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Lin Y, Agarwal AM, Marshall AG, Anderson LC. Characterization of Structural Hemoglobin Variants by Top-Down Mass Spectrometry and R Programming Tools for Rapid Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:123-130. [PMID: 34955023 DOI: 10.1021/jasms.1c00291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hemoglobinopathies are one of the most prevalent genetic disorders, affecting millions throughout the world. These are caused by pathogenic variants in genes that control the production of hemoglobin (Hb) subunits. As the number of known Hb variants has increased, it has become more challenging to obtain unambiguous results from routine chromatographic assays employed in the clinical laboratory. Top-down proteomic analysis of Hb by mass spectrometry is a definitive method to directly characterize the sequences of intact subunits. Here, we apply "chimeric ion loading" to characterize Hb β subunit variants. In this technique, product ions derived from complementary dissociation techniques are accumulated in a multipole storage device before delivery to a 21 T Fourier-transform ion cyclotron resonance mass spectrometer for simultaneous detection. To further improve the efficiency of identification of Hb variants and localization of the mutation site(s), we developed an R programming script, "Variants Identifier", to search top-down data against a database containing accurate intact mass differences and diagnostic ions from investigated Hb variants. A second R script, "PredictDiag", was developed and employed to determine relevant diagnostic ions for additional Hb variants with known sequences. These two R scripts were successfully applied to the identification of a Hb δ-β fusion protein and other Hb variants. The combination of chimeric ion loading and the above R scripts enables rapid and reliable interpretation of top-down mass spectrometry data, regardless of activation type, for Hb variant identification.
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Affiliation(s)
- Yuan Lin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32308, United States
| | - Archana M Agarwal
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, United States
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32308, United States
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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Webb IK. Recent technological developments for native mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140732. [PMID: 34653668 DOI: 10.1016/j.bbapap.2021.140732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022]
Abstract
Native mass spectrometry (MS), the analysis of proteins and protein complexes from solutions that stabilize native solution structures, is a rapidly expanding area. There is strong evidence supporting the retention of proteins' native folds in the absence of solvent under the experimental timescales of MS experiments. Therefore, instrumentation has been developed to use gas-phase native-like protein ions to exploit the speed, sensitivity, and selectivity of mass spectrometry approaches to solve emerging problems in structural biology. This article reviews some of the recent advances and applications in gas-phase instrumentation for structural proteomics.
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Affiliation(s)
- Ian K Webb
- Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, United States of America; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America.
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53
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Li C, Chu S, Tan S, Yin X, Jiang Y, Dai X, Gong X, Fang X, Tian D. Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers. Front Chem 2021; 9:813359. [PMID: 34993180 PMCID: PMC8724130 DOI: 10.3389/fchem.2021.813359] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/06/2021] [Indexed: 01/12/2023] Open
Abstract
Mass spectrometry (MS) is one of the most widely used analytical techniques in many fields. Recent developments in chemical and biological researches have drawn much attention to the measurement of substances with low abundances in samples. Continuous efforts have been made consequently to further improve the sensitivity of MS. Modifications on the mass analyzers of mass spectrometers offer a direct, universal and practical way to obtain higher sensitivity. This review provides a comprehensive overview of the latest developments in mass analyzers for the improvement of mass spectrometers' sensitivity, including quadrupole, ion trap, time-of-flight (TOF) and Fourier transform ion cyclotron (FT-ICR), as well as different combinations of these mass analyzers. The advantages and limitations of different mass analyzers and their combinations are compared and discussed. This review provides guidance to the selection of suitable mass spectrometers in chemical and biological analytical applications. It is also beneficial to the development of novel mass spectrometers.
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Affiliation(s)
- Chang Li
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
| | - Shiying Chu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Di Tian
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
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54
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Zemaitis KJ, Ye H, Nguyen HT, Wood TD. Direct Infusion Metabolomics of the Photosystem and Chlorophyll Related Metabolites within a Drought Tolerant Plant Introduction of Glycine max. Metabolites 2021; 11:metabo11120843. [PMID: 34940601 PMCID: PMC8706224 DOI: 10.3390/metabo11120843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Drought is the most prolific form of abiotic stress that legumes and cereal plants alike can endure, and the planting of an improper cultivar at the beginning of a season can cause unexpected losses up to fifty percent under water deficient conditions. Herein, a plant introduction (PI) of an exotic cultivar of soybean (Glycine max), PI 567731, which demonstrates a slow wilting (SW) canopy phenotype in maturity group III, was profiled under drought conditions in field trials in Missouri against a drought susceptible check cultivar, Pana. Metabolomic profiling was carried out on samples of leaves from each of these cultivars at V5 and R2 growth stages both while irrigated and while under drought stress for three weeks. PI 567731 was observed to have differential phytochemical content, and enhanced levels of chlorophyll (Chl) a/b and pheophytin (Pheo) were profiled by direct infusion electrospray Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Indicating drought induced changes of the photosystem and photosynthetic capabilities alongside water preservation strategies are important within the SW phenotype drought response. Subsequent multivariate analysis was able to form predictive models, encompassing the variance of growth and drought stress of the cultivar. Moreover, the existence of unique Chl-related metabolites (CRM) (m/z > 900) were confirmed through tandem mass spectrometry. The resultant coordination of fatty acids to the core of the porphyrin ring was observed and played an unknown role in the proliferation of the photosynthesis. However, the relative ratio of the most abundant CRM is undisturbed by drought stress in PI 567731, in contrast to the drought susceptible cultivar. These results provide key insights into drought related metabolic mechanisms.
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Affiliation(s)
- Kevin J. Zemaitis
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York, Buffalo, NY 14260, USA;
| | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Troy D. Wood
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York, Buffalo, NY 14260, USA;
- Correspondence:
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Ščupáková K, Adelaja OT, Balluff B, Ayyappan V, Tressler CM, Jenkinson NM, Claes BS, Bowman AP, Cimino-Mathews AM, White MJ, Argani P, Heeren RM, Glunde K. Clinical importance of high-mannose, fucosylated and complex N-glycans in breast cancermetastasis. JCI Insight 2021; 6:146945. [PMID: 34752419 PMCID: PMC8783675 DOI: 10.1172/jci.insight.146945] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND. Although aberrant glycosylation is recognized as a hallmark of cancer, glycosylation in clinical breast cancer (BC) metastasis has not yet been studied. While preclinical studies show that the glycocalyx coating of cancer cells is involved in adhesion, migration, and metastasis, glycosylation changes from primary tumor (PT) to various metastatic sites remain unknown in patients. METHODS. We investigated N-glycosylation profiles in 17 metastatic BC patients from our rapid autopsy program. Primary breast tumor, lymph node metastases, multiple systemic metastases, and various normal tissue cores from each patient were arranged on unique single-patient tissue microarrays (TMAs). We performed mass spectrometry imaging (MSI) combined with extensive pathology annotation of these TMAs, and this process enabled spatially differentiated cell-based analysis of N-glycosylation patterns in metastatic BC. RESULTS. N-glycan abundance increased during metastatic progression independently of BC subtype and treatment regimen, with high-mannose glycans most frequently elevated in BC metastases, followed by fucosylated and complex glycans. Bone metastasis, however, displayed increased core-fucosylation and decreased high-mannose glycans. Consistently, N-glycosylated proteins and N-glycan biosynthesis genes were differentially expressed during metastatic BC progression, with reduced expression of mannose-trimming enzymes and with elevated EpCAM, N-glycan branching, and sialyation enzymes in BC metastases versus PT. CONCLUSION. We show in patients that N-glycosylation of breast cancer cells undergoing metastasis occurs in a metastatic site–specific manner, supporting the clinical importance of high-mannose, fucosylated, and complex N-glycans as future diagnostic markers and therapeutic targets in metastatic BC. FUNDING. NIH grants R01CA213428, R01CA213492, R01CA264901, T32CA193145, Dutch Province Limburg “LINK”, European Union ERA-NET TRANSCAN2-643638.
