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Muni-Morgan A, Lusk MG, Heil C, Goeckner AH, Chen H, McKenna AM, Holland PS. Molecular characterization of dissolved organic matter in urban stormwater pond and municipal wastewater discharges transformed by the Florida red tide dinoflagellate Karenia brevis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166291. [PMID: 37586508 DOI: 10.1016/j.scitotenv.2023.166291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Karenia brevis blooms occur almost annually in southwest Florida, imposing significant ecological and human health impacts. Currently, 13 nutrient sources have been identified supporting blooms, including nearshore anthropogenic inputs such as stormwater and wastewater outflows. A 21-day bioassay was performed, where K. brevis cultures were inoculated with water sourced from three stormwater ponds along an age gradient (14, 18, and 34 yrs.) and one municipal wastewater effluent sample, with the aim of identifying biomolecular classes and transformations of dissolved organic matter (DOM) compounds used by K. brevis. All sample types supported K. brevis growth and showed compositional changes in their respective DOM pools. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) catalogued the molecular composition of DOM and identified specific compound classes that were biodegraded. Results showed that K. brevis utilized species across a wide range of compositions that correspond to amino sugars, humic, and lignin-like biomolecular classes. The municipal wastewater and the youngest stormwater pond (SWP 14) effluent contained the largest pools of labile DOM compounds which were bioavailable to K. brevis, which indicates younger stormwater pond effluents may be as ecologically important as wastewater effluents to blooms. Conversely, generation of DOM compounds of greater complexity and a wide range of aromaticity was observed with the older (SWP 18 and SWP 34) stormwater pond treatments. These data confirm the potential for stormwater ponds and/or wastewater to contribute nutrients which can potentially support K. brevis blooms, revealing the need for improved nutrient retention strategies to protect coastal waters from the potential ill effects of urban effluent.
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Affiliation(s)
- Amanda Muni-Morgan
- University of Florida, Gulf Coast Research and Education Center, School of Natural Resources and Environment, Wimauma, FL 33598, USA; Mote Marine Laboratory, Sarasota, FL 34236, USA
| | - Mary G Lusk
- University of Florida, Gulf Coast Research and Education Center, Soil, Water, and Ecosystem Sciences Department, Wimauma, FL 33598, USA.
| | | | - Audrey H Goeckner
- University of Florida, Soil, Water, and Ecosystem Sciences Department, 1692 McCarty Dr, Gainesville, FL 32603, USA
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University Tallahassee, FL 32310, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University Tallahassee, FL 32310, USA; Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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2
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Nisson DM, Walters CC, Chacón-Patiño ML, Weisbrod CR, Kieft TL, Sherwood Lollar B, Warr O, Castillo J, Perl SM, Cason ED, Freifeld BM, Onstott TC. Radiolytically reworked Archean organic matter in a habitable deep ancient high-temperature brine. Nat Commun 2023; 14:6163. [PMID: 37789019 PMCID: PMC10547683 DOI: 10.1038/s41467-023-41900-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
Investigations of abiotic and biotic contributions to dissolved organic carbon (DOC) are required to constrain microbial habitability in continental subsurface fluids. Here we investigate a large (101-283 mg C/L) DOC pool in an ancient (>1Ga), high temperature (45-55 °C), low biomass (102-104 cells/mL), and deep (3.2 km) brine from an uranium-enriched South African gold mine. Excitation-emission matrices (EEMs), negative electrospray ionization (-ESI) 21 tesla Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and amino acid analyses suggest the brine DOC is primarily radiolytically oxidized kerogen-rich shales or reefs, methane and ethane, with trace amounts of C3-C6 hydrocarbons and organic sulfides. δ2H and δ13C of C1-C3 hydrocarbons are consistent with abiotic origins. These findings suggest water-rock processes control redox and C cycling, helping support a meagre, slow biosphere over geologic time. A radiolytic-driven, habitable brine may signal similar settings are good targets in the search for life beyond Earth.
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Affiliation(s)
- Devan M Nisson
- Department of Geosciences, Princeton University, Princeton, NJ, 08540, USA.
| | | | | | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Thomas L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, Toronto, ON, M5S 3B1, Canada
- Institut de Physique du Globe de Paris (IPGP), Université Paris Cité, 1 rue Jussieu, 75005, Paris, France
| | - Oliver Warr
- Department of Earth Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Julio Castillo
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9300, South Africa
| | - Scott M Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Errol D Cason
- Department of Animal Sciences, University of the Free State, Bloemfontein, 9300, South Africa
| | | | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, 08540, USA
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3
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Sun X, Xia Y, Zhao X, Wang X, Zhang Y, Jia Z, Zheng F, Li Z, Zhang X, Zhao C, Lu X, Xu G. Deep Characterization of Serum Metabolome Based on the Segment-Optimized Spectral-Stitching Direct-Infusion Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Approach. Anal Chem 2023. [PMID: 37406615 DOI: 10.1021/acs.analchem.2c04995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Direct-infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FTICR MS) shows great promise for metabolomic analysis due to ultrahigh mass accuracy and resolution. However, most of the DI-FTICR MS approaches focused on high-throughput metabolomics analysis at the expense of sensitivity and resolution and the potential for metabolome characterization has not been fully explored. Here, we proposed a novel deep characterization approach of serum metabolome using a segment-optimized spectral-stitching DI-FTICR MS method integrated with high-confidence and database-independent formula assignments. With varied acquisition parameters for each segment, a highly efficient acquisition was achieved for the whole mass range with sub-ppm mass accuracy. In a pooled human serum sample, thousands of features were assigned with unambiguous formulas and possible candidates based on highly accurate mass measurements. Furthermore, a reaction network was used to select confidently unique formulas from possible candidates, which was constructed by unambiguous formulas and possible candidates connected by the formula differences resulting from biochemical and MS transformation. Compared with full-range and conventional segment acquisition, 8- and 1.2-fold increases in observed features were achieved, respectively. Assignment accuracy was 93-94% for both a standard mixture containing 190 metabolites and a spiked serum sample with the root mean square mass error of 0.15-0.16 ppm. In total, 3534 unequivocal neutral molecular formulas were assigned in the pooled serum sample, 35% of which are contained in the HMDB. This method offers great enhancement in the deep characterization of serum metabolome by DI-FTICR MS.
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Affiliation(s)
- Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Yueyi Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Xinxin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Yuqing Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, P.R. China
| | - Zhen Jia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
- Department of Cell Biology, College of Life Sciences, China Medical University, Shenyang 110122 Liaoning, P.R. China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Zaifang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning 116023, P.R. China
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4
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Bahureksa W, Borch T, Young RB, Weisbrod CR, Blakney GT, McKenna AM. Improved Dynamic Range, Resolving Power, and Sensitivity Achievable with FT-ICR Mass Spectrometry at 21 T Reveals the Hidden Complexity of Natural Organic Matter. Anal Chem 2022; 94:11382-11389. [PMID: 35917115 DOI: 10.1021/acs.analchem.2c02377] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that can resolve the molecular complexity of natural organic matter at the level of elemental composition assignment. Here, we leverage the high dynamic range, resolving power, resistance to peak coalescence, and maximum ion number and ion trapping duration in a custom built, 21 tesla hybrid linear ion trap /FT-ICR mass spectrometer for a dissolved organic matter standard (Suwanne River Fulvic Acid). We compare the effect of peak-picking threshold (3σ, 4σ, 5σ, and 6σ) on number of elemental composition assignments, mass measurement accuracy, and dynamic range for a 6.3 s transient across the mass range of m/z 200-1200 that comprises the highest achieved resolving power broadband FT-ICR mass spectrum collected to date. More than 36 000 species are assigned with signal magnitude greater than 3σ at root-mean-square mass error of 36 ppb, the most species identified reported to date for dissolved organic matter. We identify 18O and 17O isotopologues and resolve isobaric overlaps on the order of a few electrons across a wide mass range (up to m/z 1000) leveraging mass resolving powers (3 000 000 at m/z 200) only achievable by 21 T FT-ICR MS and increased by ∼30% through absorption mode data processing. Elemental compositions unique to the 3σ span a wide compositional range of aromaticity not detected at higher peak-picking thresholds. Furthermore, we leverage the high dynamic range at 21 T FT-ICR MS to provide a molecular catalogue of a widely utilized reference standard (SRFA) to the analytical community collected on the highest performing mass analyzer for complex mixture analysis to date. This instrument is available free of charge to scientists worldwide.
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Affiliation(s)
- William Bahureksa
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 United States.,Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, United States
| | - Robert B Young
- Chemical Analysis & Instrumentation Laboratory, New Mexico State University, MSC 3RES, Las Cruces, New Mexico 88003, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Greg T Blakney
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, United States.,National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
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5
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McDonough LK, Andersen MS, Behnke MI, Rutlidge H, Oudone P, Meredith K, O'Carroll DM, Santos IR, Marjo CE, Spencer RGM, McKenna AM, Baker A. A new conceptual framework for the transformation of groundwater dissolved organic matter. Nat Commun 2022; 13:2153. [PMID: 35444183 PMCID: PMC9021313 DOI: 10.1038/s41467-022-29711-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/16/2022] [Indexed: 11/09/2022] Open
Abstract
Groundwater comprises 95% of the liquid fresh water on Earth and contains a diverse mix of dissolved organic matter (DOM) molecules which play a significant role in the global carbon cycle. Currently, the storage times and degradation pathways of groundwater DOM are unclear, preventing an accurate estimate of groundwater carbon sources and sinks for global carbon budgets. Here we reveal the transformations of DOM in aging groundwater using ultra-high resolution mass spectrometry combined with radiocarbon dating. Long-term anoxia and a lack of photodegradation leads to the removal of oxidised DOM and a build-up of both reduced photodegradable formulae and aerobically biolabile formulae with a strong microbial signal. This contrasts with the degradation pathway of DOM in oxic marine, river, and lake systems. Our findings suggest that processes such as groundwater extraction and subterranean groundwater discharge to oceans could result in up to 13 Tg of highly photolabile and aerobically biolabile groundwater dissolved organic carbon released to surface environments per year, where it can be rapidly degraded. These findings highlight the importance of considering groundwater DOM in global carbon budgets.
