes the current state of the chiral MS methods without chiral chromatographic separation, which fall into five main categories: (1) the kinetic method, (2) host-guest (H-G) diastereomeric adduct formation, (3) ion/molecule (equilibrium) reactions, (4) collision-induced dissociation (CID) of diastereomeric adducts, and (5) the emerging technique for gas-phase separation using ion mobility spectrometry (IMS). It emphasizes tandem mass spectrometry (MS/MS), which provides several unique analytical advantages for quantitative chiral analysis. These include intrinsically high sensitivity, molecular specificity, and tolerance to impurities as well as the simplicity and speed of the mass spectrometric measurements. Practical prospects and current challenges in quantitative chiral MS techniques for QbD (quality-by-design)-based pharmaceutical applications are also discussed.
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Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2. Proc Natl Acad Sci U S A 2012; 109:E916-25. [PMID: 22474337 DOI: 10.1073/pnas.1121471109] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the biological roles of many members of the sirtuin family of lysine deacetylases have been well characterized, a broader understanding of their role in biology is limited by the challenges in identifying new substrates. We present here an in vitro method that combines biotinylation and mass spectrometry (MS) to identify substrates deacetylated by sirtuins. The method permits labeling of deacetylated residues with amine-reactive biotin on the ε-nitrogen of lysine. The biotin can be utilized to purify the substrate and identify the deacetylated lysine by MS. The biotinyl-lysine method was used to compare deacetylation of chemically acetylated histones by the yeast sirtuins, Sir2 and Hst2. Intriguingly, Sir2 preferentially deacetylates histone H3 lysine 79 as compared to Hst2. Although acetylation of K79 was not previously reported in Saccharomyces cerevisiae, we demonstrate that a minor population of this residue is indeed acetylated in vivo and show that Sir2, and not Hst2, regulates the acetylation state of H3 lysine 79. The in vitro biotinyl-lysine method combined with chemical acetylation made it possible to identify this previously unknown, low-abundance histone acetyl modification in vivo. This method has further potential to identify novel sirtuin deacetylation substrates in whole cell extracts, enabling large-scale screens for new deacetylase substrates.
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Prentice BM, McLuckey SA. Dipolar DC collisional activation in a “stretched” 3-D ion trap: the effect of higher order fields on rf-heating. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:736-44. [PMID: 22302588 DOI: 10.1007/s13361-011-0303-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/19/2011] [Accepted: 11/22/2011] [Indexed: 05/12/2023]
Abstract
Applying dipolar DC (DDC) to the end-cap electrodes of a 3-D ion trap operated with a bath gas at roughly 1 mTorr gives rise to ‘rf-heating’ and can result in collision-induced dissociation (CID). This approach to ion trap CID differs from the conventional single-frequency resonance excitation approach in that it does not rely on tuning a supplementary frequency to coincide with the fundamental secular frequeny of the precursor ion of interest. Simulations using the program ITSIM 5.0 indicate that application of DDC physically displaces ions solely in the axial (inter end-cap) dimension whereupon ion acceleration occurs via power absorption from the drive rf. Experimental data shows that the degree of rf-heating in a stretched 3-D ion trap is not dependent solely on the ratio of the dipolar DC voltage/radio frequency (rf) amplitude, as a model based on a pure quadrupole field suggests. Rather, ion temperatures are shown to increase as the absolute values of the dipolar DC and rf amplitude both decrease. Simulations indicate that the presence of higher order multi-pole fields underlies this unexpected behavior. These findings have important implications for the use of DDC as a broad-band activation approach in multi-pole traps.
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Affiliation(s)
- Boone M Prentice
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
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Andreasson U, Portelius E, Pannee J, Zetterberg H, Blennow K. Multiplexing and multivariate analysis in neurodegeneration. Methods 2012; 56:464-70. [PMID: 22391487 DOI: 10.1016/j.ymeth.2012.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 02/10/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022] Open
Abstract
Limited sample volume is often an obstacle in clinical research and one way to circumvent this is to use multiplex techniques where several different analytes are simultaneously measured. There is a multitude of different platforms that can be used for multiplexing and their uniqueness and similarities will be described. Multivariate analysis is a powerful tool for extracting information from multiplex data. An introduction to one such algorithm is presented followed by examples from the literature, in the field of neurodegeneration, where multiplex and multivariate methods have been used.
