1
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Robles-Lecompte A, Cheng J, McKenna AM, Chang NB. Linking pattern shifts of dissolved organic nitrogen fractional removal with microbial species richness in a cascade upflow biofiltration process. WATER RESEARCH 2024; 264:122130. [PMID: 39146847 DOI: 10.1016/j.watres.2024.122130] [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: 11/15/2023] [Revised: 07/16/2024] [Accepted: 07/20/2024] [Indexed: 08/17/2024]
Abstract
Nutrient pollution has become an important issue to solve in stormwater runoff due to the fast population growth and urbanization that impacts water quality and triggers harmful algal blooms. There is an acute need to link the dissolved organic nitrogen (DON) decomposition with the coupled nitrification and denitrification pathways to realize the pattern shifts in the nitrogen cycle. This paper presented a lab-scale cascade upflow biofiltration system for comparison of nitrate and phosphate removal from stormwater matrices through two specialty adsorbents at three influent conditions. The two specialty adsorbents are denoted as biochar iron and perlite integrated green environmental media (BIPGEM) and zero-valent iron and perlite-based green environmental media (ZIPGEM). An initial condition with stormwater runoff, a second condition with spiked nitrate, and a third condition with spiked nitrate and phosphate were used in this study. To differentiate nitrifier and denitrifier population dynamics associated with the decomposition of DON, integrative analysis of quantitative polymerase chain reaction (qPCR) and 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were performed in association with nitrate removal efficiencies for both media with or without the presence of phosphate. While the qPCR may detect one gene for a single microbe or pathogen and realize the microbial population dynamics in the bioreactors, the 21 T FT-ICR MS can separate and assign elemental compositions to identify organic compounds of DON. Results indicated that ZIPGEM obtained a higher potential for nutrient removal than BIPGEM when the influent was spiked with nitrate and phosphate simultaneously. The sustainable, scalable, and adaptable upflow bioreactors operated in sequence (in a cascade mode) can be expanded flexibly on an as-needed basis to meet the local water quality standards showing process reliability, resilience, and sustainability simultaneously.
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Affiliation(s)
- Alejandra Robles-Lecompte
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Jinxiang Cheng
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ni-Bin Chang
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA.
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2
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Maqbool T, Chen H, Wang Q, McKenna AM, Jiang D. Transformation of sedimentary dissolved organic matter in electrokinetic remediation catalogued by FT-ICR mass spectrometry. WATER RESEARCH 2024; 262:122094. [PMID: 39083902 DOI: 10.1016/j.watres.2024.122094] [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: 05/16/2024] [Revised: 06/27/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024]
Abstract
In electrokinetic remediation (EKR), the sedimentary dissolved organic matter (DOM) could impede remediation by scavenging reactive species and generating unintended byproducts. Yet its transformation and mechanisms remained largely unknown. This study conducted molecular-level characterization of the water-extractable DOM (WEOM) in EKR using negative-ion electrospray ionization coupled to 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (21 T FT-ICR MS). The results suggested that ∼55 % of the ∼7,000 WEOM compounds identified were reactive, and EKR lowered their diversity, molecular weight distribution, and double-bond equivalent (DBE) through a combination of electrochemical and microbial redox reactions. Heteroatom-containing WEOM (CHON and CHOS) were abundant (∼ 35% of the total WEOM), with CHOS generally being more reactive than CHON. Low electric potential (1 V/cm) promoted the growth of dealkylation and desulfurization bacteria, and led to anodic CO2 mineralization, anodic cleavage of -SO and -SO3, and cathodic cleavage of -SH2; high electric potential (2 V/cm) only enriched desulfurization bacteria, and differently, led to anodic oxygenation and cathodic hydrogenation of unsaturated and phenolic compounds, in addition to cathodic cleavage of -SH2. The long-term impact of these changes on soil quality and nitrogen-sulfur-carbon flux may be need to studied to identify unknown risks and new applications of EKR.
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Affiliation(s)
- Tahir Maqbool
- Department of Civil, Construction, and Environmental Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL, 32310-4005, USA
| | - Qingshi Wang
- Department of Civil, Construction, and Environmental Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL, 32310-4005, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daqian Jiang
- Department of Civil, Construction, and Environmental Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA.
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3
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B Oliveira PR, Leyva D, V Tose L, Weisbrod C, Kozhinov AN, Nagornov KO, Tsybin YO, Fernandez-Lima F. Revisiting Dissolved Organic Matter Analysis Using High-Resolution Trapped Ion Mobility and FT-ICR Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39265105 DOI: 10.1021/jasms.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
The molecular level characterization of complex mixtures remains an analytical challenge. We have shown that the integration of complementary, high-resolution, gas-phase separations allows for chemical formula level isomeric content description. In the current work, we revisited the current challenges associated with the analysis of dissolved organic matter using high-resolution trapped ion mobility separation (TIMS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). In particular, we evaluated the separation capabilities provided by TIMS-MS compared to MS alone, the use of ICR complementary data acquisition (DAQ) systems and transient processing strategies, ICR cell geometries (e.g., Infinity cell vs harmonized cell), and magnetic field strengths (7 T vs 9.4 T vs 21 T) for the case of a Harney River DOM sample. Results showed that the external high-performance DAQ enables direct representation of mass spectra in absorption mode FT (aFT), doubling the MS resolution compared to the default magnitude mode FT (mFT). Changes between half- vs full-apodization result in greater MS signal/noise vs superior MS resolving power (RP); in the case of DOM analysis, a 45% increase in assigned formulas is observed when employing the DAQ half (Kaiser-type)-apodization window and aFT when compared to the default instrument mFT. Results showed the advantages of reprocessing 2D-TIMS-FT-ICR MS data with higher RP and magnetic field chemical formulas generated list acquired (e.g., 21 T led to a 24% increase in isomers reported) or the implementation of alternative strategies.
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Affiliation(s)
- Pablo R B Oliveira
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Institute of Environment, Florida International University, Miami, Florida 33199, United States
| | - Dennys Leyva
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Institute of Environment, Florida International University, Miami, Florida 33199, United States
| | - Lilian V Tose
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Institute of Environment, Florida International University, Miami, Florida 33199, United States
| | - Chad Weisbrod
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University, Tallahassee, Florida 32310-4005, United States
| | - Anton N Kozhinov
- Spectroswiss, EPFL Innovation Park, Building 1, 1015 Lausanne, Switzerland
| | | | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, Building 1, 1015 Lausanne, Switzerland
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Institute of Environment, Florida International University, Miami, Florida 33199, United States
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4
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Palacio Lozano DC, Lester DW, Town JS, McKenna AM, Wills M. Assessment of Accelerated Aging Effect of Bio-Oil Fractions Utilizing Ultrahigh-Resolution Mass Spectrometry and k-Means Clustering of van Krevelen Compositional Space. ENERGY & FUELS : AN AMERICAN CHEMICAL SOCIETY JOURNAL 2024; 38:16473-16489. [PMID: 39257465 PMCID: PMC11382156 DOI: 10.1021/acs.energyfuels.4c02605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/12/2024]
Abstract
Bio-oils contain a substantial number of highly oxygenated hydrocarbons, which often exhibit low thermal stability during storage, handling, and refining. The primary objectives of this study are to characterize the hydroxyl group in bio-oil fractions and to investigate the relationship between the type of hydroxyl group and accelerated aging behavior. A bio-oil was fractionated into five solubility-based fractions, classified in two main groups: water-soluble and water-insoluble fractions. These fractions were then subjected to chemoselective reactions to tag molecules containing hydroxyl groups and analyzed by negative-ion electrospray ionization 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The fractions were also subjected to accelerated aging experiments and characterized by FT-ICR MS and bulk viscosity measurements. Extracting insightful information from ultrahigh-resolution data to aid in predicting upgrading methodologies and instability behaviors of bio-oils is challenging due to the complexity of the data. To address this, an unsupervised learning technique, k-means clustering analysis, was used to semiquantify molecular compositions with a close Euclidean distance within the (O/C, H/C) chemical space. The combination of k-means analysis with findings from chemoselective reactions allowed the distinctive hydroxyl functionalities across the samples to be inferred. Our results indicate that the hexane-soluble fraction contained numerous molecules containing primary and secondary alcohols, while the water-soluble fraction displayed diverse groups of oxygenated compounds, clustered near to carbohydrate-like and pyrolytic humin-like materials. Despite its high oxygen content, the water-soluble fraction showed minimal changes in viscosity during aging. In contrast, a significant increase in viscosity was observed in the water-insoluble materials, specifically, the low- and high-molecular-weight lignin fractions (LMWL and HMWL, respectively). Among these two fractions, the HMWL exhibited the highest increase in viscosity after only 4 h of accelerated aging. Our results indicate that this aging behavior is attributed to an increased number of molecular compositions containing phenolic groups. Thus, the chemical compositions within the HMWL are the major contributors to the viscosity changes in the bio-oil under accelerated aging conditions. This highlights the crucial role of oxygen functionality in bio-oil aging, suggesting that a high oxygen content alone does not necessarily correlate with an increase of viscosity. Unlike other bio-oil categorization methods based on constrained molecule locations within the van Krevelen compositional space, k-means clustering can identify patterns within ultrahigh-resolution data inherent to the unique chemical fingerprint of each sample.