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Affiliation(s)
- Klára Ščupáková
- Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Oluwatobi T Adelaja
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Vinay Ayyappan
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Caitlin M Tressler
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Nicole M Jenkinson
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Britt Sr Claes
- Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Andrew P Bowman
- Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Ashley M Cimino-Mathews
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Marissa J White
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Pedram Argani
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Ron Ma Heeren
- Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Kristine Glunde
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, United States of America
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56
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A magnetic levitation based low-gravity simulator with an unprecedented large functional volume. NPJ Microgravity 2021; 7:40. [PMID: 34716356 PMCID: PMC8556250 DOI: 10.1038/s41526-021-00174-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022] Open
Abstract
Low-gravity environment can have a profound impact on the behaviors of biological systems, the dynamics of fluids, and the growth of materials. Systematic research on the effects of gravity is crucial for advancing our knowledge and for the success of space missions. Due to the high cost and the limitations in the payload size and mass in typical spaceflight missions, ground-based low-gravity simulators have become indispensable for preparing spaceflight experiments and for serving as stand-alone research platforms. Among various simulator systems, the magnetic levitation-based simulator (MLS) has received long-lasting interest due to its easily adjustable gravity and practically unlimited operation time. However, a recognized issue with MLSs is their highly non-uniform force field. For a solenoid MLS, the functional volume V1%, where the net force results in an acceleration <1% of the Earth's gravity g, is typically a few microliters (μL) or less. In this work, we report an innovative MLS design that integrates a superconducting magnet with a gradient-field Maxwell coil. Through an optimization analysis, we show that an unprecedented V1% of over 4000 μL can be achieved in a compact coil with a diameter of 8 cm. We also discuss how such an MLS can be made using existing high-Tc-superconducting materials. When the current in this MLS is reduced to emulate the gravity on Mars (gM = 0.38g), a functional volume where the gravity varies within a few percent of gM can exceed 20,000 μL. Our design may break new ground for future low-gravity research.
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57
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Rowland SM, Smith DF, Blakney GT, Corilo YE, Hendrickson CL, Rodgers RP. Online Coupling of Liquid Chromatography with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry at 21 T Provides Fast and Unique Insight into Crude Oil Composition. Anal Chem 2021; 93:13749-13754. [PMID: 34623794 DOI: 10.1021/acs.analchem.1c01169] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
High magnetic field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry provides the highest mass resolving power and mass measurement accuracy for detailed characterization of complex chemical mixtures. Here, we report the coupling of online liquid chromatography of complex mixtures with a 21 tesla FT-ICR mass spectrometer. The high magnetic field enables large ion populations to be analyzed for each spectrum for a high dynamic range, with 3.2 million mass resolving power at m/z 400 (6.2 s transient duration) or 1.6 million (3.1 s transient duration) while maintaining high mass accuracy for molecular formula assignment (root-mean-square assignment error < 0.150 ppm). Thousands of unique elemental compositions are assigned per mass spectrum, which can be grouped by the heteroatom class, double bond equivalents (the number of rings and double bonds to carbon), and carbon number. Figures of merit are discussed, as well as characterization of an Arabian heavy vacuum gas oil in terms of the ring number, compound class, double bond equivalents, and ion type. Consideration of elemental composition and retention order provides additional structural information.
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Affiliation(s)
- Steven M Rowland
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Future Fuels Institute, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Donald F Smith
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Gregory T Blakney
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Yuri E Corilo
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Future Fuels Institute, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, Florida 32306, United States
| | - Ryan P Rodgers
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Future Fuels Institute, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, Florida 32306, United States
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58
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Walsh AN, Reddy CM, Niles SF, McKenna AM, Hansel CM, Ward CP. Plastic Formulation is an Emerging Control of Its Photochemical Fate in the Ocean. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12383-12392. [PMID: 34494430 DOI: 10.1021/acs.est.1c02272] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15-36% inorganic additives, primarily calcium carbonate (13-34%) and titanium dioxide (TiO2; 1-2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the 13C and 14C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO2-containing bags photochemically degraded into the most compositionally similar DOC, with 68-94% of photoproduced formulas in common with at least one other TiO2-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO2, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.
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Affiliation(s)
- Anna N Walsh
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher M Reddy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Sydney F Niles
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310-4005, United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310-4005, United States
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Collin P Ward
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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Maia M, Figueiredo A, Cordeiro C, Sousa Silva M. FT-ICR-MS-based metabolomics: A deep dive into plant metabolism. MASS SPECTROMETRY REVIEWS 2021. [PMID: 34545595 DOI: 10.1002/mas.21731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics involves the identification and quantification of metabolites to unravel the chemical footprints behind cellular regulatory processes and to decipher metabolic networks, opening new insights to understand the correlation between genes and metabolites. In plants, it is estimated the existence of hundreds of thousands of metabolites and the majority is still unknown. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a powerful analytical technique to tackle such challenges. The resolving power and sensitivity of this ultrahigh mass accuracy mass analyzer is such that a complex mixture, such as plant extracts, can be analyzed and thousands of metabolite signals can be detected simultaneously and distinguished based on the naturally abundant elemental isotopes. In this review, FT-ICR-MS-based plant metabolomics studies are described, emphasizing FT-ICR-MS increasing applications in plant science through targeted and untargeted approaches, allowing for a better understanding of plant development, responses to biotic and abiotic stresses, and the discovery of new natural nutraceutical compounds. Improved metabolite extraction protocols compatible with FT-ICR-MS, metabolite analysis methods and metabolite identification platforms are also explored as well as new in silico approaches. Most recent advances in MS imaging are also discussed.
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Affiliation(s)
- Marisa Maia
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Lisboa, Portugal
| | - Andreia Figueiredo
- Departamento de Biologia Vegetal, Faculdade de Ciências, Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Lisboa, Portugal
| | - Carlos Cordeiro
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Marta Sousa Silva
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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60
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Huang D, Bouza M, Gaul DA, Leach FE, Amster IJ, Schroeder FC, Edison AS, Fernández FM. Comparison of High-Resolution Fourier Transform Mass Spectrometry Platforms for Putative Metabolite Annotation. Anal Chem 2021; 93:12374-12382. [PMID: 34460220 PMCID: PMC8590398 DOI: 10.1021/acs.analchem.1c02224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fourier transform ion cyclotron resonance (FT-ICR) and Orbitrap mass spectrometry (MS) are among the highest-performing analytical platforms used in metabolomics. Non-targeted metabolomics experiments, however, yield extremely complex datasets that make metabolite annotation very challenging and sometimes impossible. The high-resolution accurate mass measurements of the leading MS platforms greatly facilitate this process by reducing mass errors and spectral overlaps. When high resolution is combined with relative isotopic abundance (RIA) measurements, heuristic rules, and constraints during searches, the number of candidate elemental formula(s) can be significantly reduced. Here, we evaluate the performance of Orbitrap ID-X and 12T solariX FT-ICR mass spectrometers in terms of mass accuracy and RIA measurements and how these factors affect the assignment of the correct elemental formulas in the metabolite annotation pipeline. Quality of the mass measurements was evaluated under various experimental conditions (resolution: 120, 240, 500 K; automatic gain control: 5 × 104, 1 × 105, 5 × 105) for the Orbitrap MS platform. High average mass accuracy (<1 ppm for UPLC-Orbitrap MS and <0.2 ppm for direct infusion FT-ICR MS) was achieved and allowed the assignment of correct elemental formulas for over 90% (m/z 75-466) of the 104 investigated metabolites. 13C1 and 18O1 RIA measurements further improved annotation certainty by reducing the number of candidates. Overall, our study provides a systematic evaluation for two leading Fourier transform (FT)-based MS platforms utilized in metabolite annotation and provides the basis for applying these, individually or in combination, to metabolomics studies of biological systems.
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Affiliation(s)
- Danning Huang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Marcos Bouza
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David A Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Franklin E Leach
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602, United States
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department to Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Arthur S Edison
- Departments of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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61
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Collins SL, Koo I, Peters JM, Smith PB, Patterson AD. Current Challenges and Recent Developments in Mass Spectrometry-Based Metabolomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:467-487. [PMID: 34314226 DOI: 10.1146/annurev-anchem-091620-015205] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry-based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.