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Affiliation(s)
- Ulf Andreasson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.
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Garimella S, Xu W, Huang G, Harper JD, Cooks RG, Ouyang Z. Gas-flow assisted ion transfer for mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:201-207. [PMID: 22359330 DOI: 10.1002/jms.2955] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Methods and devices that use gas flows to collect ions and transfer them over long distances for mass spectrometric analysis have been developed. Gas flows derived from the ionization source itself or provided by means of additional pumping were used to generate a laminar flow inside cylindrical tube. Hydrodynamic simulations and experimental tests demonstrate that laminar flow can transfer ions over long distance. The typical angular discrimination effects encountered when sampling ions from ambient ionization sources are minimized, and the sampling of relatively large surface areas is demonstrated with desorption electrospray ionization (DESI). Ion transfer over 6 m has been achieved and its application to multiplexed chemical analysis is demonstrated on samples at locations remote from the mass spectrometer.
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Affiliation(s)
- Sandilya Garimella
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
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36
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Unkefer CJ, Martinez RA. The use of stable isotope labelling for the analytical chemistry of drugs. Drug Test Anal 2011; 4:303-7. [DOI: 10.1002/dta.361] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 08/12/2011] [Accepted: 08/13/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Clifford J. Unkefer
- Los Alamos National Laboratory; National Stable Isotope Resource; Los Alamos; NM; USA
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37
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Abstract
Lipidomics, a major part of metabolomics, constitutes the detailed analysis and global characterization, both spatial and temporal, of the structure and function of lipids (the lipidome) within a living system. As with proteomics, mass spectrometry has earned a central analytical role in lipidomics, and this role will continue to grow with technological developments. Currently, there exist two mass spectrometry-based lipidomics approaches, one based on a division of lipids into categories and classes prior to analysis, the "comprehensive lipidomics analysis by separation simplification" (CLASS), and the other in which all lipid species are analyzed together without prior separation, shotgun. In exploring the lipidome of various living systems, novel lipids are being discovered, and mass spectrometry is helping characterize their chemical structure. Deuterium exchange mass spectrometry (DXMS) is being used to investigate the association of lipids and membranes with proteins and enzymes, and imaging mass spectrometry (IMS) is being applied to the in situ analysis of lipids in tissues.
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Affiliation(s)
- Richard Harkewicz
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California 92093-0601, USA.
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Vessecchi R, Lopes JNC, Lopes NP, Galembeck SE. Application of the Atoms in Molecules Theory and Computational Chemistry in Mass Spectrometry Analysis of 1,4-Naphthoquinone Derivatives. J Phys Chem A 2011; 115:12780-8. [DOI: 10.1021/jp203912d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
| | - José N. C. Lopes
- Lychnoflora Pesquisa e Desenvolvimento em Produtos Naturais LTDA, Av. dos Bandeirantes 3900, Incubadora Supera - Campus da USP, 14040-903 Ribeirão Preto - SP, Brazil
| | - Norberto P. Lopes
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
| | - Sérgio E. Galembeck
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto - SP, Brazil
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Graham AWG, Ray SJ, Enke CG, Barinaga CJ, Koppenaal DW, Hieftje GM. First distance-of-flight instrument: opening a new paradigm in mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:110-117. [PMID: 21472549 DOI: 10.1007/s13361-010-0005-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 10/11/2010] [Indexed: 05/30/2023]
Abstract
A new instrumental concept, distance-of-flight mass spectrometry (DOFMS), is demonstrated experimentally. In DOFMS the mass-to-charge ratio of ions is determined by the distance each ion travels during a fixed time period; the mass spectrum is then recorded with a position-sensitive detector. The DOF approach provides a new way to separate and quantify components of complex samples. Initial results are demonstrated with a glow discharge ion source and a microchannel plate-phosphor screen detector assembly for atomic ion determination. This detection system demonstrated mass spectral peak widths of approximately 0.65 mm, corresponding to resolving powers of approximately 400-600 for a number of elemental samples.