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Affiliation(s)
| | - Daniel W Lester
- Polymer Characterisation Research Technology Platform, University of Warwick, Coventry CV4 7AL, U.K
| | - J S Town
- Polymer Characterisation Research Technology Platform, University of Warwick, Coventry CV4 7AL, U.K
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Martin Wills
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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5
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Schneider E, Neumann A, Chacón-Patiño ML, Somero M, Ruppel MM, Ihalainen M, Köster K, Sippula O, Czech H, Rüger CP, Zimmermann R. Accessing the Low-Polar Molecular Composition of Boreal and Arctic Peat-Burning Organic Aerosol via Thermal Analysis and Ultrahigh-Resolution Mass Spectrometry: Structural Motifs and Their Formation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1713-1725. [PMID: 38950165 DOI: 10.1021/jasms.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Peatland fires emit organic carbon-rich particulate matter into the atmosphere. Boreal and Arctic peatlands are becoming more vulnerable to wildfires, resulting in a need for better understanding of the emissions of these special fires. Extractable, nonpolar, and low-polar organic aerosol species emitted from laboratory-based boreal and Arctic peat-burning experiments are analyzed by direct-infusion atmospheric pressure photoionization (APPI) ultrahigh-resolution mass spectrometry (UHRMS) and compared to time-resolved APPI UHRMS evolved gas analysis from the thermal analysis of peat under inert nitrogen (pyrolysis) and oxidative atmosphere. The chemical composition is characterized on a molecular level, revealing abundant aromatic compounds that partially contain oxygen, nitrogen, or sulfur and are formed at characteristic temperatures. Two main structural motifs are identified, single core and multicore, and their temperature-dependent formation is assigned to the thermal degradation of the lignocellulose building blocks and other parts of peat.
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Affiliation(s)
- Eric Schneider
- Joint Mass Spectrometry Centre, Department of Analytical and Technical Chemistry, University of Rostock, 18059 Rostock, Germany
- Department Life, Light & Matter (LL&M), University of Rostock, 18059 Rostock, Germany
| | - Anika Neumann
- Joint Mass Spectrometry Centre, Department of Analytical and Technical Chemistry, University of Rostock, 18059 Rostock, Germany
- Department Life, Light & Matter (LL&M), University of Rostock, 18059 Rostock, Germany
| | - Martha L Chacón-Patiño
- National High Magnetic Field Laboratory, Florida State University, 32310 Tallahassee, United States
| | - Markus Somero
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Meri M Ruppel
- Atmospheric Composition Unit, Finnish Meteorological Institute, 00014 Helsinki, Finland
| | - Mika Ihalainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Kajar Köster
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Olli Sippula
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210 Kuopio, Finland
- Department of Chemistry, University of Eastern Finland, 80101 Joensuu, Finland
| | - Hendryk Czech
- Joint Mass Spectrometry Centre, Department of Analytical and Technical Chemistry, University of Rostock, 18059 Rostock, Germany
- Joint Mass Spectrometry Centre, Cooperation Group "Comprehensive Molecular Analytics" (CMA), Helmholtz Centre Munich, 85764 Neuherberg, Germany
| | - Christopher P Rüger
- Joint Mass Spectrometry Centre, Department of Analytical and Technical Chemistry, University of Rostock, 18059 Rostock, Germany
- Department Life, Light & Matter (LL&M), University of Rostock, 18059 Rostock, Germany
| | - Ralf Zimmermann
- Joint Mass Spectrometry Centre, Department of Analytical and Technical Chemistry, University of Rostock, 18059 Rostock, Germany
- Department Life, Light & Matter (LL&M), University of Rostock, 18059 Rostock, Germany
- Joint Mass Spectrometry Centre, Cooperation Group "Comprehensive Molecular Analytics" (CMA), Helmholtz Centre Munich, 85764 Neuherberg, Germany
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6
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Leach FE, Nagornov KO, Kozhinov AN, Tsybin YO. External Data Systems Enable Enhanced (and Sustainable) Fourier Transform Mass Spectrometry Imaging for Legacy Hybrid Linear Ion Trap-Orbitrap Platforms. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39031087 DOI: 10.1021/jasms.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
Legacy Fourier transform (FT) mass spectrometers provide robust platforms for bioanalytical mass spectrometry (MS) yet lack the most modern performance capabilities. For many laboratories, the routine investment in next generation instrumentation is cost prohibitive. Field-based upgrades provide a direct path to extend the usable lifespan of MS platforms which may be considered antiquated based on performance specifications at the time of manufacture. Here we demonstrate and evaluate the performance of a hybrid linear ion trap (LTQ)-Orbitrap mass spectrometer that has been enhanced via an external high-performance data acquisition and processing system to provide true absorption mode FT processing during an experimental acquisition. For the application to mass spectrometry imaging, several performance metrics have been improved including mass resolving power, mass accuracy, and dynamic range to provide an FTMS system comparable to current platforms. We also demonstrate, perhaps, the unexpected ability of these legacy platforms to detect usable time-domain signals up to 5 s in duration to achieve a mass resolving power 8× higher than the original platform specification.
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Affiliation(s)
- Franklin E Leach
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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7
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Mo X, Du P, Chan TWD, Shaw PC, Chow ATS. Fostering Adequate Data Reporting of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry-Based Environmental Studies. ACS ES&T WATER 2024; 4:2779-2781. [PMID: 39021581 PMCID: PMC11249965 DOI: 10.1021/acsestwater.4c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 07/20/2024]
Affiliation(s)
- Xiaohan Mo
- Earth
and Environmental Sciences Programme, The
Chinese University of Hong Kong, Shatin 999077, Hong
Kong SAR, China
| | - Penghui Du
- Earth
and Environmental Sciences Programme, The
Chinese University of Hong Kong, Shatin 999077, Hong
Kong SAR, China
| | - T.-W. Dominic Chan
- Department
of Chemistry, The Chinese University of
Hong Kong, Shatin 999077, Hong Kong SAR, China
| | - Pang Chui Shaw
- School
of Life Sciences, The Chinese University
of Hong Kong, Shatin 999077, Hong Kong SAR, China
- Li Dak
Sum Yip Yio Chin R&D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin 999077, Hong
Kong SAR, China
| | - Alex Tat-Shing Chow
- Earth
and Environmental Sciences Programme, The
Chinese University of Hong Kong, Shatin 999077, Hong
Kong SAR, China
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8
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Cheng J, Robles-Lecompte A, McKenna AM, Chang NB. Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system. CHEMOSPHERE 2024; 357:142042. [PMID: 38621490 DOI: 10.1016/j.chemosphere.2024.142042] [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: 02/23/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.
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Affiliation(s)
- Jinxiang Cheng
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Alejandra Robles-Lecompte
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ni-Bin Chang
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA.
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9
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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10
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Cai YH, Wang CC, Hsiao CH, Wang YS. Experimental Validation of Comprehensive Calculation for High-Resolution Linear MALDI-TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:992-998. [PMID: 38634762 PMCID: PMC11066958 DOI: 10.1021/jasms.4c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
This work discusses the effectiveness of the previously developed comprehensive calculation model to optimize linear MALDI-TOF mass spectrometers. The model couples space- and velocity-focusing to precisely analyze the flight-time distribution of ions and predict optimal experimental parameters for the highest mass resolving power. Experimental validation was conducted using a laboratory-made instrument to analyze CsI3 and angiotensin I ions in low to medium m/z range. The results indicate that the predicted optimal extraction voltage and delay were reasonably accurate and effective. In the low m/z range, the peak width obtained using optimal parameters reached the sub nanosecond range, corresponding to a mass resolving power of 10 000-17 000, or 20 000-34 000 if shot-to-shot random fluctuations were minimized by the dynamic data correction method. The observed optimal mass resolving power in the current experiment is 4.8-7.8 times that of commercial instruments. Practical limitations resulting in the gap between the observed and theoretical ultimate mass resolving power are discussed.