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Affiliation(s)
- Liza K McDonough
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia. .,Connected Waters Initiative Research Centre, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Martin S Andersen
- Connected Waters Initiative Research Centre, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Megan I Behnke
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, 32310, USA
| | - Helen Rutlidge
- Connected Waters Initiative Research Centre, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Phetdala Oudone
- Connected Waters Initiative Research Centre, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Karina Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia
| | - Denis M O'Carroll
- Connected Waters Initiative Research Centre, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Isaac R Santos
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, 2450, Australia
| | - Christopher E Marjo
- Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Robert G M Spencer
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, 32310, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310-4005, USA
| | - Andy Baker
- Connected Waters Initiative Research Centre, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
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6
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Li C, Chu S, Tan S, Yin X, Jiang Y, Dai X, Gong X, Fang X, Tian D. Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers. Front Chem 2021; 9:813359. [PMID: 34993180 PMCID: PMC8724130 DOI: 10.3389/fchem.2021.813359] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/06/2021] [Indexed: 01/12/2023] Open
Abstract
Mass spectrometry (MS) is one of the most widely used analytical techniques in many fields. Recent developments in chemical and biological researches have drawn much attention to the measurement of substances with low abundances in samples. Continuous efforts have been made consequently to further improve the sensitivity of MS. Modifications on the mass analyzers of mass spectrometers offer a direct, universal and practical way to obtain higher sensitivity. This review provides a comprehensive overview of the latest developments in mass analyzers for the improvement of mass spectrometers' sensitivity, including quadrupole, ion trap, time-of-flight (TOF) and Fourier transform ion cyclotron (FT-ICR), as well as different combinations of these mass analyzers. The advantages and limitations of different mass analyzers and their combinations are compared and discussed. This review provides guidance to the selection of suitable mass spectrometers in chemical and biological analytical applications. It is also beneficial to the development of novel mass spectrometers.
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Affiliation(s)
- Chang Li
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
| | - Shiying Chu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Di Tian
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
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7
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Rowland SM, Smith DF, Blakney GT, Corilo YE, Hendrickson CL, Rodgers RP. Online Coupling of Liquid Chromatography with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry at 21 T Provides Fast and Unique Insight into Crude Oil Composition. Anal Chem 2021; 93:13749-13754. [PMID: 34623794 DOI: 10.1021/acs.analchem.1c01169] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
High magnetic field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry provides the highest mass resolving power and mass measurement accuracy for detailed characterization of complex chemical mixtures. Here, we report the coupling of online liquid chromatography of complex mixtures with a 21 tesla FT-ICR mass spectrometer. The high magnetic field enables large ion populations to be analyzed for each spectrum for a high dynamic range, with 3.2 million mass resolving power at m/z 400 (6.2 s transient duration) or 1.6 million (3.1 s transient duration) while maintaining high mass accuracy for molecular formula assignment (root-mean-square assignment error < 0.150 ppm). Thousands of unique elemental compositions are assigned per mass spectrum, which can be grouped by the heteroatom class, double bond equivalents (the number of rings and double bonds to carbon), and carbon number. Figures of merit are discussed, as well as characterization of an Arabian heavy vacuum gas oil in terms of the ring number, compound class, double bond equivalents, and ion type. Consideration of elemental composition and retention order provides additional structural information.