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Affiliation(s)
- Stephanie L Collins
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jeffrey M Peters
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Philip B Smith
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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62
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Chavez JD, Wippel HH, Tang X, Keller A, Bruce JE. In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. Chem Rev 2021; 122:7647-7689. [PMID: 34232610 PMCID: PMC8966414 DOI: 10.1021/acs.chemrev.1c00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biological systems have evolved to utilize proteins to accomplish nearly all functional roles needed to sustain life. A majority of biological functions occur within the crowded environment inside cells and subcellular compartments where proteins exist in a densely packed complex network of protein-protein interactions. The structural biology field has experienced a renaissance with recent advances in crystallography, NMR, and CryoEM that now produce stunning models of large and complex structures previously unimaginable. Nevertheless, measurements of such structural detail within cellular environments remain elusive. This review will highlight how advances in mass spectrometry, chemical labeling, and informatics capabilities are merging to provide structural insights on proteins, complexes, and networks that exist inside cells. Because of the molecular detection specificity provided by mass spectrometry and proteomics, these approaches provide systems-level information that not only benefits from conventional structural analysis, but also is highly complementary. Although far from comprehensive in their current form, these approaches are currently providing systems structural biology information that can uniquely reveal how conformations and interactions involving many proteins change inside cells with perturbations such as disease, drug treatment, or phenotypic differences. With continued advancements and more widespread adaptation, systems structural biology based on in-cell labeling and mass spectrometry will provide an even greater wealth of structural knowledge.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
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63
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Kösling P, Rüger CP, Schade J, Fort KL, Ehlert S, Irsig R, Kozhinov AN, Nagornov KO, Makarov A, Rigler M, Tsybin YO, Walte A, Zimmermann R. Vacuum Laser Photoionization inside the C-trap of an Orbitrap Mass Spectrometer: Resonance-Enhanced Multiphoton Ionization High-Resolution Mass Spectrometry. Anal Chem 2021; 93:9418-9427. [PMID: 34170684 DOI: 10.1021/acs.analchem.1c01018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
State-of-the-art mass spectrometry with ultraviolet (UV) photoionization is mostly limited to time-of-flight (ToF) mass spectrometers with 1000-10 000 m/Δm mass resolution. However, higher resolution and higher spectral dynamic range mass spectrometry may be indispensable in complex mixture characterization. Here, we present the concept, implementation, and initial evaluation of a compact ultrahigh-resolution mass spectrometer with gas-phase laser ionization. The concept is based on direct laser photoionization in the ion accumulation and ejection trap (C-trap) of an Orbitrap mass spectrometer. Resonance-enhanced multiphoton ionization (REMPI) using 266 nm UV pulses from a frequency-quadrupled Nd:YAG laser was applied for selective and efficient ionization of monocyclic and polycyclic aromatic hydrocarbons. The system is equipped with a gas inlet for volatile compounds and a heated gas chromatography coupling. The former can be employed for rapid system m/z-calibration and performance evaluation, whereas the latter enables analysis of semivolatile and higher-molecular-weight compounds. The capability to evaluate complex mixtures is demonstrated for selected petrochemical materials. In these experiments, several hundred to over a thousand compounds could be attributed with a root-mean-square mass error generally below 1 ppm and a mass resolution of over 140 000 at 200 m/z. Isobaric interferences could be resolved, and narrow mass splits, such as 3.4 mDa (SH4/C3), are determined. Single laser shots provided limits of detection in the 20-ppb range for p-xylene and 1,2,4-trimethylbenzene, similar to compact vacuum REMPI-ToF systems.
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Affiliation(s)
- Paul Kösling
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany
| | - Christopher P Rüger
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany
| | - Julian Schade
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany
| | - Kyle L Fort
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Sven Ehlert
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany.,Photonion GmbH, 19061 Schwerin, Germany
| | - Robert Irsig
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany.,Photonion GmbH, 19061 Schwerin, Germany
| | | | | | | | | | | | | | - Ralf Zimmermann
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany.,Joint Mass Spectrometry Centre, Cooperation Group "Comprehensive Molecular Analytics", Helmholtz Zentrum Muenchen, Neuherberg D-85764, Germany
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64
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Weisbrod CR, Anderson LC, Hendrickson CL, Schaffer LV, Shortreed MR, Smith LM, Shabanowitz J, Hunt DF. Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal Chem 2021; 93:9119-9128. [PMID: 34165955 DOI: 10.1021/acs.analchem.1c00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer reactions (PTRs) have emerged as a powerful tool for the study of intact proteins. When coupled with m/z-selective kinetic excitation, such as parallel ion parking (PIP), one can exert exquisite control over rates of reaction with a high degree of specificity. This allows one to "concentrate", in the gas phase, nearly all the signals from an intact protein charge state envelope into a single charge state, improving the signal-to-noise ratio (S/N) by 10× or more. While this approach has been previously reported, here we show that implementing these technologies on a 21 T FT-ICR MS provides a tremendous advantage for intact protein analysis. Advanced strategies for performing PTR with PIP were developed to complement this unique instrument, including subjecting all analyte ions entering the mass spectrometer to PTR and PIP. This experiment, which we call "PTR-MS1-PIP", generates a pseudo-MS1 spectrum derived from ions that are exposed to the PTR reagent and PIP waveforms but have not undergone any prior true mass filtering or ion isolation. The result is an extremely rapid and significant improvement in the spectral S/N of intact proteins. This permits the observation of many more proteoforms and reduces ion injection periods for subsequent tandem mass spectrometry characterization. Additionally, the product ion parking waveform has been optimized to enhance the PTR rate without compromise to the parking efficiency. We demonstrate that this process, called "rapid park", can improve reaction rates by 5-10× and explore critical factors discovered to influence this process. Finally, we demonstrate how coupling PTR-MS1 and rapid park provides a 10-fold reduction in ion injection time, improving the rate of tandem MS sequencing.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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65
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Zhang J, McKenna AM, Zhu M. Macromolecular Characterization of Compound Selectivity for Oxidation and Oxidative Alterations of Dissolved Organic Matter by Manganese Oxide. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7741-7751. [PMID: 33973466 DOI: 10.1021/acs.est.1c01283] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Manganese (Mn) oxides can oxidize dissolved organic matter (DOM) and alter its chemical properties and microbial degradability, but the compound selectivity for oxidation and oxidative alterations remain to be determined. We applied ultrahigh mass spectrometry to catalog the macromolecular composition of Suwannee River fulvic acid (SRFA) before and after oxidation by a Mn oxide (δ-MnO2) at pH 4 or 6. Polycyclic aromatic hydrocarbons, polyphenols, and carbohydrates were more reactive in reducing δ-MnO2 than highly unsaturated and phenolic (HuPh) compounds and aliphatics, but highly abundant HuPh contributed the most (∼50%) to the overall reduction of δ-MnO2. On average, oxidized species had higher molecular weights, aromaticity, carbon unsaturation degree, nominal oxidation state of carbon, and oxygen and nitrogen contents but were lower in hydrogen content compared to unoxidized species. The oxidation decreased these molecular indices and oxygen and nitrogen contents but increased the hydrogen content, with stronger changes at the lower pH. This DOM oxidation on polar mineral surfaces was more selective but shared similar selectivity rules to adsorption. The abiotic oxidation resembles microbial oxidative degradation of organic matter, and Mn oxide-oxidizable carbon may be a useful index for detection and identification of labile organic carbon.
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Affiliation(s)
- Jianchao Zhang
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Mengqiang Zhu
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
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66
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Huang X, Liu H, Lu D, Lin Y, Liu J, Liu Q, Nie Z, Jiang G. Mass spectrometry for multi-dimensional characterization of natural and synthetic materials at the nanoscale. Chem Soc Rev 2021; 50:5243-5280. [PMID: 33656017 DOI: 10.1039/d0cs00714e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Characterization of materials at the nanoscale plays a crucial role in in-depth understanding the nature and processes of the substances. Mass spectrometry (MS) has characterization capabilities for nanomaterials (NMs) and nanostructures by offering reliable multi-dimensional information consisting of accurate mass, isotopic, and molecular structural information. In the last decade, MS has emerged as a powerful nano-characterization technique. This review comprehensively summarizes the capabilities of MS in various aspects of nano-characterization that greatly enrich the toolbox of nano research. Compared with other characterization techniques, MS has unique capabilities for real-time monitoring and tracking reaction intermediates and by-products. Moreover, MS has shown application potential in some novel aspects, such as MS imaging of the biodistribution and fate of NMs in animals and humans, stable isotopic tracing of NMs, and risk assessment of NMs, which deserve update and integration into the current knowledge framework of nano-characterization.