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Affiliation(s)
- Yi-Hong Cai
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan ROC
| | - Chia-Chen Wang
- Instrumentation
Center, National Taiwan Normal University, Taipei 106, Taiwan ROC
| | - Chih-Hao Hsiao
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan ROC
| | - Yi-Sheng Wang
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan ROC
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11
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VanderRoest JP, Fowler JA, Rhoades CC, Roth HK, Broeckling CD, Fegel TS, McKenna AM, Bechtold EK, Boot CM, Wilkins MJ, Borch T. Fire Impacts on the Soil Metabolome and Organic Matter Biodegradability. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4167-4180. [PMID: 38385432 DOI: 10.1021/acs.est.3c09797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Global wildfire activity has increased since the 1970s and is projected to intensify throughout the 21st century. Wildfires change the composition and biodegradability of soil organic matter (SOM) which contains nutrients that fuel microbial metabolism. Though persistent forms of SOM often increase postfire, the response of more biodegradable SOM remains unclear. Here we simulated severe wildfires through a controlled "pyrocosm" approach to identify biodegradable sources of SOM and characterize the soil metabolome immediately postfire. Using microbial amplicon (16S/ITS) sequencing and gas chromatography-mass spectrometry, heterotrophic microbes (Actinobacteria, Firmicutes, and Protobacteria) and specific metabolites (glycine, protocatechuate, citric cycle intermediates) were enriched in burned soils, indicating that burned soils contain a variety of substrates that support microbial metabolism. Molecular formulas assigned by 21 T Fourier transform ion cyclotron resonance mass spectrometry showed that SOM in burned soil was lower in molecular weight and featured 20 to 43% more nitrogen-containing molecular formulas than unburned soil. We also measured higher water extractable organic carbon concentrations and higher CO2 efflux in burned soils. The observed enrichment of biodegradable SOM and microbial heterotrophs demonstrates the resilience of these soils to severe burning, providing important implications for postfire soil microbial and plant recolonization and ecosystem recovery.
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Affiliation(s)
- Jacob P VanderRoest
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Julie A Fowler
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Holly K Roth
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Corey D Broeckling
- Bioanalysis and Omics Center, Analytical Resources Core, Colorado State University, Fort Collins, 80521, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Emily K Bechtold
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Claudia M Boot
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
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12
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Ivanova B. Special Issue with Research Topics on "Recent Analysis and Applications of Mass Spectra on Biochemistry". Int J Mol Sci 2024; 25:1995. [PMID: 38396673 PMCID: PMC10888122 DOI: 10.3390/ijms25041995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Analytical mass spectrometry applies irreplaceable mass spectrometric (MS) methods to analytical chemistry and chemical analysis, among other areas of analytical science [...].
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
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13
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Hu Z, McKenna AM, Wen K, Zhang B, Mao H, Goual L, Feng X, Zhu M. Controls of Mineral Solubility on Adsorption-Induced Molecular Fractionation of Dissolved Organic Matter Revealed by 21 T FT-ICR MS. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2313-2322. [PMID: 38266164 DOI: 10.1021/acs.est.3c08123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Mineral adsorption-induced molecular fractionation of dissolved organic matter (DOM) affects the composition of both DOM and OM adsorbed and thus stabilized by minerals. However, it remains unclear what mineral properties control the magnitude of DOM fractionation. Using a combined technique approach that leverages the molecular composition identified by ultrahigh resolution 21 T Fourier transform ion cyclotron resonance mass spectrometry and adsorption isotherms, we catalogue the compositional differences that occur at the molecular level that results in fractionation due to adsorption of Suwannee River fulvic acid on aluminum (Al) and iron (Fe) oxides and a phyllosilicate (allophane) species of contrasting properties. The minerals of high solubility (i.e., amorphous Al oxide, boehmite, and allophane) exhibited much stronger DOM fractionation capabilities than the minerals of low solubility (i.e., gibbsite and Fe oxides). Specifically, the former released Al3+ to solution (0.05-0.35 mM) that formed complexes with OM and likely reduced the surface hydrophobicity of the mineral-OM assemblage, thus increasing the preference for adsorbing polar DOM molecules. The impacts of mineral solubility are exacerbated by the fact that interactions with DOM also enhance metal release from minerals. For sparsely soluble minerals, the mineral surface hydrophobicity, instead of solubility, appeared to be the primary control of their DOM fractionation power. Other chemical properties seemed less directly relevant than surface hydrophobicity and solubility in fractionating DOM.
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Affiliation(s)
- Zhen Hu
- Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Hubei Hongshan Laboratory, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430063, China
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Ke Wen
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Bingjun Zhang
- Department of Petroleum Engineering, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Hairuo Mao
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Lamia Goual
- Department of Petroleum Engineering, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Xionghan Feng
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengqiang Zhu
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
- Department of Geology, University of Maryland, College Park, Maryland 20742, United States
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14
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Mallick SP, Patel HV, Gawande S, Wadee A, Chen H, McKenna AM, Brazil B, Yu W, Zhao R. Using landfill leachate to indicate the chemical and biochemical activities in elevated temperature landfills. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119719. [PMID: 38043306 DOI: 10.1016/j.jenvman.2023.119719] [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: 09/10/2023] [Revised: 11/05/2023] [Accepted: 11/23/2023] [Indexed: 12/05/2023]
Abstract
Landfill leachate properties contain important information and can be a unique indicator for the chemical and biochemical activities in landfills. In the recent decade, more landfills are experiencing elevated temperature, causing an imbalance in the decomposition of solid waste and affecting the properties of the landfill leachate. This study analyzes the properties of leachate from two landfills that were experiencing elevated temperature (ETLFs), samples were collected from both elevated temperature impacted and non-impacted areas in each landfill. The accumulation of volatile fatty acids (VFA) in leachates from elevated temperature impacted areas of both landfill sites revealed that methanogenesis was inhibited by the elevated temperature, which was further confirmed by the more acidic pH, higher H/C elemental ratio, and lower degree of aromaticity of the elevated temperature impacted leachates. Also, carbohydrates depletion indicated possible enhancement of hydrolysis and acidogenesis by elevated temperature, which was supported by compositional comparison of isolated acidic species by negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS) at 21 T derived from both elevated temperature impacted and non-impacted areas in the same landfill site. Furthermore, leachate organics fractionation showed that leachates not impacted by elevated temperature contain less hydrophilic fraction and more humic fraction than elevated temperature-impacted leachates for both ETLFs.
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Affiliation(s)
| | - Harsh V Patel
- Department of Civil, Architectural and Environmental Engineering, North Carolina A&T State University, Greensboro, NC, 27411, USA
| | - Sailee Gawande
- Texas Commission on Environmental Quality (TCEQ), Fort Worth, TX, 76118, USA
| | | | - Huan Chen
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310-4205, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310-4205, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Brian Brazil
- Waste Management Inc. Gaithersburg, MD, 20878, USA
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Renzun Zhao
- Department of Civil, Architectural and Environmental Engineering, North Carolina A&T State University, Greensboro, NC, 27411, USA.
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15
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Grgic A, Nagornov KO, Kozhinov AN, Michael JA, Anthony IG, Tsybin YO, Heeren RM, Ellis SR. Ultrahigh-Mass Resolution Mass Spectrometry Imaging with an Orbitrap Externally Coupled to a High-Performance Data Acquisition System. Anal Chem 2024; 96:794-801. [PMID: 38127459 PMCID: PMC10794996 DOI: 10.1021/acs.analchem.3c04146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) is a powerful analytical tool that enables molecular sample analysis while simultaneously providing the spatial context of hundreds or even thousands of analytes. However, because of the lack of a separation step prior to ionization and the immense diversity of biomolecules, such as lipids, including numerous isobaric species, the coupling of ultrahigh mass resolution (UHR) with MSI presents one way in which this complexity can be resolved at the spectrum level. Until now, UHR MSI platforms have been restricted to Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. Here, we demonstrate the capabilities of an Orbitrap-based UHR MSI platform to reach over 1,000,000 mass resolution in a lipid mass range (600-950 Da). Externally coupling the Orbitrap Q Exactive HF with the high-performance data acquisition system FTMS Booster X2 provided access to the unreduced data in the form of full-profile absorption-mode FT mass spectra. In addition, it allowed us to increase the time-domain transient length from 0.5 to 10 s, providing improvement in the mass resolution, signal-to-noise ratio, and mass accuracy. The resulting UHR performance generates high-quality MALDI MSI images and simplifies the identification of lipids. Collectively, these improvements resulted in a 1.5-fold increase in annotations, demonstrating the advantages of this UHR imaging platform for spatial lipidomics using MALDI-MSI.