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Nizkorodov SA, Laskin J, Laskin A. Molecular chemistry of organic aerosols through the application of high resolution mass spectrometry. Phys Chem Chem Phys 2011; 13:3612-29. [DOI: 10.1039/c0cp02032j] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Hummel J, Segu S, Li Y, Irgang S, Jueppner J, Giavalisco P. Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. FRONTIERS IN PLANT SCIENCE 2011; 2:54. [PMID: 22629264 PMCID: PMC3355513 DOI: 10.3389/fpls.2011.00054] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Accepted: 09/05/2011] [Indexed: 05/13/2023]
Abstract
Holistic analysis of lipids is becoming increasingly popular in the life sciences. Recently, several interesting, mass spectrometry-based studies have been conducted, especially in plant biology. However, while great advancements have been made we are still far from detecting all the lipids species in an organism. In this study we developed an ultra performance liquid chromatography-based method using a high resolution, accurate mass, mass spectrometer for the comprehensive profiling of more than 260 polar and non-polar Arabidopsis thaliana leaf lipids. The method is fully compatible to the commonly used lipid extraction protocols and provides a viable alternative to the commonly used direct infusion-based shotgun lipidomics approaches. The whole process is described in detail and compared to alternative lipidomic approaches. Next to the developed method we also introduce an in-house developed database search software (GoBioSpace), which allows one to perform targeted or un-targeted lipidomic and metabolomic analysis on mass spectrometric data of every kind.
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Affiliation(s)
- Jan Hummel
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Shruthi Segu
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Yan Li
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Susann Irgang
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Jessica Jueppner
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
- *Correspondence: Patrick Giavalisco, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Golm, 14476 Potsdam, Germany. e-mail:
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42
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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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43
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Hart-Smith G, Barner-Kowollik C. Contemporary Mass Spectrometry and the Analysis of Synthetic Polymers: Trends, Techniques and Untapped Potential. MACROMOL CHEM PHYS 2010. [DOI: 10.1002/macp.201000107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Dangi BB, Sassin NA, Ervin KM. Pulsed ion extraction diagnostics in a quadrupole ion trap linear time-of-flight mass spectrometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:063302. [PMID: 20590232 DOI: 10.1063/1.3436659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Pulsed extraction techniques are investigated for a quadrupole ion trap (QIT) interfaced to a linear time-of-flight (TOF) mass analyzer. A nonfocusing short-pulse mode of operation is developed and characterized. The short-pulse mode creates a near-monoenergetic ion packet, which is useful for reaction kinetics experiments and for making diagnostic measurements of the ion cloud size in the trap. Monopolar and bipolar pulsing modes, with the voltage pulses applied to one or both QIT endcaps to extract the ions into the TOF region, are compared. Ion TOF peak distributions are characterized experimentally and by ion trajectory simulations. Also, first-order spatial (Wiley-McLaren) focusing of ions is characterized for the conventional long-pulse extraction mode. The nonparallel fields in the QIT, which serves as the first acceleration region in the linear-TOF mass spectrometer, are shown to degrade spatial focusing and mass resolution.
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Affiliation(s)
- Beni B Dangi
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, 1664 N. Virginia St., MS 216, Reno, Nevada 89557-0216, USA
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45
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Knyazev VD, Stein SE. Monte Carlo/RRKM/Classical Trajectories Modeling of Collisional Excitation and Dissociation of n-Butylbenzene Ion in Multipole Collision Cells of Tandem Mass Spectrometers. J Phys Chem A 2010; 114:6384-93. [DOI: 10.1021/jp101526m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vadim D. Knyazev
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and Research Center for Chemical Kinetics, Department of Chemistry, The Catholic University of America, Washington, D.C. 20064
| | - Stephen E. Stein
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and Research Center for Chemical Kinetics, Department of Chemistry, The Catholic University of America, Washington, D.C. 20064
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46
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Knyazev VD, Stein SE. Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and tert-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:425-439. [PMID: 20060316 DOI: 10.1016/j.jasms.2009.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 11/24/2009] [Accepted: 11/24/2009] [Indexed: 05/28/2023]
Abstract
Collision-induced dissociation of the benzylammonium and the 4-tert-butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined as functions of the kinetic energy of ions and the collider gas (argon) pressure. A theoretical Monte Carlo model of ion collisional excitation, scattering, and decomposition was developed. The model includes simulation of the trajectories of the parent and the product ions flight through the hexapole collision cell, quasiclassical trajectory modeling of collisional activation and scattering of ions, and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the parent ion decomposition. The results of modeling demonstrate a general agreement between calculations and experiment. Calculated values of ion fragmentation efficiency are sensitive to initial vibrational excitation of ions, scattering of product ions from the collision cell, and distribution of initial ion velocities orthogonal to the axis of the collision cell. Three critical parameters of the model were adjusted to reproduce the experimental data on the dissociation of the benzylammonium ion: reaction enthalpy and initial internal and translational temperatures of the ions. Subsequent application of the model to decomposition of the t-butyl benzylammonium ion required adjustment of the internal ion temperature only. Energy distribution functions obtained in modeling depend on the average numbers of collisions between the ion and the atoms of the collider gas and, in general, have non-Boltzmann shapes.