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Affiliation(s)
- Xiu Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dawei Lu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Yue Lin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jingfu Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and University of Chinese Academy of Sciences, Beijing 100049, China and Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Zongxiu Nie
- University of Chinese Academy of Sciences, Beijing 100049, China and Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and University of Chinese Academy of Sciences, Beijing 100049, China
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67
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McKenna AM, Chen H, Weisbrod CR, Blakney GT. Molecular Comparison of Solid-Phase Extraction and Liquid/Liquid Extraction of Water-Soluble Petroleum Compounds Produced through Photodegradation and Biodegradation by FT-ICR Mass Spectrometry. Anal Chem 2021; 93:4611-4618. [PMID: 33660499 DOI: 10.1021/acs.analchem.0c05230] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We apply two widely used extraction techniques, liquid/liquid extraction and solid-phase extraction with styrene-divinylbenzene polymer with a proprietary nonpolar surface priority pollutant (PPL) to water-soluble compounds generated through photodegradation and biodegradation of petroleum. We compare the molecular composition of bio- and photodegraded water-soluble organic (WSO) acids by 21 T negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). We highlight the compositional differences between the two extraction techniques for abiotic and biotic degradation processes and identify known toxic species (naphthenic acids) produced through hydrocarbon biodegradation identified by liquid/liquid extraction (LLE) that are not detected with solid-phase extraction (SPE) of the same sample. Photodegraded WSO compounds extracted by SPE-PPL correspond to species with higher O/C ratio and carbon number compared to LLE extracted compounds. Naphthenic acids, a recalcitrant class of nonaromatic carboxylic acids and known acute toxicants formed through biodegradation of oil, are detected in LLE extracts (up to C30 and double-bond equivalents, DBE < 3) but are not detected in SPE-PPL extracts. This suggests that LLE and SPE-PPL retain different water-soluble oil species based on the dominant type of oil weathering process.
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Affiliation(s)
- Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Gregory T Blakney
- National High Magnetic Field Laboratory, Florida State University,1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
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68
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Müller MA, Kompauer M, Strupat K, Heiles S, Spengler B. Implementation of a High-Repetition-Rate Laser in an AP-SMALDI MSI System for Enhanced Measurement Performance. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:465-472. [PMID: 33370109 DOI: 10.1021/jasms.0c00368] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging is a promising tool in the life sciences for obtaining spatial and chemical information from complex biological samples. State-of-the-art setups combine high mass resolution and high mass accuracy with high lateral resolution, offering untargeted insights into biochemical processes on the single-cell length scale. Despite recent technological breakthroughs, the sensitivity and acquisition speed of many setups are often in competition with achievable pixel resolutions below 25 μm. New measurement modes were developed by implementing a high-repetition-rate laser into an AP-SMALDI10 ion source, coupled to an orbital trapping mass spectrometer. These new MSI modes allow for a modular use of the new setup. We demonstrate that the system allows single cell features to be visualized in mouse brain tissue sections at a pixel resolution of 5 μm and an imaging speed of 18 pixels/s. Furthermore, the analytical sensitivity was improved in another measurement mode by applying multiple pulses of a highly focused laser beam over larger square pixels ≥25 μm edge length, increasing ion signal intensities up to 20-fold on tissue and decreasing the limit of detection by 1 order of magnitude.
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Affiliation(s)
- Max A Müller
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Mario Kompauer
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Kerstin Strupat
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
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69
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Nikolaev E, Lioznov A. How to Increase Further the Resolving Power of the Ultrahigh Magnetic Field FT ICR Instruments? The New Concept of the FT ICR Cell-the Open Dynamically Harmonized Cell as a Part of the Vacuum System Wall. Anal Chem 2021; 93:1249-1253. [PMID: 33352037 DOI: 10.1021/acs.analchem.0c03237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
FT ICR mass spectrometry continues to be the leader in the resolving power among all mass spectrometry methods. With the introduction of the dynamically harmonized FT ICR cell, it has become possible to achieve the resolving power of more than 10 million at m/q = 1000 with moderate magnetic fields of about 7 T. A further increase in the mass resolving power is desirable mainly for two reasons: with this we are increasing the number of resolved components in analyses of complex mixtures (like oil and natural organic matter (NOM)) and increasing the number of the mass of molecules for which a fine structure can be resolved. In recent years, some attempts have been made to further increase the mass resolving power by increasing the magnetic field and using the multielectrode detection method. An increase in the magnetic field to 21 T did not show a proportional increase in the mass resolving power. Likely, the reason for this is an insufficiently high vacuum to satisfy the requirement of an increase in the mean free path of ions with the increasing magnetic field power. We offer a new design for the FT ICR cell and the whole mass spectrometer, in which an open, dynamically harmonized FT ICR cell is integrated into a vacuum system with the outer surfaces of the cell electrodes at atmospheric pressure. In this design, the trap electrodes are the walls of the vacuum system and have the minimized active surfaces by combining the vacuum system surface and the cell surface into one. In this design, the pumping process is accelerated, and the factor of insufficient vacuum in FT ICR mass spectrometers with an ultrahigh magnetic field is eliminated.
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Affiliation(s)
- Evgeny Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, Russia 121205
| | - Anton Lioznov
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, Russia 121205
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70
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Wologo E, Shakil S, Zolkos S, Textor S, Ewing S, Klassen J, Spencer RGM, Podgorski DC, Tank SE, Baker MA, O'Donnell JA, Wickland KP, Foks SSW, Zarnetske JP, Lee‐Cullin J, Liu F, Yang Y, Kortelainen P, Kolehmainen J, Dean JF, Vonk JE, Holmes RM, Pinay G, Powell MM, Howe J, Frei RJ, Bratsman SP, Abbott BW. Stream Dissolved Organic Matter in Permafrost Regions Shows Surprising Compositional Similarities but Negative Priming and Nutrient Effects. GLOBAL BIOGEOCHEMICAL CYCLES 2021; 35:e2020GB006719. [PMID: 33519064 PMCID: PMC7816262 DOI: 10.1029/2020gb006719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 05/04/2023]
Abstract
Permafrost degradation is delivering bioavailable dissolved organic matter (DOM) and inorganic nutrients to surface water networks. While these permafrost subsidies represent a small portion of total fluvial DOM and nutrient fluxes, they could influence food webs and net ecosystem carbon balance via priming or nutrient effects that destabilize background DOM. We investigated how addition of biolabile carbon (acetate) and inorganic nutrients (nitrogen and phosphorus) affected DOM decomposition with 28-day incubations. We incubated late-summer stream water from 23 locations nested in seven northern or high-altitude regions in Asia, Europe, and North America. DOM loss ranged from 3% to 52%, showing a variety of longitudinal patterns within stream networks. DOM optical properties varied widely, but DOM showed compositional similarity based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. Addition of acetate and nutrients decreased bulk DOM mineralization (i.e., negative priming), with more negative effects on biodegradable DOM but neutral or positive effects on stable DOM. Unexpectedly, acetate and nutrients triggered breakdown of colored DOM (CDOM), with median decreases of 1.6% in the control and 22% in the amended treatment. Additionally, the uptake of added acetate was strongly limited by nutrient availability across sites. These findings suggest that biolabile DOM and nutrients released from degrading permafrost may decrease background DOM mineralization but alter stoichiometry and light conditions in receiving waterbodies. We conclude that priming and nutrient effects are coupled in northern aquatic ecosystems and that quantifying two-way interactions between DOM properties and environmental conditions could resolve conflicting observations about the drivers of DOM in permafrost zone waterways.