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Affiliation(s)
- Steven M Rowland
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Future Fuels Institute, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Donald F Smith
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Gregory T Blakney
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Yuri E Corilo
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Future Fuels Institute, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, Florida 32306, United States
| | - Ryan P Rodgers
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Future Fuels Institute, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, Florida 32306, United States
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8
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Weisbrod CR, Anderson LC, Hendrickson CL, Schaffer LV, Shortreed MR, Smith LM, Shabanowitz J, Hunt DF. Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal Chem 2021; 93:9119-9128. [PMID: 34165955 DOI: 10.1021/acs.analchem.1c00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer reactions (PTRs) have emerged as a powerful tool for the study of intact proteins. When coupled with m/z-selective kinetic excitation, such as parallel ion parking (PIP), one can exert exquisite control over rates of reaction with a high degree of specificity. This allows one to "concentrate", in the gas phase, nearly all the signals from an intact protein charge state envelope into a single charge state, improving the signal-to-noise ratio (S/N) by 10× or more. While this approach has been previously reported, here we show that implementing these technologies on a 21 T FT-ICR MS provides a tremendous advantage for intact protein analysis. Advanced strategies for performing PTR with PIP were developed to complement this unique instrument, including subjecting all analyte ions entering the mass spectrometer to PTR and PIP. This experiment, which we call "PTR-MS1-PIP", generates a pseudo-MS1 spectrum derived from ions that are exposed to the PTR reagent and PIP waveforms but have not undergone any prior true mass filtering or ion isolation. The result is an extremely rapid and significant improvement in the spectral S/N of intact proteins. This permits the observation of many more proteoforms and reduces ion injection periods for subsequent tandem mass spectrometry characterization. Additionally, the product ion parking waveform has been optimized to enhance the PTR rate without compromise to the parking efficiency. We demonstrate that this process, called "rapid park", can improve reaction rates by 5-10× and explore critical factors discovered to influence this process. Finally, we demonstrate how coupling PTR-MS1 and rapid park provides a 10-fold reduction in ion injection time, improving the rate of tandem MS sequencing.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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9
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Monda H, McKenna AM, Fountain R, Lamar RT. Bioactivity of Humic Acids Extracted From Shale Ore: Molecular Characterization and Structure-Activity Relationship With Tomato Plant Yield Under Nutritional Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:660224. [PMID: 34122481 PMCID: PMC8195337 DOI: 10.3389/fpls.2021.660224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
The increasing demands for biostimulants in the agricultural market over the last years have posed the problem of regulating this product category by requiring the industry to make available the information about efficacy and safety, including the explanation of mode of action and the definition of bioactive constituents. In the present study, we tested the biostimulant proprieties of a sedimentary shale ore-extracted humic acid (HA) on Micro Tom tomato plants under increasing nutritional stress and investigated the correlation with the chemical features of HA by means of ultra-high resolution FT-ICR MS, FT-ATR, and 13C-NMR. Humic acid application proved effective in alleviating the nutritional stress by improving nutrient use efficiency, with results comparable to the control treatment supplied with higher NPK nutrition. Increased yield (up to +19%) and fruit quality (in the range +10-24%), higher ascorbic acid content and a better root growth were the main parameters affected by HA application. Molecular-level characterization identified the possible chemical drivers of bioactivity, and included flavonoids, quinones, and alkaloids among the most represented molecules, some of which exhibiting antioxidant, pro-oxidant, and antimicrobial activity. The redox effect was discussed as a determinant of the delicate homeostasis balance, capable of triggering plant defense response and eventually inducing a protective priming effect on the plants.
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Affiliation(s)
- Hiarhi Monda
- Humic R&D Lab, Bio Huma Netics, Inc., Gilbert, AZ, United States
| | - Amy M. McKenna
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Tallahassee, FL, United States
| | - Ryan Fountain
- Humic R&D Lab, Bio Huma Netics, Inc., Gilbert, AZ, United States
| | - Richard T. Lamar
- Humic R&D Lab, Bio Huma Netics, Inc., Gilbert, AZ, United States
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10
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Classification of the Biogenicity of Complex Organic Mixtures for the Detection of Extraterrestrial Life. Life (Basel) 2021; 11:life11030234. [PMID: 33809046 PMCID: PMC8001260 DOI: 10.3390/life11030234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/02/2021] [Accepted: 03/07/2021] [Indexed: 11/17/2022] Open
Abstract
Searching for life in the Universe depends on unambiguously distinguishing biological features from background signals, which could take the form of chemical, morphological, or spectral signatures. The discovery and direct measurement of organic compounds unambiguously indicative of extraterrestrial (ET) life is a major goal of Solar System exploration. Biology processes matter and energy differently from abiological systems, and materials produced by biological systems may become enriched in planetary environments where biology is operative. However, ET biology might be composed of different components than terrestrial life. As ET sample return is difficult, in situ methods for identifying biology will be useful. Mass spectrometry (MS) is a potentially versatile life detection technique, which will be used to analyze numerous Solar System environments in the near future. We show here that simple algorithmic analysis of MS data from abiotic synthesis (natural and synthetic), microbial cells, and thermally processed biological materials (lab-grown organisms and petroleum) easily identifies relational organic compound distributions that distinguish pristine and aged biological and abiological materials, which likely can be attributed to the types of compounds these processes produce, as well as how they are formed and decompose. To our knowledge this is the first comprehensive demonstration of the utility of this analytical technique for the detection of biology. This method is independent of the detection of particular masses or molecular species samples may contain. This suggests a general method to agnostically detect evidence of biology using MS given a sufficiently strong signal in which the majority of the material in a sample has either a biological or abiological origin. Such metrics are also likely to be useful for studies of possible emergent living phenomena, and paleobiological samples.