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Affiliation(s)
- Andrej Grgic
- The
Maastricht MultiModal Molecular Imaging (M4I) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229-ER Maastricht, Netherlands
| | | | | | - Jesse A. Michael
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Ian G.M. Anthony
- The
Maastricht MultiModal Molecular Imaging (M4I) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229-ER Maastricht, Netherlands
| | | | - Ron M.A. Heeren
- The
Maastricht MultiModal Molecular Imaging (M4I) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229-ER Maastricht, Netherlands
| | - Shane R. Ellis
- The
Maastricht MultiModal Molecular Imaging (M4I) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229-ER Maastricht, Netherlands
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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16
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Champiny RE, Bacon AR, Brush ID, McKenna AM, Colopietro DJ, Lin Y. Unraveling the persistence of deep podzolized carbon: Insights from organic matter characterization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167382. [PMID: 37774867 DOI: 10.1016/j.scitotenv.2023.167382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/14/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
Abstract
Over a billion tons of terrestrial carbon (C) is stored in deep soils from the Southeastern Coastal Plain of the United States. While the size and extent of this pool, known as deep podzolized carbon (DPC), have been reported in recent studies, the stabilization mechanisms responsible for its persistence are unclear. The main hypothesis of DPC stabilization is that hydrology, specifically water table fluctuations in the phreatic zone, slow microbial degradation and promote C accumulation. This accounts for the characteristic properties and distribution of DPC and provides a mechanistic distinction between DPC and shallow podzolized C in the region's soils, however it has yet to be tested. We characterized the organic matter composition of the bulk and dissolved fractions of DPC using elemental analysis, solvent extraction, infrared spectroscopy, and high-resolution mass spectrometry. Consistent with past work, the majority of DPC organic matter was extractable by sodium pyrophosphate solution; the influence of metal association was also observable in the water extractable fraction of DPC with large species being preferentially removed and a low compound diversity compared to those from other horizons overlying DPC. Only water extractable species with low molecular mass (m/z < 375 Da) showed significant change in average nominal oxidation state of carbon (NOSC) values, indicative of oxygen-limitation influence on the processing of these species. Infrared spectroscopy revealed an increase in abundance of aliphatic (C-H:C-O) bonds relative to polysaccharide bonds with depth whereas aromatic (C=C:C-O) bonds decreased with depth in DPC relative to other subsurface horizons. Our work shows that DPC is significantly more refractory than overlying surface soil C, and yet slightly more labile than the subsoils above DPC. Together our results suggest that the maintenance of low redox conditions via persistent water saturation contributes to the stabilization and persistence of DPC.
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Affiliation(s)
- Ryan E Champiny
- Department of Soil, Water, and Ecosystem Science, University of Florida, Gainesville, FL 32611, USA.
| | - Allan R Bacon
- Department of Soil, Water, and Ecosystem Science, University of Florida, Gainesville, FL 32611, USA
| | - Isabella D Brush
- Department of Soil, Water, and Ecosystem Science, University of Florida, Gainesville, FL 32611, USA
| | - Amy M McKenna
- National Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Daniel J Colopietro
- Department of Soil, Water, and Ecosystem Science, University of Florida, Gainesville, FL 32611, USA
| | - Yang Lin
- Department of Soil, Water, and Ecosystem Science, University of Florida, Gainesville, FL 32611, USA
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17
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Meng L, Xue J, Zhao C, Huang T, Yang H, Zhao K, Yu Z, Yuan L, Zhou Q, Kellerman AM, McKenna AM, Spencer RGM, Huang C. N-containing dissolved organic matter promotes dissolved inorganic carbon supersaturation in the Yangtze River, China. WATER RESEARCH 2023; 247:120808. [PMID: 37924684 DOI: 10.1016/j.watres.2023.120808] [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: 06/28/2023] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023]
Abstract
Dissolved inorganic carbon (DIC) represents a major global carbon pool and the flux from rivers to oceans has been observed to be increasing. The effect of weathering with respect to increasing DIC has been widely studied in recent decades; however, the influence of dissolved organic matter (DOM) on increasing DIC in large rivers remains unclear. This study employed stable carbon isotopes and Fourier transform ion cyclotron mass spectrometry (FT-ICR MS) to investigate the effect of the molecular composition of DOM on the DIC in the Yangtze River. The results showed that organic matter is an important source of DIC in the Yangtze River, accounting for 40.0 ± 12.1 % and 32.0 ± 7.2 % of DIC in wet and dry seasons, respectively, and increased along the river by approximately three times. Nitrogen (N)-containing DOM, an important composition in DOM with a percentage of ∼40 %, showed superior oxidation state than non N-containing DOM, suggesting that the presence of N could improve the degradable potential of DOM. Positive relationship between organic sourced DIC (DICOC) and N-containing DOM formulae indicated that N-containing DOM is crucial to facilitate the mineralization of DOM to DICOC. N-containg molecular formular with low H/C and O/C ratio were positively correlated with DICOC further verified these energy-rich and biolabile compounds are preferentially decomposed by bacteria to produce DIC. N-containing components significantly accelerated the degradation of DOM to DICOC, which is important for understanding the CO2 emission and carbon cycling in large rivers.
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Affiliation(s)
- Lize Meng
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Jingya Xue
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Chu Zhao
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Tao Huang
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China.
| | - Hao Yang
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Kan Zhao
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Zhaoyuan Yu
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Linwang Yuan
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Qichao Zhou
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, PR China
| | - Anne M Kellerman
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert G M Spencer
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Changchun Huang
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; School of Geography, Nanjing Normal University, Nanjing 210023, PR China.
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18
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Counihan KL, McKenna AM, Hebert D, Tomco P, Zito P. Photo-Enhanced Oil Toxicity to Alcid Immune Function. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:2701-2711. [PMID: 37671848 DOI: 10.1002/etc.5742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/23/2023] [Accepted: 08/30/2023] [Indexed: 09/07/2023]
Abstract
Oil spills are devastating to seabirds, causing high levels of mortality and toxic physiological effects, especially to immune function. Sunlight exposure can further enhance the toxicity of oil to marine species by generating photodegradation products. Photo-enhanced oil toxicity to marine birds has not been studied. Therefore, the goal of the present study was to investigate the toxicity and photo-enhanced toxicity of oil to lymphocyte proliferation, macrophage phagocytosis, and reactive oxygen species production in three alcid species, common murres (Uria aalge), tufted puffins (Fratercula cirrhata), and horned puffins (Fratercula corniculata). Intrinsic factors (species, age, and sex) had a more significant effect on lymphocyte proliferation than exposure to oil or photoactivated oil. Macrophage phagocytosis was significantly reduced in oil and photoactivated oil treatments, whereas hydrogen peroxide production was significantly increased. Interestingly, nonphotoactivated oil stimulated significantly more hydrogen peroxide than photoactivated oil. The results suggest that alcid immune function could be variably influenced during an oil spill depending on the species, sex, and age of the bird as well as the season and level of sunlight exposure. Environ Toxicol Chem 2023;42:2701-2711. © 2023 SETAC.
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Affiliation(s)
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University, Tallahassee, Florida, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Deja Hebert
- Department of Chemistry, Chemical Analysis & Mass Spectrometry Facility, University of New Orleans, New Orleans, Louisiana, USA
| | - Patrick Tomco
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska, USA
| | - Phoebe Zito
- Department of Chemistry, Chemical Analysis & Mass Spectrometry Facility, University of New Orleans, New Orleans, Louisiana, USA
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska, USA
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19
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Dong H, Cuthbertson AA, Plewa MJ, Weisbrod CR, McKenna AM, Richardson SD. Unravelling High-Molecular-Weight DBP Toxicity Drivers in Chlorinated and Chloraminated Drinking Water: Effect-Directed Analysis of Molecular Weight Fractions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18788-18800. [PMID: 37418586 DOI: 10.1021/acs.est.3c00771] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
As disinfection byproducts (DBPs) are ubiquitous sources of chemical exposure in disinfected drinking water, identifying unknown DBPs, especially unknown drivers of toxicity, is one of the major challenges in the safe supply of drinking water. While >700 low-molecular-weight DBPs have been identified, the molecular composition of high-molecular-weight DBPs remains poorly understood. Moreover, due to the absence of chemical standards for most DBPs, it is difficult to assess toxicity contributions for new DBPs identified. Based on effect-directed analysis, this study combined predictive cytotoxicity and quantitative genotoxicity analyses and Fourier transform ion cyclotron resonance mass spectrometry (21 T FT-ICR-MS) identification to resolve molecular weight fractions that induce toxicity in chloraminated and chlorinated drinking waters, along with the molecular composition of these DBP drivers. Fractionation using ultrafiltration membranes allowed the investigation of <1 kD, 1-3 kD, 3-5 kD, and >5 kD molecular weight fractions. Thiol reactivity based predictive cytotoxicity and single-cell gel electrophoresis based genotoxicity assays revealed that the <1 kD fraction for both chloraminated and chlorinated waters exhibited the highest levels of predictive cytotoxicity and direct genotoxicity. The <1 kD target fraction was used for subsequent molecular composition identification. Ultrahigh-resolution MS identified singly charged species (as evidenced by the 1 Da spacing in 13C isotopologues), including 3599 chlorine-containing DBPs in the <1 kD fraction with the empirical formulas CHOCl, CHOCl2, and CHOCl3, with a relative abundance order of CHOCl > CHOCl2 ≫ CHOCl3. Interestingly, more high-molecular-weight CHOCl1-3 DBPs were identified in the chloraminated vs chlorinated waters. This may be due to slower reactions of NH2Cl. Most of the DBPs formed in chloraminated waters were composed of high-molecular-weight Cl-DBPs (up to 1 kD) rather than known low-molecular-weight DBPs. Moreover, with the increase of chlorine number in the high-molecular-weight DBPs detected, the O/C ratio exhibited an increasing trend, while the modified aromaticity index (AImod) showed an opposite trend. In drinking water treatment processes, the removal of natural organic matter fractions with high O/C ratio and high AImod value should be strengthened to minimize the formation of known and unknown DBPs.