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Affiliation(s)
- Ethan Wologo
- Department of Land Resources and Environmental SciencesMontana State UniversityBozemanMTUSA
| | - Sarah Shakil
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Scott Zolkos
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Woods Hole Research CenterWoods HoleMAUSA
| | - Sadie Textor
- Department of Earth, Ocean and Atmospheric Science and National High Magnetic Field Laboratory Geochemistry GroupFlorida State UniversityTallahasseeFLUSA
| | - Stephanie Ewing
- Department of Land Resources and Environmental SciencesMontana State UniversityBozemanMTUSA
| | - Jane Klassen
- Department of Land Resources and Environmental SciencesMontana State UniversityBozemanMTUSA
| | - Robert G. M. Spencer
- Department of Earth, Ocean and Atmospheric Science and National High Magnetic Field Laboratory Geochemistry GroupFlorida State UniversityTallahasseeFLUSA
| | - David C. Podgorski
- Department of Earth, Ocean and Atmospheric Science and National High Magnetic Field Laboratory Geochemistry GroupFlorida State UniversityTallahasseeFLUSA
| | - Suzanne E. Tank
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Michelle A. Baker
- Department of Biology and Ecology CenterUtah State UniversityLoganUTUSA
| | | | | | | | - Jay P. Zarnetske
- Department of Earth and Environmental SciencesMichigan State UniversityEast LansingMIUSA
| | - Joseph Lee‐Cullin
- Department of Earth and Environmental SciencesMichigan State UniversityEast LansingMIUSA
| | - Futing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of BotanyChinese Academy of SciencesBeijingChina
| | | | | | - Joshua F. Dean
- Department of Earth SciencesVrije Universiteit AmsterdamAmsterdamNetherlands
- School of Environmental SciencesUniversity of LiverpoolLiverpoolUK
| | - Jorien E. Vonk
- Department of Earth SciencesVrije Universiteit AmsterdamAmsterdamNetherlands
| | | | - Gilles Pinay
- Environnement‐Ville‐Société (UMR5600) ‐ Centre National de la Recherche Scientifique (CNRS)LyonFrance
| | - Michaela M. Powell
- Department of Land Resources and Environmental SciencesMontana State UniversityBozemanMTUSA
| | - Jansen Howe
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUTUSA
| | - Rebecca J. Frei
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUTUSA
- Department of Renewable ResourcesUniversity of AlbertaEdmontonAlbertaCanada
| | - Samuel P. Bratsman
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUTUSA
| | - Benjamin W. Abbott
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUTUSA
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71
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Maillard JF, Le Maître J, Rüger CP, Ridgeway M, Thompson CJ, Paupy B, Hubert-Roux M, Park M, Afonso C, Giusti P. Structural analysis of petroporphyrins from asphaltene by trapped ion mobility coupled with Fourier transform ion cyclotron resonance mass spectrometry. Analyst 2021; 146:4161-4171. [PMID: 34047731 DOI: 10.1039/d1an00140j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular characterization of compounds present in highly complex mixtures such as petroleum is proving to be one of the main analytical challenges. Heavy fractions, such as asphaltenes, exhibit immense molecular and isomeric complexity. Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) with its unequalled resolving power, mass accuracy and dynamic range can address the isobaric complexity. Nevertheless, isomers remain largely inaccessible. Therefore, another dimension of separation is required. Recently, ion mobility mass spectrometry has revealed great potential for isomer description. In this study, the combination of trapped ion mobility and Fourier transform ion cyclotron resonance mass spectrometry (TIMS-FTICR) is used to obtain information on the structural features and isomeric diversity of vanadium petroporphyrins present in heavy petroleum fractions. The ion mobility spectra provided information on the isomeric diversity of the different classes of porphyrins. The determination of the collision cross section (CCS) from the peak apex allows us to hypothesize about the structural aspects of the petroleum molecules. In addition, the ion mobility signal full width at half maximum (FWHM) was used as a measure for isomeric diversity. Finally, theoretical CCS determinations were conducted first on core structures and then on alkylated petroporphyrins taking advantage of the linear correlation between the CCS and the alkylation level. This allowed the proposal of putative structures in agreement with the experimental results. The authors believe that the presented workflow will be useful for the structural prediction of real unknowns in highly complex mixtures.
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Affiliation(s)
- Julien F Maillard
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Johann Le Maître
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and TOTAL Refining & Chemicals, Total Research & Technology Gonfreville, BP 27, 76700 Harfleur, France and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Christopher P Rüger
- International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France and Joint Mass Spectrometry Centre/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany and Department Life, Light & Matter (LLM), University of Rostock, 18051 Rostock, Germany
| | | | | | - Benoit Paupy
- TOTAL Refining & Chemicals, Total Research & Technology Gonfreville, BP 27, 76700 Harfleur, France and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Marie Hubert-Roux
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | | | - Carlos Afonso
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Pierre Giusti
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and TOTAL Refining & Chemicals, Total Research & Technology Gonfreville, BP 27, 76700 Harfleur, France and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
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72
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Ivanova B, Spiteller M. Stochastic dynamic mass spectrometric quantification of steroids in mixture - Part II. Steroids 2020; 164:108750. [PMID: 33069721 DOI: 10.1016/j.steroids.2020.108750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/04/2020] [Indexed: 01/25/2023]
Abstract
This paper deals with quantification of the following steroids in mixture: hydrocortisone (1), deoxycorticosterone (2), progesterone (3) and methyltestosterone (4) by means of mass spectrometry and implementing our innovative stochatic dynamic functional relationship between the analyte concentration in solution and the experimental variable intensity. The mass spectrometric data are correlated independently using chromatography. Chemometric analysis is carried out.
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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, Nordrhein-Westfalen, Germany.
| | - Michael Spiteller
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Nordrhein-Westfalen, Germany
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73
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Xie YR, Castro DC, Lam F, Sweedler JV. Accelerating Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Imaging Using a Subspace Approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2338-2347. [PMID: 33064944 PMCID: PMC7682253 DOI: 10.1021/jasms.0c00276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We present a subspace method that accelerates data acquisition using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry imaging (MSI). For MSI of biological tissue samples, there is a finite number of heterogeneous tissue types with distinct chemical profiles that introduce redundancy in the high-dimensional measurements. Our subspace model exploits the redundancy in data measured from whole-slice tissue samples by decomposing the transient signals into linear combinations of a set of basis transients with the desired spectral resolution. This decomposition allowed us to design a strategy that acquires a subset of long transients for basis determination and short transients for the remaining pixels, drastically reducing the acquisition time. The computational reconstruction strategy can maintain high-mass-resolution and spatial-resolution MSI while providing a 10-fold improvement in throughput. We validated the capability of the subspace model using a rat sagittal brain slice imaging data set. Comprehensive evaluation of the quality of the mass spectral and ion images demonstrated that the reconstructed data produced by the reported method required only 15% of the typical acquisition time and exhibited both qualitative and quantitative consistency when compared to the original data. Our method enables either higher sample throughput or higher-resolution images at similar acquisition lengths, providing greater flexibility in obtaining FT-ICR MSI measurements.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Daniel C. Castro
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Fan Lam
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Corresponding Authors: Fan Lam, Postal: 405 N. Mathews Avenue, Urbana, IL 61801, , Jonathan V. Sweedler, Postal: 600 S. Mathews Avenue, Urbana, IL 61801,
| | - Jonathan V. Sweedler
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Corresponding Authors: Fan Lam, Postal: 405 N. Mathews Avenue, Urbana, IL 61801, , Jonathan V. Sweedler, Postal: 600 S. Mathews Avenue, Urbana, IL 61801,
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74
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Nagornov KO, Kozhinov AN, Nicol E, Tsybin OY, Touboul D, Brunelle A, Tsybin YO. Narrow Aperture Detection Electrodes ICR Cell with Quadrupolar Ion Detection for FT-ICR MS at the Cyclotron Frequency. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2258-2269. [PMID: 32966078 DOI: 10.1021/jasms.0c00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion signal detection at the true (unperturbed) cyclotron frequency instead of the conventional reduced cyclotron frequency has remained a formidable challenge since the inception of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Recently, routine FT-ICR MS at the true cyclotron frequency has become a reality with the implementation of ICR cells with narrow aperture detection electrodes (NADEL). Here, we describe the development and implementation of the next generation of these cells, namely, a 2xNADEL ICR cell, which comprises four flat detect and four ∼45° cylindrical excite electrodes, enabling independent ion excitation and quadrupolar ion detection. The performance of the 2xNADEL ICR cell was evaluated on two commercial FT-ICR MS platforms, 10 T LTQ FT from Thermo Scientific and 9.4 T SolariX XR from Bruker Daltonics. The cells provided accurate mass measurements in the analyses of singly and multiply charged peptides (root-mean-square, RMS, mass error Δm/m of 90 ppb), proteins (Δm/m = 200 ppb), and petroleum fractions (Δm/m < 200 ppb). Due to the reduced influence of measured frequency on the space charge and external (trapping) electric fields, the 2xNADEL ICR cells exhibited stable performance in a wide range of trapping potentials (1-20 V). Similarly, in a 13 h rat brain MALDI imaging experiment, the RMS mass error did not exceed 600 ppb even for low signal-to-noise ratio analyte peaks. Notably, the same set of calibration constants was applicable to Fourier spectra in all pixels, reducing the need for recalibration at the individual pixel level. Overall, these results support further experimental development and fundamentals investigation of this promising technology.