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11
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Weisbrod CR, Anderson LC, Greer JB, DeHart CJ, Hendrickson CL. Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading. Anal Chem 2020; 92:12193-12200. [PMID: 32812743 DOI: 10.1021/acs.analchem.0c01064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fourier transform mass spectrometers routinely provide high mass resolution, mass measurement accuracy, and mass spectral dynamic range. In this work, we utilize 21 T Fourier transform ion cyclotron resonance (FT-ICR) to analyze product ions derived from the application of multiple dissociation techniques and/or multiple precursor ions within a single transient acquisition. This ion loading technique, which we call, "chimeric ion loading", saves valuable acquisition time, decreases sample consumption, and improves top-down protein sequence coverage. In the analysis of MCF7 cell lysate, we show collision-induced dissociation (CID) and electron-transfer dissociation (ETD) on each precursor on a liquid chromatography-mass spectrometry (LC-MS) timescale and improve mean sequence coverage dramatically (CID-only 15% vs chimeric 33%), even during discovery-based acquisition. This approach can also be utilized to multiplex the acquisition of product ion spectra of multiple charge states from a single protein precursor or multiple ETD/proton-transfer reactions (PTR) reaction periods. The analytical utility of chimeric ion loading is demonstrated for top-down proteomics, but it is also likely to be impactful for tandem mass spectrometry applications in other areas.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Caroline J DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
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12
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Takemori A, Butcher DS, Harman VM, Brownridge P, Shima K, Higo D, Ishizaki J, Hasegawa H, Suzuki J, Yamashita M, Loo JA, Loo RRO, Beynon RJ, Anderson LC, Takemori N. PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry. J Proteome Res 2020; 19:3779-3791. [PMID: 32538093 DOI: 10.1021/acs.jproteome.0c00303] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prefractionation of complex mixtures of proteins derived from biological samples is indispensable for proteome analysis via top-down mass spectrometry (MS). Polyacrylamide gel electrophoresis (PAGE), which enables high-resolution protein separation based on molecular size, is a widely used technique in biochemical experiments and has the potential to be useful in sample fractionation for top-down MS analysis. However, the lack of a means to efficiently recover the separated proteins in-gel has always been a barrier to its use in sample prefractionation. In this study, we present a novel experimental workflow, called Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS ("PEPPI-MS"), which allows top-down MS of PAGE-separated proteins. The optimization of Coomassie brilliant blue staining followed by the passive extraction step in the PEPPI-MS workflow enabled the efficient recovery of proteins, separated on commercial precast gels, from a wide range of molecular weight regions in under 10 min. Two-dimensional separation combining offline PEPPI-MS with online reversed-phase liquid chromatographic separation resulted in identification of over 1000 proteoforms recovered from the target region of the gel (≤50 kDa). Given the widespread availability and relatively low cost of traditional sodium dodecyl sulfate (SDS)-PAGE equipment, the PEPPI-MS workflow will be a powerful prefractionation strategy for top-down proteomics.
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Affiliation(s)
- Ayako Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 791-0295, Ehime, Japan
| | - David S Butcher
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Victoria M Harman
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Philip Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Keisuke Shima
- Shimadzu Corporation, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Daisuke Higo
- Thermo Fisher Scientific K.K., Yokohama 221-0022, Kanagawa, Japan
| | - Jun Ishizaki
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Hitoshi Hasegawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Junpei Suzuki
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States.,Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Nobuaki Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 791-0295, Ehime, Japan
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13
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Dehghanizadeh M, Cheng F, Jarvis JM, Holguin FO, Brewer CE. Characterization of resin extracted from guayule ( Parthenium argentatum): A dataset including GC-MS and FT-ICR MS. Data Brief 2020; 31:105989. [PMID: 32715039 PMCID: PMC7371977 DOI: 10.1016/j.dib.2020.105989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 11/29/2022] Open
Abstract
Guayule (Parthenium argentatum), a shrub native to the arid region of the U.S. southwest and Mexico belonging to the Asteraceae family, is a source of high quality, hypoallergenic natural rubber with applications in pharmaceutical, tire, and food industries. Production of rubber results in a substantial amount of resin-containing residues which contain a wide variety of secondary metabolites (sesquiterpene esters, triterpene alcohols, fatty acids, etc.). In order to enhance the economic viability of guayule as an industrial crop, value-added use of the residues is needed and has the potential to reduce gross rubber production costs. The main objective of this research is the characterization of guayule resin using rapid and accurate analytical techniques to identify compounds of potential commercial value. Guayule resin is inherently complex and includes many high-molecular-weight and non-volatile compounds that are not easy to observe using traditional chromatographic techniques. The combination of two mass spectroscopy techniques: gas chromatography mass spectroscopy (GC–MS) and high-resolution Fourier transform ion cyclotron resonance mass spectroscopy (FT-ICR MS), were used to characterize the composition of the extracted resin from guayule (Parthenium argentatum). FT-ICR MS was used to characterize hundreds of compounds with over a wide range of molecular weights and degrees of aromaticity at higher levels of mass accuracy than other forms of mass spectrometry. GC–MS was used to identify volatile compounds like mono- and sesquiterpene compounds.