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Affiliation(s)
- Huiyu Dong
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Beijing 100085, People's Republic of China
| | - Amy A Cuthbertson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Michael J Plewa
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Susan D Richardson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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20
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Lai YH, Wang YS. Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions. MASS SPECTROMETRY REVIEWS 2023; 42:2426-2445. [PMID: 35686331 DOI: 10.1002/mas.21790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/27/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.
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Affiliation(s)
- Yin-Hung Lai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National United University, Miaoli, Taiwan, R.O.C
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, R.O.C
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
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21
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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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22
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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23
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Maillard J, Carrasco N, Rüger CP, Chatain A, Schmitz-Afonso I, Weisbrod CR, Bailly L, Petit E, Gautier T, McKenna AM, Afonso C. Humid Evolution of Haze in the Atmosphere of Super-Earths in the Habitable Zone. ASTROBIOLOGY 2023; 23:723-732. [PMID: 37229532 DOI: 10.1089/ast.2022.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Abstract Photochemical hazes are expected to form and significantly contribute to the chemical and radiative balance of exoplanets with relatively moderate temperatures, possibly in the habitable zone of their host star. In the presence of humidity, haze particles might thus serve as cloud condensation nuclei and trigger the formation of water droplets. In the present work, we are interested in the chemical impact of such a close interaction between photochemical hazes and humidity on the organic content composing the hazes and on the capacity to generate organic molecules with high prebiotic potential. For this purpose, we explore experimentally the sweet spot by combining N-dominated super-Earth exoplanets in agreement with Titan's rich organic photochemistry and humid conditions expected for exoplanets in habitable zones. A logarithmic increase with time is observed for the relative abundance of oxygenated species, with O-containing molecules dominating after 1 month only. The rapidity of the process suggests that the humid evolution of N-rich organic haze provides an efficient source of molecules with high prebiotic potential.
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Affiliation(s)
- Julien Maillard
- Université Paris-Saclay, UVSQ, CNRS, LATMOS, Guyancourt, France
- Normandie Univ, COBRA UMR 6014 et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, Mont-Saint-Aignan, France
| | | | - Christopher P Rüger
- Normandie Univ, COBRA UMR 6014 et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, Mont-Saint-Aignan, France
| | - Audrey Chatain
- Université Paris-Saclay, UVSQ, CNRS, LATMOS, Guyancourt, France
| | - Isabelle Schmitz-Afonso
- Normandie Univ, COBRA UMR 6014 et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, Mont-Saint-Aignan, France
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Laetitia Bailly
- Normandie Univ, COBRA UMR 6014 et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, Mont-Saint-Aignan, France
| | - Emilie Petit
- Normandie Univ, COBRA UMR 6014 et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, Mont-Saint-Aignan, France
| | - Thomas Gautier
- Université Paris-Saclay, UVSQ, CNRS, LATMOS, Guyancourt, France
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Carlos Afonso
- Normandie Univ, COBRA UMR 6014 et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, Mont-Saint-Aignan, France
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24
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Gosset-Erard C, Aubriet F, Leize-Wagner E, François YN, Chaimbault P. Hyphenation of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with separation methods: The art of compromises and the possible - A review. Talanta 2023; 257:124324. [PMID: 36780779 DOI: 10.1016/j.talanta.2023.124324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
This review provides an overview of the online hyphenation of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with separation methods to date. The online coupling between separation techniques (gas and liquid chromatography, capillary electrophoresis) and FT-ICR MS essentially raises questions of compromise and is not look as straightforward as hyphenation with other analyzers (QTOF-MS for instance). FT-ICR MS requires time to reach its highest resolving power and accuracy in mass measurement capabilities whereas chromatographic and electrophoretic peaks are transient. In many applications, the strengths and the weaknesses of each technique are balanced by their hyphenation. Untargeted "Omics" (e.g. proteomics, metabolomics, petroleomics, …) is one of the main areas of application for FT-ICR MS hyphenated to online separation techniques because of the complexity of the sample. FT-ICR MS achieves the required high mass measurement accuracy to determine accurate molecular formulae and resolution for isobar distinction. Meanwhile separation techniques highlight isomers and reduce the ion suppression effects extending the dynamic range. Even if the implementation of FT-ICR MS hyphenated with online separation methods is a little trickier (the art of compromise), this review shows that it provides unparalleled results to the scientific community (the art of the possible), along with raising the issue of its future in the field with the relentless technological progress.
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Affiliation(s)
- Clarisse Gosset-Erard
- Université de Lorraine, LCP-A2MC, F-57000, Metz, France; Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
| | | | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
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25
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Castro DC, Smith KW, Norsworthy MD, Rubakhin SS, Weisbrod CR, Hendrickson CL, Sweedler JV. Single-Cell and Subcellular Analysis Using Ultrahigh Resolution 21 T MALDI FTICR Mass Spectrometry. Anal Chem 2023; 95:6980-6988. [PMID: 37070980 PMCID: PMC10190686 DOI: 10.1021/acs.analchem.3c00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The mammalian brain contains ∼20,000 distinct lipid species that contribute to its structural organization and function. The lipid profiles of cells change in response to a variety of cellular signals and environmental conditions that result in modulation of cell function through alteration of phenotype. The limited sample material combined with the vast chemical diversity of lipids makes comprehensive lipid profiling of individual cells challenging. Here, we leverage the resolving power of a 21 T Fourier-transform ion cyclotron resonance (FTICR) mass spectrometer for chemical characterization of individual hippocampal cells at ultrahigh mass resolution. The accuracy of the acquired data allowed differentiation of freshly isolated and cultured hippocampal cell populations, as well as finding differences in lipids between the soma and neuronal processes of the same cell. Differences in lipids include TG 42:2 observed solely in the cell bodies and SM 34:1;O2 found only in the cellular processes. The work represents the first mammalian single cells analyzed at ultrahigh resolution and is an advance in the performance of mass spectrometry (MS) for single-cell research.
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Affiliation(s)
- Daniel C. Castro
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
| | - Karl W. Smith
- National High Magnetic Field Laboratory, Florida State University, 1801 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Miles D. Norsworthy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801 United States
| | - Stanislav S. Rubakhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana IL 61801, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
| | - Chad R. Weisbrod
- National High Magnetic Field Laboratory, Florida State University, 1801 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Christopher L. Hendrickson
- National High Magnetic Field Laboratory, Florida State University, 1801 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Jonathan V. Sweedler
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana IL 61801, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, IL 61801, United States
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26
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Lioznov A, Nikolaev E. The analytical solution for the optimum voltage on regularizing electrodes of the open dynamically harmonized cell. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:97-101. [PMID: 36922755 DOI: 10.1177/14690667231164552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The Fourier transform ion cyclotron resonance method holds the lead in mass accuracy and resolving power among all other mass spectrometry methods. The dynamically harmonized cell is largely responsible for the supremacy. This cell has an ideal hyperbolic trapping potential after averaging over fast cyclotron motion. Recently we have introduced an open modification of the cell (especially useful with ultrahigh magnetic fields) and have found the analytical solution for the averaged potential inside it. The voltage on specific "regularizing" electrodes determines how close a potential is to the hyperbolic one. In this article, we find the optimal voltage on these "regularizing" electrodes analytically. This will assist with both further analysis and tuning of the trap after manufacturing.
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Affiliation(s)
- Anton Lioznov
- Center of Life Science, 366033Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgeny Nikolaev
- Center of Life Science, 366033Skolkovo Institute of Science and Technology, Moscow, Russia
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27
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Claesen J, Rockwood A, Gorshkov M, Valkenborg D. The isotope distribution: A rose with thorns. MASS SPECTROMETRY REVIEWS 2023. [PMID: 36744702 DOI: 10.1002/mas.21820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/03/2022] [Accepted: 10/21/2022] [Indexed: 06/18/2023]
Abstract
The isotope distribution, which reflects the number and probabilities of occurrence of different isotopologues of a molecule, can be theoretically calculated. With the current generation of (ultra)-high-resolution mass spectrometers, the isotope distribution of molecules can be measured with high sensitivity, resolution, and mass accuracy. However, the observed isotope distribution can differ substantially from the expected isotope distribution. Although differences between the observed and expected isotope distribution can complicate the analysis and interpretation of mass spectral data, they can be helpful in a number of specific applications. These applications include, yet are not limited to, the identification of peptides in proteomics, elucidation of the elemental composition of small organic molecules and metabolites, as well as wading through peaks in mass spectra of complex bioorganic mixtures such as petroleum and humus. In this review, we give a nonexhaustive overview of factors that have an impact on the observed isotope distribution, such as elemental isotope deviations, ion sampling, ion interactions, electronic noise and dephasing, centroiding, and apodization. These factors occur at different stages of obtaining the isotope distribution: during the collection of the sample, during the ionization and intake of a molecule in a mass spectrometer, during the mass separation and detection of ionized molecules, and during signal processing.