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Affiliation(s)
| | | | - Edith Nicol
- Laboratoire de Chimie Moléculaire, CNRS UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Oleg Yu Tsybin
- Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Alain Brunelle
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
- Laboratoire d'Archéologie Moléculaire et Structurale, LAMS UMR8220, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, 1015 Lausanne, Switzerland
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75
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Schaffer LV, Anderson LC, Butcher DS, Shortreed MR, Miller RM, Pavelec C, Smith LM. Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. J Proteome Res 2020; 20:317-325. [PMID: 33074679 DOI: 10.1021/acs.jproteome.0c00403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Identification of proteoforms, the different forms of a protein, is important to understand biological processes. A proteoform family is the set of different proteoforms from the same gene. We previously developed the software program Proteoform Suite, which constructs proteoform families and identifies proteoforms by intact-mass analysis. Here, we have applied this approach to top-down proteomic data acquired at the National High Magnetic Field Laboratory 21 tesla Fourier transform ion cyclotron resonance mass spectrometer (data available on the MassIVE platform with identifier MSV000085978). We explored the ability to construct proteoform families and identify proteoforms from the high mass accuracy data that this instrument provides for a complex cell lysate sample from the MCF-7 human breast cancer cell line. There were 2830 observed experimental proteforms, of which 932 were identified, 44 were ambiguous, and 1854 were unidentified. Of the 932 unique identified proteoforms, 766 were identified by top-down MS2 analysis at 1% false discovery rate (FDR) using TDPortal, and 166 were additional intact-mass identifications (∼4.7% calculated global FDR) made using Proteoform Suite. We recently published a proteoform level schema to represent ambiguity in proteoform identifications. We implemented this proteoform level classification in Proteoform Suite for intact-mass identifications, which enables users to determine the ambiguity levels and sources of ambiguity for each intact-mass proteoform identification.
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Affiliation(s)
- Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - David S Butcher
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Caitlin Pavelec
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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76
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Thompson CJ, Witt M, Forcisi S, Moritz F, Kessler N, Laukien FH, Schmitt-Kopplin P. An Enhanced Isotopic Fine Structure Method for Exact Mass Analysis in Discovery Metabolomics: FIA-CASI-FTMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2025-2034. [PMID: 32857936 DOI: 10.1021/jasms.0c00047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A major bottleneck in metabolomics is the annotation of a molecular formula as a first step to a tentative structure assignment of known and unknown metabolites. The direct observation of an isotopic fine structure (IFS) provides the ability to confidently assign an unknown's molecular formula out of a complex mass spectrum. However, the majority of mass spectrometers deployed for metabolomic studies do not have sufficient resolving power and high-fidelity isotope ratios in the mass range of interest to determine molecular formulas from IFS data. To increase the number of unknowns for which IFS can be determined, a segmented "boxcar" approach using a selection quadrupole as a broadband mass filter is used. In this longer, enhanced dynamic range discovery experiment, selected ions in a specific mass range are accumulated before detection by the analyzer cell. The mass filter window is then moved across the entire mass range resulting in a composite mass spectrum covering the m/z range of interest for phenomics research. The effectiveness of the FIA-CASI-FTMS workflow utilizing IFS for molecular formula assignment is realized with the implementation of the dynamically harmonized cell, which distinguishes the approach from other segmented workflows because of the analytical properties of the cell. The discovery approach was applied to a human plasma sample to confidently assign an unknown molecular formula as part of the quest to illuminate its metabolic "dark matter" via high-fidelity IFS ratio determinations. The FIA-CASI-FTMS workflow showed a 2.6-fold increase in both matching with the Human Metabolome Database and an increase in the IFS pattern.
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Affiliation(s)
| | | | - Sara Forcisi
- Helmholtz Center Munich, Analytical BioGeoChemistry, Munich 85764, Germany
| | - Franco Moritz
- Helmholtz Center Munich, Analytical BioGeoChemistry, Munich 85764, Germany
| | | | - Frank H Laukien
- Bruker Daltonics Inc, Billerica, Massachusetts 01821, United States
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77
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Pinder J, Lacy JH, Willetts R, Cridland Mathad A, Uribe A, Verdú J. Planar, strong magnetic field source for a chip ion trap. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:103201. [PMID: 33138568 DOI: 10.1063/5.0024735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
We present a planar, scalable magnetic field source, originally conceived for a chip ion trap. It consists of two symmetric sections, each with several independent currents arranged in coplanar, concentric rectangular loops. The currents allow for tuning the strength of the field and its lowest-order derivatives at one discretional position along the source's vertical symmetry axis, a few mm above its surface. We describe the construction and calibration of the device and the cryogenic setup. The two most important current configurations for a Penning ion trap, the homogeneous field and the magnetic bottle, are investigated experimentally. Homogeneous fields around 0.5 T are routinely reached. We discuss the maximum attainable field, and we briefly describe ongoing further developments aiming at homogeneous fields well above 1 T.
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Affiliation(s)
- Jonathan Pinder
- Department of Physics and Astronomy, University of Sussex, Falmer BN1 9QH, United Kingdom
| | - John H Lacy
- Physics Department, Williams College, Williamstown, Massachusetts 01267, USA
| | - Ryan Willetts
- Department of Physics and Astronomy, University of Sussex, Falmer BN1 9QH, United Kingdom
| | | | - Alberto Uribe
- Department of Physics and Astronomy, University of Sussex, Falmer BN1 9QH, United Kingdom
| | - José Verdú
- Department of Physics and Astronomy, University of Sussex, Falmer BN1 9QH, United Kingdom
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78
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Weisbrod CR, Anderson LC, Greer JB, DeHart CJ, Hendrickson CL. Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading. Anal Chem 2020; 92:12193-12200. [PMID: 32812743 DOI: 10.1021/acs.analchem.0c01064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fourier transform mass spectrometers routinely provide high mass resolution, mass measurement accuracy, and mass spectral dynamic range. In this work, we utilize 21 T Fourier transform ion cyclotron resonance (FT-ICR) to analyze product ions derived from the application of multiple dissociation techniques and/or multiple precursor ions within a single transient acquisition. This ion loading technique, which we call, "chimeric ion loading", saves valuable acquisition time, decreases sample consumption, and improves top-down protein sequence coverage. In the analysis of MCF7 cell lysate, we show collision-induced dissociation (CID) and electron-transfer dissociation (ETD) on each precursor on a liquid chromatography-mass spectrometry (LC-MS) timescale and improve mean sequence coverage dramatically (CID-only 15% vs chimeric 33%), even during discovery-based acquisition. This approach can also be utilized to multiplex the acquisition of product ion spectra of multiple charge states from a single protein precursor or multiple ETD/proton-transfer reactions (PTR) reaction periods. The analytical utility of chimeric ion loading is demonstrated for top-down proteomics, but it is also likely to be impactful for tandem mass spectrometry applications in other areas.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Caroline J DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
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79
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Liberatore HK, Westerman DC, Allen JM, Plewa MJ, Wagner ED, McKenna AM, Weisbrod CR, McCord JP, Liberatore RJ, Burnett DB, Cizmas LH, Richardson SD. High-Resolution Mass Spectrometry Identification of Novel Surfactant-Derived Sulfur-Containing Disinfection Byproducts from Gas Extraction Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9374-9386. [PMID: 32600038 PMCID: PMC7469867 DOI: 10.1021/acs.est.0c01997] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Introduction of oil and gas extraction wastewaters (OGWs) to surface water leads to elevated halide levels from geogenic bromide and iodide, as well as enhanced formation of brominated and iodinated disinfection byproducts (DBPs) when treated. OGWs contain high levels of chemical additives used to optimize extraction activities, such as surfactants, which have the potential to serve as organic DBP precursors in OGW-impacted water sources. We report the first identification of olefin sulfonate surfactant-derived DBPs from laboratory-disinfected gas extraction wastewater. Over 300 sulfur-containing DBPs, with 43 unique molecular formulas, were found by high-resolution mass spectrometry, following bench-scale chlor(am)ination. DBPs consisted of mostly brominated species, including bromohydrin sulfonates, dihalo-bromosulfonates, and bromosultone sulfonates, with chlorinated/iodinated analogues formed to a lesser extent. Disinfection of a commercial C12-olefin sulfonate surfactant mixture revealed dodecene sulfonate as a likely precursor for most detected DBPs; disulfur-containing DBPs, like bromosultone sulfonate and bromohydrin disulfonate, originated from olefin disulfonate species, present as side-products of olefin sulfonate production. Disinfection of wastewaters increased mammalian cytotoxicity several orders of magnitude, with chloraminated water being more toxic. This finding is important to OGW-impacted source waters because drinking water plants with high-bromide source waters may switch to chloramination to meet DBP regulations.