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Affiliation(s)
- Mostafa Dehghanizadeh
- Department of Chemical and Materials Engineering, New Mexico State University, P.O. Box 30001 MSC 3805, Las Cruces, NM 88003, USA
| | - Feng Cheng
- Department of Chemical and Materials Engineering, New Mexico State University, P.O. Box 30001 MSC 3805, Las Cruces, NM 88003, USA
| | - Jacqueline M Jarvis
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - F Omar Holguin
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Catherine E Brewer
- Department of Chemical and Materials Engineering, New Mexico State University, P.O. Box 30001 MSC 3805, Las Cruces, NM 88003, USA
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14
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McDonough LK, O'Carroll DM, Meredith K, Andersen MS, Brügger C, Huang H, Rutlidge H, Behnke MI, Spencer RGM, McKenna A, Marjo CE, Oudone P, Baker A. Changes in groundwater dissolved organic matter character in a coastal sand aquifer due to rainfall recharge. WATER RESEARCH 2020; 169:115201. [PMID: 31675607 DOI: 10.1016/j.watres.2019.115201] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Dissolved organic matter (DOM) in groundwater is fundamentally important with respect to biogeochemical reactions, global carbon cycling, heavy metal transport, water treatability and potability. One source of DOM to groundwater is from the transport of organic matter from the vadose zone by rainfall recharge. Changes in precipitation patterns associated with natural climate variability and climate change are expected to alter the load and character of organic matter released from these areas, which ultimately impacts on groundwater quality and DOM treatability. In order to investigate potential changes in groundwater DOM character after rainfall recharge, we sampled shallow groundwater from a coastal peat-rich sand aquifer in New South Wales, Australia, during an extended period of low precipitation (average daily precipitation rate < 1.6 mm day-1 over the 8 months prior to sampling), and after two heavy precipitation events (84 mm day-1 and 98 mm day-1 respectively). We assess changes in DOM composition after correcting for dilution by a novel combination of two advanced analytical techniques: liquid chromatography organic carbon detection (LC-OCD) and negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). We also assess changes in water chemistry pre- and post-rainfall. Post-rainfall, we show that the dilution-corrected amount of highly aromatic DOM molecular formulae (i.e. those categorised into the groups polyphenolics and condensed aromatics) were 1.7 and 2.0 times higher respectively than in pre-rainfall samples. We attribute this to the flushing of peat-derived DOM from buried organic material into the groundwater. We also identify that periods of low precipitation can lead to low hydrophilic/HOC ratios in groundwater (median = 4.9, n = 14). Redundancy analysis (RDA) was used to compare the HOC fraction with FT-ICR MS compound groups. We show that HOC has a more aromatic character in pre-rainfall samples, and is less similar to the aromatic groups in post-rainfall samples. This suggests that the decline in water-borne hydrophobics observed post-rainfall could be associated with preferential adsorption of the hydrophobic aromatic DOM, making post-rainfall samples less treatable for potable water supply. Post-rainfall we also observe significant increases in arsenic (leading to concentrations greater than 3 times the World Health Organisation drinking water limit of 10 μg / L). Increases in coastal rainfall due to climate change may therefore alter the composition of groundwater DOM in coastal peatland areas in ways that may impact DOM bioavailability, and increase arsenic concentrations, reducing the ease of water treatment for human consumption. To the best of our knowledge, this is the first study to identify the chemical and molecular changes of shallow groundwater DOM pre-rainfall and post-rainfall in a sedimentary organic carbon rich environment through multiple analytical techniques.
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Affiliation(s)
- Liza K McDonough
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW, 2052, Australia.