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Affiliation(s)
- Jürgen Claesen
- Department of Epidemiology and Data Science, Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, The Netherlands
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Alan Rockwood
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Mikhail Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Dirk Valkenborg
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
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28
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Lin Y, Agarwal AM, Anderson LC, Marshall AG. Discovery of a biomarker for β-Thalassemia by HPLC-MS and improvement from Proton Transfer Reaction - Parallel Ion Parking. J Mass Spectrom Adv Clin Lab 2023; 28:20-26. [PMID: 36814695 PMCID: PMC9939715 DOI: 10.1016/j.jmsacl.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
β-thalassemia is a quantitative hemoglobin (Hb) disorder resulting in reduced production of Hb A and increased levels of Hb A2. Diagnosis of β-thalassemia can be problematic when combined with other structural Hb variants, so that the separation approaches in routine clinical centers are not sufficiently decisive to obtain accurate results. Here, we separate the intact Hb subunits by high-performance liquid chromatography, followed by top-down tandem mass spectrometry of intact subunits to distinguish Hb variants. Proton transfer reaction-parallel ion parking (PTR-PIP), in which a radical anion removes protons from multiply charged precursor ions and produces charge-reduced ions spanning a limited m/z range, was used to increase the signal-to-noise ratio of the subunits of interest. We demonstrate that the δ/β ratio can act as a biomarker to identify β-thalassemia in normal electrospray ionization MS1 and PTR-PIP MS1. The application of PTR-PIP significantly increases the sensitivity and specificity of the HPLC-MS method to identify δ/β ratio as a thalassemia biomarker.
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Key Words
- ACN, Acetonitrile
- AUC, Areas under the curve
- CID, Collision-induced dissociation
- ESI, Electrospray ionization
- ETD, Electron-transfer dissociation
- FA, Formic acid
- FN, False-negative
- FP, False-positive
- FT-ICR
- FT-ICR, MS Fourier transform ion cyclotron resonance mass spectrometer
- FTMS
- Fourier transform ion cyclotron resonance
- Hb A, Normal adult Hb
- Hb, Hemoglobin
- HbA1d, Hb β with glutathione
- IFCC, International Federation of Clinical Chemistry and Laboratory Medicine
- IQR, Interquartile range
- J, Youden Index
- MCW, Methanol/chloroform/water
- MS, Mass spectrometry
- PTM, Post-translational modification
- PTR-PIP, Proton transfer reaction-parallel ion parking
- ROC, Receiver operating characteristic
- S/N, Signal-to-noise ratios
- Se(c), Sensitivity, the probability of a true positive)
- Sp(c), Specificity, the probability of a true negative)
- TIC, Total ion chromatogram
- TN, True negative
- TP, True positive
- Top-down
- XIC, Extracted ion chromatograms
- m/z, Mass-to-charge ratios
- δ/β ratio
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Affiliation(s)
- Yuan Lin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States
| | - Archana M. Agarwal
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, United States,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, United States
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States,Corresponding authors at: Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States (A.G. Marshall).
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States,Corresponding authors at: Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States (A.G. Marshall).
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29
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Popovic Z, Anderson LC, Zhang X, Butcher DS, Blakney GT, Zubarev RA, Marshall AG. Analysis of Isotopically Depleted Proteins Derived from Escherichia coli and Caenorhabditis elegans Cell Lines by Liquid Chromatography 21 T Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:137-144. [PMID: 36656140 DOI: 10.1021/jasms.2c00242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Protein mass measurement by mass spectrometry is complicated by wide isotopic distributions that result from incorporation of heavy isotopes of C, H, N, O, and S, thereby limiting signal-to-noise ratio (SNR) and accurate intact mass determination, particularly for larger proteins [Fenselau et al. Anal. Chem. 1983, 55 (2), 353-356]. Observation of the monoisotopic mass-to-charge ratio (m/z) is the simplest and most accurate way to determine intact protein mass, but as mass increases, the relative abundance of the monoisotopic peak becomes so low that it is often undetectable. Here, we used an isotopically depleted growth medium to culture bacterial cells (Escherichia coli), resulting in isotopically depleted proteins. Isotopically depleted proteins show increased sequence coverage, mass measurement accuracy, and increased S/N of the monoisotopic peak by Fourier transform ion cyclotron resonance mass spectrometry analysis. We then grew Caenorhabditis elegans cells in a medium containing living isotopically depleted E. coli cells, thereby producing the first isotopically depleted eukaryotic proteins. This is the first time isotopic depletion has been implemented for four isotopes (1H, 12C, 14N, and 16O), resulting in the highest degree of depletion ever used for protein analysis and further improving MS analysis.
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Affiliation(s)
- Zeljka Popovic
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Xuepei Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavagen 1, Solna, 171 77 Stockholm, Sweden
| | - David S Butcher
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Greg T Blakney
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Roman A Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavagen 1, Solna, 171 77 Stockholm, Sweden
| | - Alan G Marshall
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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30
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Adams LM, DeHart CJ, Drown BS, Anderson LC, Bocik W, Boja ES, Hiltke TM, Hendrickson CL, Rodriguez H, Caldwell M, Vafabakhsh R, Kelleher NL. Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling. J Biol Chem 2022; 299:102768. [PMID: 36470426 PMCID: PMC9808003 DOI: 10.1016/j.jbc.2022.102768] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
The KRAS gene is one of the most frequently mutated oncogenes in human cancer and gives rise to two isoforms, KRAS4A and KRAS4B. KRAS post-translational modifications (PTMs) have the potential to influence downstream signaling. However, the relationship between KRAS PTMs and oncogenic mutations remains unclear, and the extent of isoform-specific modification is unknown. Here, we present the first top-down proteomics study evaluating both KRAS4A and KRAS4B, resulting in 39 completely characterized proteoforms across colorectal cancer cell lines and primary tumor samples. We determined which KRAS PTMs are present, along with their relative abundance, and that proteoforms of KRAS4A versus KRAS4B are differentially modified. Moreover, we identified a subset of KRAS4B proteoforms lacking the C185 residue and associated C-terminal PTMs. By confocal microscopy, we confirmed that this truncated GFP-KRAS4BC185∗ proteoform is unable to associate with the plasma membrane, resulting in a decrease in mitogen-activated protein kinase signaling pathway activation. Collectively, our study provides a reference set of functionally distinct KRAS proteoforms and the colorectal cancer contexts in which they are present.
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Affiliation(s)
- Lauren M. Adams
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Caroline J. DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bryon S. Drown
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - William Bocik
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Emily S. Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | - Tara M. Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | | | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | - Michael Caldwell
- Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA,Department of Chemistry, Northwestern University, Evanston, Illinois, USA,Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA,For correspondence: Neil L. Kelleher
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31
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Creydt M, Fischer M. Food metabolomics: Latest hardware-developments for nontargeted food authenticity and food safety testing. Electrophoresis 2022; 43:2334-2350. [PMID: 36104152 DOI: 10.1002/elps.202200126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 12/14/2022]
Abstract
The analytical requirements for food testing have increased significantly in recent years. On the one hand, because food fraud is becoming an ever-greater challenge worldwide, and on the other hand because food safety is often difficult to monitor due to the far-reaching trade chains. In addition, the expectations of consumers on the quality of food have increased, and they are demanding extensive information. Cutting-edge analytical methods are required to meet these demands. In this context, non-targeted metabolomics strategies using mass and nuclear magnetic resonance spectrometers (mass spectrometry [MS]) have proven to be very suitable. MS-based approaches are of particular importance as they provide a comparatively high analytical coverage of the metabolome. Accordingly, the efficiency to address even challenging issues is high. A variety of hardware developments, which are explained in this review, have contributed to these advances. In addition, the potential of future developments is highlighted, some of which are currently not yet commercially available or only used to a comparatively small extent but are expected to gain in importance in the coming years.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Hamburg, Germany
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32
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Lioznov A, Nikolaev E. Generalization of an Open Dynamically Harmonized Cell for Ultrahigh FT ICR Resolution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2032-2037. [PMID: 36251283 DOI: 10.1021/jasms.2c00133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
FT ICR mass spectrometry is the leader in resolving power among all mass spectrometry methods. Introduction of the dynamically harmonized measuring cell─a closed-cylindrical cell with specifically shaped electrodes─helps to reach the resolving power of more than 107 with a magnetic field of about 7 T. From the theory of FT ICR mass spectrometry it follows that the resolving power of this type of instrument depends linearly on the magnetic field under various conditions. However, the results obtained on this type of mass spectrometer with the maximum magnetic field achievable today did not show a proportional increase in resolving power. In one of our previous papers, we assumed that the reason for this was insufficient vacuum inside the cell, since vacuum quality should be at least proportional to the magnetic field, since the mean free run time decreases proportionally to the magnetic field growth. We have presented an open modification of the dynamically harmonized cell that can help improve the cell pumping conditions. However, the electric potential distribution inside this new cell is slightly different from the ideal (harmonic) one, obtained inside the closed version of the cell, and the resolving power may have been limited by this difference.