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Affiliation(s)
- Hannah K Liberatore
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Danielle C Westerman
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Joshua M Allen
- 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
- Safe Global Water Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Elizabeth D Wagner
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Safe Global Water Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - James P McCord
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | | | - David B Burnett
- Department of Petroleum Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Leslie H Cizmas
- Department of Environmental and Occupational Health, School of Public Health, Texas A&M University, College Station, Texas 77843, United States
| | - Susan D Richardson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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80
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Takemori A, Butcher DS, Harman VM, Brownridge P, Shima K, Higo D, Ishizaki J, Hasegawa H, Suzuki J, Yamashita M, Loo JA, Loo RRO, Beynon RJ, Anderson LC, Takemori N. PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry. J Proteome Res 2020; 19:3779-3791. [PMID: 32538093 DOI: 10.1021/acs.jproteome.0c00303] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prefractionation of complex mixtures of proteins derived from biological samples is indispensable for proteome analysis via top-down mass spectrometry (MS). Polyacrylamide gel electrophoresis (PAGE), which enables high-resolution protein separation based on molecular size, is a widely used technique in biochemical experiments and has the potential to be useful in sample fractionation for top-down MS analysis. However, the lack of a means to efficiently recover the separated proteins in-gel has always been a barrier to its use in sample prefractionation. In this study, we present a novel experimental workflow, called Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS ("PEPPI-MS"), which allows top-down MS of PAGE-separated proteins. The optimization of Coomassie brilliant blue staining followed by the passive extraction step in the PEPPI-MS workflow enabled the efficient recovery of proteins, separated on commercial precast gels, from a wide range of molecular weight regions in under 10 min. Two-dimensional separation combining offline PEPPI-MS with online reversed-phase liquid chromatographic separation resulted in identification of over 1000 proteoforms recovered from the target region of the gel (≤50 kDa). Given the widespread availability and relatively low cost of traditional sodium dodecyl sulfate (SDS)-PAGE equipment, the PEPPI-MS workflow will be a powerful prefractionation strategy for top-down proteomics.
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Affiliation(s)
- Ayako Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 791-0295, Ehime, Japan
| | - David S Butcher
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Victoria M Harman
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Philip Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Keisuke Shima
- Shimadzu Corporation, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Daisuke Higo
- Thermo Fisher Scientific K.K., Yokohama 221-0022, Kanagawa, Japan
| | - Jun Ishizaki
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Hitoshi Hasegawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Junpei Suzuki
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States.,Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Nobuaki Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 791-0295, Ehime, Japan
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81
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Affiliation(s)
- Mateusz K. Łącki
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz 55131, Germany
| | - Dirk Valkenborg
- Data Science Institute, Hasselt University, BE3500 Hasselt, Belgium
- Interuniversity Institute of Biostatistics and Statistical Bioinformatics, Hasselt University, BE3500 Hasselt, Belgium
- Center for Proteomics, University of Antwerp, 2000 Antwerp, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), 2400 Mol, Belgium
| | - Michał P. Startek
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
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82
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Reymond C, Le Masle A, Colas C, Charon N. Input of an Off-Line, Comprehensive, Three-Dimensional Method (CPC×SFC/HRMS) to Quantify Polycyclic Aromatic Hydrocarbons in Vacuum Gas Oils. Anal Chem 2020; 92:6684-6692. [DOI: 10.1021/acs.analchem.0c00605] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Carole Reymond
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, BP 3, 69360 Solaize, France
| | - Agnès Le Masle
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, BP 3, 69360 Solaize, France
| | - Cyril Colas
- Institut de Chimie Organique et Analytique, Université d’Orléans, CNRS UMR 7311, Rue de Chartres, 45067 Orléans, France
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Université d’Orléans, Rue Charles Sadron, 45071 Orléans, France
| | - Nadège Charon
- IFP Energies nouvelles, Rond-point de l’échangeur de Solaize, BP 3, 69360 Solaize, France
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83
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Rodgers RP, Mapolelo MM, Robbins WK, Chacón-Patiño ML, Putman JC, Niles SF, Rowland SM, Marshall AG. Combating selective ionization in the high resolution mass spectral characterization of complex mixtures. Faraday Discuss 2020; 218:29-51. [PMID: 31184658 DOI: 10.1039/c9fd00005d] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Direct "dilute and shoot" mass spectral analysis of complex naturally-occurring mixtures has become the "standard" analysis in environmental and petrochemical science, as well as in many other areas of research. Despite recent advances in ionization methods, that approach still suffers several limitations for the comprehensive characterization of compositionally complex matrices. Foremost, the selective ionization of highly acidic (negative electrospray ionization ((-) ESI)) and/or basic (positive electrospray ionization ((+) ESI)) species limits the detection of weakly acidic/basic species, and similar issues (matrix effects) complicate atmospheric pressure photo-ionization (APPI)/atmospheric pressure chemical ionization (APCI) analyses. Furthermore, given the wide range of chemical functionalities and structural motifs in these compositionally complex mixtures, aggregation can similarly limit the observed species to a small (10-20%) mass fraction of the whole sample. Finally, irrespective of the ionization method, the mass analyzer must be capable of resolving tens-of-thousands of mass spectral peaks and provide the mass accuracy (typically 50-300 ppb mass measurement error) required for elemental composition assignment, and thus is generally limited to high-field Fourier transform ion cyclotron mass spectrometry (FT-ICR MS). Here, we describe three approaches to combat the above issues for (+) ESI, (-) ESI, and (+) APPI FT-ICR MS analysis of petroleum samples. Each approach relies on chromatographic fractionation to help reduce selective ionization discrimination and target either specific chemical functionalities (pyridinic and pyrrolic species (nitrogen) or carboxylic acids (oxygen)) or specific structural motifs (single aromatic core (island) or multi-core aromatics (archipelago)) known to be related to ionization efficiency. Each fractionation method yields a 2-10-fold increase in the compositional coverage, exposes species that are undetectable using direct "dilute and shoot" analysis, and provides coarse selectivity in chemical functionalities that can both increase the assignment confidence and optimize ionization conditions to maximize compositional coverage.
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Affiliation(s)
- Ryan P Rodgers
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA.