| | - Denis M O'Carroll
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Karina Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia
| | - Martin S Andersen
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Clément Brügger
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia
| | - Hanxue Huang
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Helen Rutlidge
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Megan I Behnke
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Florida, 32310, USA
| | - Robert G M Spencer
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Florida, 32310, USA
| | - Amy McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310-4005, USA
| | - Christopher E Marjo
- Mark Wainwright Analytical Centre, UNSW Sydney, NSW, 2052, Sydney, Australia
| | - Phetdala Oudone
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Andy Baker
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW, 2052, Australia
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15
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21 Tesla FT-ICR Mass Spectrometer for Ultrahigh-Resolution Analysis of Complex Organic Mixtures. Anal Chem 2018; 90:2041-2047. [PMID: 29303558 DOI: 10.1021/acs.analchem.7b04159] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We describe complex organic mixture analysis by 21 tesla (T) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ultrahigh mass-resolving power (m/Δm50% > 2 700 000 at m/z 400) and mass accuracy (80 ppb rms) enable resolution and confident identification of tens of thousands of unique elemental compositions. We demonstrate 2.2-fold higher mass-resolving power, 2.6-fold better mass measurement accuracy, and 1.3-fold more assigned molecular formulas compared to our custom-built, state-of-the-art 9.4 T FT-ICR mass spectrometer for petroleum and dissolved organic matter (DOM) analyses. Analysis of a heavy petroleum distillate exemplifies the need for ultrahigh-performance mass spectrometry (49 040 assigned molecular formulas for 21 T versus 29 012 for 9.4 T) and extends the identification of previously unresolved Oo, SsOo, and NOo classes. Mass selective ion accumulation (20 Thompson isolation) of an asphalt volcano sample yields 462 resolved mass spectral peaks at m/z 677 and reveals previously unresolved CcHhNnOoSs mass differences at high mass (m/z > 600). Similar performance gains are realized in the analysis of dissolved organic matter, where doubly charged Oo species are resolved from singly charged SOo species, which requires a mass-resolving power greater than 1 400 000 (at m/z 600). This direct comparison reveals the continued need for higher mass-resolving power and better mass accuracy for comprehensive molecular characterization of the most complex organic mixtures.
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16
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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17
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Anderson LC, Håkansson M, Walse B, Nilsson CL. Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1796-1804. [PMID: 28681360 PMCID: PMC5556139 DOI: 10.1007/s13361-017-1705-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/16/2023]
Abstract
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a ~45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. Graphical Abstract ᅟ.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Carol L Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX, 77555-1074, USA.
- Institute of Clinical Sciences-Lund, Lund University, SE-221 85, Lund, Sweden.
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18
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Weisbrod CR, Kaiser NK, Syka JEP, Early L, Mullen C, Dunyach JJ, English AM, Anderson LC, Blakney GT, Shabanowitz J, Hendrickson CL, Marshall AG, Hunt DF. Front-End Electron Transfer Dissociation Coupled to a 21 Tesla FT-ICR Mass Spectrometer for Intact Protein Sequence Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1787-1795. [PMID: 28721671 PMCID: PMC5711562 DOI: 10.1007/s13361-017-1702-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/13/2023]
Abstract
High resolution mass spectrometry is a key technology for in-depth protein characterization. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enables high-level interrogation of intact proteins in the most detail to date. However, an appropriate complement of fragmentation technologies must be paired with FTMS to provide comprehensive sequence coverage, as well as characterization of sequence variants, and post-translational modifications. Here we describe the integration of front-end electron transfer dissociation (FETD) with a custom-built 21 tesla FT-ICR mass spectrometer, which yields unprecedented sequence coverage for proteins ranging from 2.8 to 29 kDa, without the need for extensive spectral averaging (e.g., ~60% sequence coverage for apo-myoglobin with four averaged acquisitions). The system is equipped with a multipole storage device separate from the ETD reaction device, which allows accumulation of multiple ETD fragment ion fills. Consequently, an optimally large product ion population is accumulated prior to transfer to the ICR cell for mass analysis, which improves mass spectral signal-to-noise ratio, dynamic range, and scan rate. We find a linear relationship between protein molecular weight and minimum number of ETD reaction fills to achieve optimum sequence coverage, thereby enabling more efficient use of instrument data acquisition time. Finally, real-time scaling of the number of ETD reactions fills during method-based acquisition is shown, and the implications for LC-MS/MS top-down analysis are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Chad R Weisbrod
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA.
| | - Nathan K Kaiser
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | | | - Lee Early
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | | | - A Michelle English
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Lissa C Anderson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Greg T Blakney
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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19
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Cawley KM, Hohner AK, Podgorski DC, Cooper WT, Korak JA, Rosario-Ortiz FL. Molecular and Spectroscopic Characterization of Water Extractable Organic Matter from Thermally Altered Soils Reveal Insight into Disinfection Byproduct Precursors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:771-779. [PMID: 28032509 DOI: 10.1021/acs.est.6b05126] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To characterize the effects of thermal-alteration on water extractable organic matter (WEOM), soil samples were heated in a laboratory at 225, 350, and 500 °C. Next, heated and unheated soils were leached, filtered, and analyzed for dissolved organic carbon (DOC) concentration, optical properties, molecular size distribution, molecular composition, and disinfection byproduct (DBP) formation following the addition of chlorine. The soils heated to 225 °C leached the greatest DOC and had the highest C- and N-DBP precursor reactivity per unit carbon compared to the unheated material or soils heated to 350 or 500 °C. The molecular weight of the soluble compounds decreased with increasing heating temperature. Compared to the unheated soil leachates, all DBP yields were higher for the leachates of soils heated to 225 °C. However, only haloacetonitrile yields (μg/mgC) were higher for leachates of the soils heated to 350 °C, whereas trihalomethane, haloacetic acid and chloropicrin yields were lower compared to unheated soil leachates. Soluble N-containing compounds comprised a high number of molecular formulas for leachates of heated soils, which may explain the higher yield of haloacetonitriles for heated soil leachates. Overall, heating soils altered the quantity, quality, and reactivity of the WEOM pool. These results may be useful for inferring how thermal alteration of soil by wildfire can affect water quality.