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Affiliation(s)
- Anton Lioznov
- Center of Life Science, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow121205Russia
| | - Evgeny Nikolaev
- Center of Life Science, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow121205Russia
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33
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Ijaz A, Kew W, China S, Schum SK, Mazzoleni LR. Molecular Characterization of Organophosphorus Compounds in Wildfire Smoke Using 21-T Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2022; 94:14537-14545. [PMID: 36215705 PMCID: PMC9610683 DOI: 10.1021/acs.analchem.2c00916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/16/2022] [Indexed: 11/28/2022]
Abstract
We present a detailed molecular characterization of organophosphorus compounds in ambient organic aerosol influenced by wildfire smoke. Biomass burning organic aerosol (BBOA) is an important source of phosphorus (P) to surface waters, where even a small imbalance in the P flux can lead to substantial effects on water quality, such as eutrophication, algal blooms, and oxygen depletion. We aimed to exploit the ultrahigh resolving power, mass accuracy, and sensitivity of Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) to explore the molecular composition of an ambient BBOA sample collected downwind of Pacific Northwest wildfires. The 21-T FT-ICR MS yielded 10 533 distinct formulae, which included molecular species comprising C, H, O, and P with or without N, i.e., organophosphorus compounds that have long been quantified in wildfire smoke but have not yet been characterized at the molecular level. The lack of detailed molecular characterization of organophosphorus compounds in BBOA is primarily due to their inherently low concentrations in aerosols and poor ionization efficiency in complex mixtures. We demonstrate that the exceptional sensitivity of the 21-T FT-ICR MS allows qualitative analysis of a previously uncharacterized fraction of BBOA without its selective concentration from the organic matrix, exemplifying the need for ultrahigh-resolution tools for a more detailed and accurate molecular depiction of such complex mixtures.
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Affiliation(s)
- Amna Ijaz
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - William Kew
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Swarup China
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Simeon K. Schum
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Lynn R. Mazzoleni
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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34
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Roth HK, Nelson AR, McKenna AM, Fegel TS, Young RB, Rhoades CC, Wilkins MJ, Borch T. Impact of beaver ponds on biogeochemistry of organic carbon and nitrogen along a fire-impacted stream. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1661-1677. [PMID: 36004537 DOI: 10.1039/d2em00184e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wildfires, which are increasing in frequency and severity in the western U.S., impact water quality through increases in erosion, and transport of nutrients and metals. Meanwhile, beaver populations have been increasing since the early 1900s, and the ponds they create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). However, it remains unknown how the presence of beaver ponds in burned watersheds may impact retention and transformation of chemical constituents originating in burned uplands (e.g., pyrogenic dissolved organic matter; pyDOM) and the consequences for downstream water quality. Here, we investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments. The chemistry and microbiology of surface water and sediment changed along a stream sequence starting upstream of fire and flowing through multiple beaver ponds and interconnecting stream reaches within a burned high-elevation forest watershed. The relative abundance of N-containing compounds increased in surface water of the burned beaver ponds, which corresponded to lower C/N and O/C, and higher aromaticity as characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The resident microbial communities lack the capacity to process such aromatic pyDOM, though genomic analyses demonstrate their potential to metabolize various compounds in the anaerobic sediments of the beaver ponds. Collectively, this work highlights the role of beaver ponds as biological "hotspots" with unique biogeochemistry in fire-impacted systems.
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Affiliation(s)
- Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University, FL, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis & Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
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35
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Papanastasiou D, Kounadis D, Lekkas A, Orfanopoulos I, Mpozatzidis A, Smyrnakis A, Panagiotopoulos E, Kosmopoulou M, Reinhardt-Szyba M, Fort K, Makarov A, Zubarev RA. The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1990-2007. [PMID: 36113052 PMCID: PMC9850925 DOI: 10.1021/jasms.2c00214] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.
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Affiliation(s)
- Dimitris Papanastasiou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Diamantis Kounadis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Alexandros Lekkas
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Ioannis Orfanopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Andreas Mpozatzidis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Athanasios Smyrnakis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Elias Panagiotopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Mariangela Kosmopoulou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | | | - Kyle Fort
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Alexander Makarov
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Roman A. Zubarev
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
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36
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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: 14] [Impact Index Per Article: 7.0] [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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37
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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38
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
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39
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Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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40
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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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41
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Fornelli L, Toby TK. Characterization of large intact protein ions by mass spectrometry: What directions should we follow? BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140758. [PMID: 35077914 DOI: 10.1016/j.bbapap.2022.140758] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Theoretically, the gas-phase interrogation of whole proteoforms via mass spectrometry, known as top-down proteomics, bypasses the protein inference problem that afflicts peptide-centric proteomic approaches. Despite this obvious advantage, the application of top-down proteomics remains rare, mainly due to limited throughput and difficulty of analyzing proteins >30 kDa. Here we will discuss some of the problems encountered during the characterization of large proteoforms, and guided by a combination of theoretical background and experimental evidence we will describe some innovative data acquisition strategies and novel mass spectrometry technologies that can at least partially overcome such limitations.
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Affiliation(s)
- Luca Fornelli
- University of Oklahoma, Department of Biology, 730 Van Vleet oval, Norman, OK 73109, United States of America; University of Oklahoma, Department Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73109, United States of America.
| | - Timothy K Toby
- DiscernDx, 2478 Embarcadero Way, Palo Alto, CA 94303, United States of America
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42
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Dunham SD, Sanders JD, Holden DD, Brodbelt JS. Improving the Center Section Sequence Coverage of Large Proteins Using Stepped-Fragment Ion Protection Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:446-456. [PMID: 35119856 DOI: 10.1021/jasms.1c00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry has gained attention in recent years for its ability to provide high sequence coverage of intact proteins. However, secondary dissociation of fragment ions, in which fragment ions subjected to multiple laser pulses decompose into small products, is a common phenomenon during UVPD that contributes to limited coverage in the midsection of protein sequences. To counter secondary dissociation, a method involving the application of notched waveforms to modulate the trajectories of fragment ions away from the laser beam, termed fragment ion protection (FIP), was previously developed to reduce the probability of secondary dissociation. This, in turn, increased the number of identified large fragment ions. In the present study, FIP was applied to UVPD of large proteins ranging in size from 29 to 55 kDa, enhancing the abundances of large fragment ions. A stepped-FIP strategy was implemented in which UVPD mass spectra were collected using multiple different amplitudes of the FIP waveforms and then the results from the mass spectra were combined. By using stepped-FIP, the number of fragment ions in the midsections of the sequences increased for all proteins. For example, whereas no fragment ions were identified in the middle section of the sequence for glutamate dehydrogenase (55 kDa, 55+ charge state), 10 sequence ions were identified by using UVPD-FIP.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Dustin D Holden
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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43
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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44
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Chavez JD, Park SG, Mohr JP, Bruce JE. Applications and advancements of FT-ICR-MS for interactome studies. MASS SPECTROMETRY REVIEWS 2022; 41:248-261. [PMID: 33289940 PMCID: PMC8184889 DOI: 10.1002/mas.21675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 05/05/2023]
Abstract
The set of all intra- and intermolecular interactions, collectively known as the interactome, is currently an unmet challenge for any analytical method, but if measured, could provide unparalleled insight on molecular function in living systems. Developments and applications of chemical cross-linking and high-performance mass spectrometry technologies are beginning to reveal details on how proteins interact in cells and how protein conformations and interactions inside cells change with phenotype or during drug treatment or other perturbations. A major contributor to these advances is Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) technology and its implementation with accurate mass measurements on cross-linked peptide-pair precursor and fragment ions to enable improved identification methods. However, these applications place increased demands on mass spectrometer performance in terms of high-resolution spectral acquisition rates for on-line MSn experiments. Moreover, FT-ICR-MS also offers unique opportunities to develop and implement parallel ICR cells for multiplexed signal acquisition and the potential to greatly advance accurate mass acquisition rates for interactome studies. This review highlights our efforts to exploit accurate mass FT-ICR-MS technologies with chemical cross-linking and developments being pursued to realize parallel MS array capabilities that will further advance visualization of the interactome.