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Affiliation(s)
- Vadim D Knyazev
- National Institute of Standards and Technology, Physical and Chemical Properties Division, Gaithersburg, Maryland, USA.
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47
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Zhao NW, Yao JT. Characterization and sequence identification of angiotensin II by a novel method involving ultra-fast liquid chromatography assay coupled with matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight five tandem mass spectrometry analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:663-671. [PMID: 21173463 DOI: 10.1255/ejms.1099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
High-throughput proteomics aims to investigate dynamically changing proteins expressed by a full organism, specific tissue or cellular compartment under certain conditions. High-sensitivity mass spectrometry has gradually become a significant tool for characterizing peptides. Here, we analyzed angiotensin II using ultra-fast liquid chromatography (UFLC) coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). First, we applied UFLC in isolating and collecting the angiotensin II, and then Axima-Resonance (MALDI-QIT-ToF MS(5)) was adopted, which enables collision-induced dissociation-MS(5) analysis for fine structural characterization of angiotensin II. Resultant MS, MS(2), MS(3) and MS(4) spectra of interested [M+H](+) ions selected as precursor ions yielded detailed information about the sites of fragmentation as well as the amino acid sequence for angiotensin II; meanwhile, the average deviation between theoretical mass and actually measured mass from MS to MS(5) spectra was only 0.32 Da. It indicated that Axima-Resonance was capable of analyzing the peptide sequence accurately and provide the corresponding fragmentation information thoroughly, thus suggesting a potential strategy involving UFLC assay coupled with MALDI-QIT-ToF MS(5) analysis on high-throughput proteomics study in future.
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Affiliation(s)
- Ning-wei Zhao
- Shimadzu Global COE for Application & Technical Development, Shanghai 200052, China.
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48
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The incorporation of metal cations into polymer backbones: An important consideration in the interpretation of ESI-MS spectra. POLYMER 2009. [DOI: 10.1016/j.polymer.2009.09.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Voinov VG, Beckman JS, Deinzer ML, Barofsky DF. Electron-capture dissociation (ECD), collision-induced dissociation (CID) and ECD/CID in a linear radio-frequency-free magnetic cell. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3028-30. [PMID: 19685479 PMCID: PMC3057201 DOI: 10.1002/rcm.4209] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Valery G. Voinov
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
- Pacific Institute of Bioorganic Chemistry, Vladivostok 690022, Russia
- Correspondence to: V. G. Voinov, Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
| | - Joseph S. Beckman
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | - Max L. Deinzer
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
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50
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Zellner M, Veitinger M, Umlauf E. The role of proteomics in dementia and Alzheimer's disease. Acta Neuropathol 2009; 118:181-95. [PMID: 19259691 DOI: 10.1007/s00401-009-0502-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 02/15/2009] [Accepted: 02/16/2009] [Indexed: 12/20/2022]
Abstract
Proteomic analysis enables us to identify dementia-related protein profiles of both genetic and environmental origins. In this review, current proteomics technologies are described including many examples of clinical proteomics studies. Many of these studies present only results of the discovery phase. Progression to the validation phase was achieved by developing more advanced proteomics technologies such as fluorescence two-dimensional differential gel electrophoresis or isobaric tagging for relative and absolute protein quantification. These technologies will lead to the design of several new Alzheimer's disease-related protein panels for the analysis of CSF. On these new panels, established markers such as tau and Abeta42 will be used in combination with novel markers, for example beta-2-microglobulin, brain-derived neurotrophic factor 1 and fragments of cystatin C. However, there are still limitations to using proteomic assays. The preparation of homogeneous sample material is difficult due the complexity of brain tissue. Laser capture microdissection and recently developed more sensitive proteomics methods, for example fluorescence saturation labelling, will overcome these limitations. Combining proteomics with approaches at the level of the genome and transcriptome followed by interpretation by systems biology will soon shed further light on dementia-related pathogenesis.
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