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Affiliation(s)
- Kaelin M Cawley
- Department of Civil, Environmental and Architectural Engineering, University of Colorado , 4001 Discovery Drive, Boulder, Colorado 80309-0607, United States
- National Ecological Observatory Network (NEON) , 1685 38th Street, Suite 100, Boulder, Colorado 80301, United States
| | - Amanda K Hohner
- Department of Civil, Environmental and Architectural Engineering, University of Colorado , 4001 Discovery Drive, Boulder, Colorado 80309-0607, United States
| | - David C Podgorski
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - William T Cooper
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Julie A Korak
- Department of Civil, Environmental and Architectural Engineering, University of Colorado , 4001 Discovery Drive, Boulder, Colorado 80309-0607, United States
| | - Fernando L Rosario-Ortiz
- Department of Civil, Environmental and Architectural Engineering, University of Colorado , 4001 Discovery Drive, Boulder, Colorado 80309-0607, United States
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20
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Anderson LC, DeHart CJ, Kaiser NK, Fellers RT, Smith DF, Greer JB, LeDuc RD, Blakney GT, Thomas PM, Kelleher NL, Hendrickson CL. Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry. J Proteome Res 2016; 16:1087-1096. [PMID: 27936753 DOI: 10.1021/acs.jproteome.6b00696] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Successful high-throughput characterization of intact proteins from complex biological samples by mass spectrometry requires instrumentation capable of high mass resolving power, mass accuracy, sensitivity, and spectral acquisition rate. These limitations often necessitate the performance of hundreds of LC-MS/MS experiments to obtain reasonable coverage of the targeted proteome, which is still typically limited to molecular weights below 30 kDa. The National High Magnetic Field Laboratory (NHMFL) recently installed a 21 T FT-ICR mass spectrometer, which is part of the NHMFL FT-ICR User Facility and available to all qualified users. Here we demonstrate top-down LC-21 T FT-ICR MS/MS of intact proteins derived from human colorectal cancer cell lysate. We identified a combined total of 684 unique protein entries observed as 3238 unique proteoforms at a 1% false discovery rate, based on rapid, data-dependent acquisition of collision-induced and electron-transfer dissociation tandem mass spectra from just 40 LC-MS/MS experiments. Our identifications included 372 proteoforms with molecular weights over 30 kDa detected at isotopic resolution, which substantially extends the accessible mass range for high-throughput top-down LC-MS/MS.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Caroline J DeHart
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Nathan K Kaiser
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Donald F Smith
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Greg T Blakney
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry and Molecular Biosciences and the Division of Hematology-Oncology, Northwestern University , Evanston, Illinois 60208, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32304, United States
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Hendrickson CL, Quinn JP, Kaiser NK, Smith DF, Blakney GT, Chen T, Marshall AG, Weisbrod CR, Beu SC. 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: A National Resource for Ultrahigh Resolution Mass Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1626-32. [PMID: 26091892 DOI: 10.1007/s13361-015-1182-2] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 05/16/2023]
Abstract
We describe the design and initial performance of the first 21 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The 21 tesla magnet is the highest field superconducting magnet ever used for FT-ICR and features high spatial homogeneity, high temporal stability, and negligible liquid helium consumption. The instrument includes a commercial dual linear quadrupole trap front end that features high sensitivity, precise control of trapped ion number, and collisional and electron transfer dissociation. A third linear quadrupole trap offers high ion capacity and ejection efficiency, and rf quadrupole ion injection optics deliver ions to a novel dynamically harmonized ICR cell. Mass resolving power of 150,000 (m/Δm(50%)) is achieved for bovine serum albumin (66 kDa) for a 0.38 s detection period, and greater than 2,000,000 resolving power is achieved for a 12 s detection period. Externally calibrated broadband mass measurement accuracy is typically less than 150 ppb rms, with resolving power greater than 300,000 at m/z 400 for a 0.76 s detection period. Combined analysis of electron transfer and collisional dissociation spectra results in 68% sequence coverage for carbonic anhydrase. The instrument is part of the NSF High-Field FT-ICR User Facility and is available free of charge to qualified users.
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Affiliation(s)
- Christopher L Hendrickson
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA,
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