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Affiliation(s)
- Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
| | - Sung-Gun Park
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
| | - Jared P. Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
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Nagornov KO, Tsybin OY, Nicol E, Kozhinov AN, Tsybin YO. Fourier transform ion cyclotron resonance mass spectrometry at the true cyclotron frequency. MASS SPECTROMETRY REVIEWS 2022; 41:314-337. [PMID: 33462876 DOI: 10.1002/mas.21681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Ion cyclotron resonance (ICR) cells provide stability and coherence of ion oscillations in crossed electric and magnetic fields over extended periods of time. Using the Fourier transform enables precise measurements of ion oscillation frequencies. These precisely measured frequencies are converted into highly accurate mass-to-charge ratios of the analyte ions by calibration procedures. In terms of resolution and mass accuracy, Fourier transform ICR mass spectrometry (FT-ICR MS) offers the highest performance of any MS technology. This is reflected in its wide range of applications. However, in the most challenging MS application, for example, imaging, enhancements in the mass accuracy of fluctuating ion fluxes are required to continue advancing the field. One approach is to shift the ion signal power into the peak corresponding to the true cyclotron frequency instead of the reduced cyclotron frequency peak. The benefits of measuring the true cyclotron frequency include increased tolerance to electric fields within the ICR cell, which enhances frequency measurement precision. As a result, many attempts to implement this mode of FT-ICR MS operation have occurred. Examples of true cyclotron frequency measurements include detection of magnetron inter-harmonics of the reduced cyclotron frequency (i.e., the sidebands), trapping field-free (i.e., screened) ICR cells, and hyperbolic ICR cells with quadrupolar ion detection. More recently, ICR cells with spatially distributed ion clouds have demonstrated attractive performance characteristics for true cyclotron frequency ion detection. Here, we review the corresponding developments in FT-ICR MS over the past 40 years.
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Affiliation(s)
| | - Oleg Y Tsybin
- Ion Physics and Mass Spectrometry Laboratory, Peter The Great State Polytechnic University, Saint-Petersburg, Russia
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire, CNRS, UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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Marshall AG. A PERSONAL SCIENTIFIC HISTORY. MASS SPECTROMETRY REVIEWS 2022; 41:243-247. [PMID: 33094852 DOI: 10.1002/mas.21666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/24/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Alan G Marshall
- Robert O. Lawton Professor of Chemistry & Biochemistry, Founding Director and Chief Scientist, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory*, Florida State University, 1800 E. Paul Dirac Drive, Tallahassee, FL, 32310-4005
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Young RB, Pica NE, Sharifan H, Chen H, Roth HK, Blakney GT, Borch T, Higgins CP, Kornuc JJ, McKenna AM, Blotevogel J. PFAS Analysis with Ultrahigh Resolution 21T FT-ICR MS: Suspect and Nontargeted Screening with Unrivaled Mass Resolving Power and Accuracy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2455-2465. [PMID: 35099180 DOI: 10.1021/acs.est.1c08143] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are a large family of thousands of chemicals, many of which have been identified using nontargeted time-of-flight and Orbitrap mass spectrometry methods. Comprehensive characterization of complex PFAS mixtures is critical to assess their environmental transport, transformation, exposure, and uptake. Because 21 tesla (T) Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest available mass resolving power and sub-ppm mass errors across a wide molecular weight range, we developed a nontargeted 21 T FT-ICR MS method to screen for PFASs in an aqueous film-forming foam (AFFF) using suspect screening, a targeted formula database (C, H, Cl, F, N, O, P, S; ≤865 Da), isotopologues, and Kendrick-analogous mass difference networks (KAMDNs). False-positive PFAS identifications in a natural organic matter (NOM) sample, which served as the negative control, suggested that a minimum length of 3 should be imposed when annotating CF2-homologous series with positive mass defects. We putatively identified 163 known PFASs during suspect screening, as well as 134 novel PFASs during nontargeted screening, including a suspected polyethoxylated perfluoroalkane sulfonamide series. This study shows that 21 T FT-ICR MS analysis can provide unique insights into complex PFAS composition and expand our understanding of PFAS chemistries in impacted matrices.
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Affiliation(s)
- Robert B Young
- Chemical Analysis & Instrumentation Laboratory, New Mexico State University, Las Cruces, New Mexico 88003, United States
| | - Nasim E Pica
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
- Weston Solutions, Lakewood, Colorado 80401, United States
| | - Hamidreza Sharifan
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Natural Science, Albany State University, Albany, Georgia 31705, United States
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Greg T Blakney
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Thomas Borch
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Christopher P Higgins
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - John J Kornuc
- NAVFAC EXWC, 1100 23rd Avenue, Port Hueneme, California 93041, United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Jens Blotevogel
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
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Roth HK, Borch T, Young RB, Bahureksa W, Blakney GT, Nelson AR, Wilkins MJ, McKenna AM. Enhanced Speciation of Pyrogenic Organic Matter from Wildfires Enabled by 21 T FT-ICR Mass Spectrometry. Anal Chem 2022; 94:2973-2980. [PMID: 35107981 DOI: 10.1021/acs.analchem.1c05018] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Wildfires affect soils through the formation of pyrogenic organic matter (pyOM) (e.g., char and soot). While many studies examine the connection between pyOM persistence and carbon (C) composition, nitrogen (N) transformation in wildfire-impacted systems remains poorly understood. Thermal reactions in wildfires transform biomass into a highly complex, polyfunctional, and polydisperse organic mixture that challenges most mass analyzers. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that achieves resolving powers sufficient to separate species that differ in mass by the mass of an electron across a wide molecular weight range (m/z 150-1500). We report enhanced speciation of organic N by positive-ion electrospray ionization (ESI) that leverages ultrahigh resolving power (m/Δm50% = 1 800 000 at m/z 400) and mass accuracy (<10-100 ppb) achieved by FT-ICR MS at 21 T. Isobaric overlaps, roughly the mass of an electron (Me- = 548 μDa), are resolved across a wide molecular weight range and are more prevalent in positive ESI than negative ESI. The custom-built 21 T FT-ICR MS instrument identifies previously unresolved mass differences in CcHhNnOoSs formulas and assigns more than 30 000 peaks in a pyOM sample. This is the first molecular catalogue of pyOM by positive-ion ESI 21 T FT-ICR MS and presents a method to provide new insight into terrestrial cycling of organic carbon and nitrogen in wildfire impacted ecosystems.
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Affiliation(s)
- Holly K Roth
- 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
| | - William Bahureksa
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, 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
| | - Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States.,Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, United States
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Letourneau DR, Volmer DA. Constellation: An Open-Source Web Application for Unsupervised Systematic Trend Detection in High-Resolution Mass Spectrometry Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:382-389. [PMID: 35014266 DOI: 10.1021/jasms.1c00371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The increasing popularity of high-resolution mass spectrometry has led to many custom software solutions to process, interpret, and reveal information from high-resolution mass spectra. Although there are numerous software packages for peak-picking, calibration, and formula-finding, there are additional layers of information available when it comes to detecting repeated motifs from polymers or molecules with repeating structures or products of chemical or biochemical transformations that exhibit systematic, serial chemical changes of mass. Constellation is an open-source, Python-based web application that allows the user first to expand their high-resolution mass data into the mass defect space, after which a trend finding algorithm is used for supervised or unsupervised detection of repeating motifs. Many adjustable parameters allow the user to tailor their trend-search to target particular chemical moieties or repeating units, or search for all potential motifs within certain limits. The algorithm has a built-in optimization routine to provide a good starting point for the main trend finding parameters before user customization. Visualization tools allow interrogation of the data and any trends/patterns to a highly specific degree and save publication-quality images directly from the interface. As Constellation is deployed as a web application, it is easily used by anyone with a web browser; no software download or high-powered computer is required, as computations are performed on a remote high-powered data server run by our group.
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Affiliation(s)
- Dane R Letourneau
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
| | - Dietrich A Volmer
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
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50
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Melani RD, Gerbasi VR, Anderson LC, Sikora JW, Toby TK, Hutton JE, Butcher DS, Negrão F, Seckler HS, Srzentić K, Fornelli L, Camarillo JM, LeDuc RD, Cesnik AJ, Lundberg E, Greer JB, Fellers RT, Robey MT, DeHart CJ, Forte E, Hendrickson CL, Abbatiello SE, Thomas PM, Kokaji AI, Levitsky J, Kelleher NL. The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells. Science 2022; 375:411-418. [PMID: 35084980 PMCID: PMC9097315 DOI: 10.1126/science.aaz5284] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of ~30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma from human blood and bone marrow. The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. We demonstrate the potential for clinical application, by interrogating the BPA in the context of liver transplantation and identifying cell and proteoform signatures that distinguish normal graft function from acute rejection and other causes of graft dysfunction.
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Affiliation(s)
- Rafael D. Melani
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Vincent R. Gerbasi
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Lissa C. Anderson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | - Jacek W. Sikora
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Timothy K. Toby
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Josiah E. Hutton
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - David S. Butcher
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | - Fernanda Negrão
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Henrique S. Seckler
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Kristina Srzentić
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeannie M. Camarillo
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Richard D. LeDuc
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Anthony J. Cesnik
- Department of Genetics, Stanford University, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Department of Genetics, Stanford University, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Joseph B. Greer
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T. Fellers
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Matthew T. Robey
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Caroline J. DeHart
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | - Paul M. Thomas
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | - Josh Levitsky
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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