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84
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Park SG, Anderson GA, Bruce JE. Parallel Detection of Fundamental and Sixth Harmonic Signals Using an ICR Cell with Dipole and Sixth Harmonic Detectors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:719-726. [PMID: 31967815 PMCID: PMC7970440 DOI: 10.1021/jasms.9b00144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is a powerful instrument for high-resolution analysis of biomolecules. However, relatively long signal acquisition periods are needed to achieve mass spectra with high resolution. The use of multiple detector electrodes for detection of harmonic frequencies has been introduced as one approach to increase scan rate for a given resolving power or to obtain increased resolving power for a given detection period. The achieved resolving power and scan rate increase linearly with the order of detected harmonic signals. In recent years, ICR cell geometries have been investigated to increase the order of the harmonic frequencies and enhance harmonic signal intensities. In this study, we demonstrated PCB-based ICR cell designs with dipole and sixth harmonic detectors for parallel detection of fundamental and harmonic (6f) signals. The sixth harmonic signals from the sixth harmonic detector showed an expected 6 times higher resolving power with (M + 3H)3+ charge state insulin ions as compared with that from fundamental signals from the dipole detector. Moreover, the insulin isotopic peaks with sixth harmonic frequency signals acquired with the sixth harmonic detector were resolved for a 40 ms data acquisition period but unresolved with the same duration dipole detector signals, corresponding to a 6-fold improvement in achievable spectral acquisition rates for a given resolving power.
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Affiliation(s)
- Sung-Gun Park
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Gordon A Anderson
- GAA Custom Engineering, LLC, Benton City, Washington 99320, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
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85
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Drake TW, Podgorski DC, Dinga B, Chanton JP, Six J, Spencer RGM. Land-use controls on carbon biogeochemistry in lowland streams of the Congo Basin. GLOBAL CHANGE BIOLOGY 2020; 26:1374-1389. [PMID: 31665558 DOI: 10.1111/gcb.14889] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
The flux and composition of carbon (C) from land to rivers represents a critical component of the global C cycle as well as a powerful integrator of landscape-level processes. In the Congo Basin, an expansive network of streams and rivers transport and cycle terrigenous C sourced from the largest swathe of pristine tropical forest on Earth. Increasing rates of deforestation and conversion to agriculture in the Basin are altering the current regime of terrestrial-to-aquatic biogeochemical cycling of C. To investigate the role of deforestation on dissolved organic and inorganic C (DOC and DIC, respectively) biogeochemistry in the Congo Basin, six lowland streams that drain catchments of varying forest proportion (12%-77%) were sampled monthly for 1 year. Annual mean concentrations of DOC exhibited an asymptotic response to forest loss, while DIC concentrations increased continuously with forest loss. The isotopic signature of DIC became significantly more enriched with deforestation, indicating a shift in source and processes controlling DIC production. The composition of dissolved organic matter (DOM), as revealed by ultra-high-resolution mass spectrometry, indicated that deforested catchments export relatively more aliphatic and heteroatomic DOM sourced from microbial biomass in soils. The DOM compositional results imply that DOM from the deforested sites is more biolabile than DOM from the forest, consistent with the corresponding elevated stream CO2 concentrations. In short, forest loss results in significant and comprehensive shifts in the C biogeochemistry of the associated streams. It is apparent that land-use conversion has the potential to dramatically affect the C cycle in the Congo Basin by reducing the downstream flux of stable, vascular-plant derived DOC while increasing the transfer of biolabile soil C to the atmosphere.
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Affiliation(s)
- Travis W Drake
- National High Magnetic Field Laboratory Geochemistry Group and Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
- Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - David C Podgorski
- Department of Chemistry, Pontchartrain Institute for Environmental Sciences, University of New Orleans, New Orleans, LA, USA
| | - Bienvenu Dinga
- Institut de Recherche en Sciences et Exactes et Naturelles, Brazzaville, Republic of Congo
| | - Jeffrey P Chanton
- National High Magnetic Field Laboratory Geochemistry Group and Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Johan Six
- Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Robert G M Spencer
- National High Magnetic Field Laboratory Geochemistry Group and Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
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86
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Wang H, Lu L, Chen H, McKenna AM, Lu J, Jin S, Zuo Y, Rosario-Ortiz FL, Ren ZJ. Molecular Transformation of Crude Oil Contaminated Soil after Bioelectrochemical Degradation Revealed by FT-ICR Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2500-2509. [PMID: 31986023 DOI: 10.1021/acs.est.9b06164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bioremediation is a low-cost approach for crude oil spill remediation, but it is often limited by electron acceptor availability. In addition, the biodegradation products of crude oil contaminants are complex, and transformation pathways are difficult to decipher. This study demonstrates that bioelectrochemical systems (BESs) can be effective in crude oil degradation by integrating biological and electrochemical pathways, and more importantly, it provides the first understanding on the daughter products of bioelectrochemical hydrocarbon degradation. Using electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and two-dimensional gas chromatography (GC × GC), the results showed that the active BES reactor improved the total petroleum hydrocarbon (TPH) degradation by ∼70% than open circuit control reactors. After separating the daughter products into nine fractions (MA1-MA9) according to the molecular weight (m/z 200-1000) by modified aminopropyl silica (MAPS) fractionation, we found that active BES remediation resulted in 50% more polar, oxygen-containing naphthenic (NAP) acids. The MA4 fraction (centered at ∼550 Da) increased by 47%, and MA5 and MA7 fractions with higher molucular weight increased by a maximum of ∼7- and 9-fold, respectively. These results are in accordance with the variation of bulk elemental compositions in O2 species, where daughter transformation products doubled relative to parent oil extract. The contribution of newly generated NAP acids was mainly from higher-order oxygen species (O5-O6) with increased hydrophobicity in conjunction with a decreased abundance in lower-order oxygen species (O1). Overall, the study suggests that n-alkane degradation occurred via β-oxidation to oxygenated transformation products with lower molecular weight, such as n-alcohols in O1 class and subsequently to n-fatty acids in O2 class.
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Affiliation(s)
- Huan Wang
- Department of Civil and Environmental Engineering and the Andlinger Center for Energy and the Environment , Princeton University , Princeton , New Jersey 08544 , United States
- Department of Civil, Environmental and Architectural Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Lu Lu
- Department of Civil and Environmental Engineering and the Andlinger Center for Energy and the Environment , Princeton University , Princeton , New Jersey 08544 , United States
| | - Huan Chen
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Jie Lu
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Song Jin
- Advanced Environmental Technologies, LLC , Fort Collins , Colorado 80525 , United States
| | - Yi Zuo
- Chevron Energy Technology Company , San Ramon , California 94583 , United States
| | - Fernando L Rosario-Ortiz
- Department of Civil, Environmental and Architectural Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Zhiyong Jason Ren
- Department of Civil and Environmental Engineering and the Andlinger Center for Energy and the Environment , Princeton University , Princeton , New Jersey 08544 , United States
- Department of Civil, Environmental and Architectural Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
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87
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Smith DF, Blakney GT, Beu SC, Anderson LC, Weisbrod CR, Hendrickson CL. Ultrahigh Resolution Ion Isolation by Stored Waveform Inverse Fourier Transform 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2020; 92:3213-3219. [PMID: 32011122 DOI: 10.1021/acs.analchem.9b04954] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Stored waveform inverse Fourier transform (SWIFT) is a versatile method to generate complex isolation/ejection waveforms for precursor isolation prior to tandem mass spectrometry experiments. Here, we report ultrahigh resolving power ion isolation by SWIFT on a 21 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Individual histone proteoforms are isolated (0.6 m/z isolation window) with near 100% efficiency using a 52 ms SWIFT isolation, followed by in-cell fragmentation by ultraviolet photodissociation (UVPD). Ion isolation resolving power of 175 000 (m/Δm) is demonstrated by isolation of individual peaks at a spacing of 0.0034 Da at m/z 597 from a complex mixture of Canadian bitumen. An individual m/z ion, which corresponds to a single elemental composition, from a complex mixture is isolated and fragmented by infrared multiphoton dissociation (IRMPD). Theoretical and experimental considerations that limit achievable ion isolation resolving power are discussed.
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Affiliation(s)
- Donald F Smith
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Greg T Blakney
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Steven C Beu
- S.C. Beu Consulting , 12449 Los Indios Trail, Austin , Texas 78729 , United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States.,Department of Chemistry and Biochemistry , Florida State University , 95 Chieftain Way , Tallahassee , Florida 32306 , United States
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88
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Bowman AP, Blakney GT, Hendrickson CL, Ellis SR, Heeren RMA, Smith DF. Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS. Anal Chem 2020; 92:3133-3142. [PMID: 31955581 PMCID: PMC7031845 DOI: 10.1021/acs.analchem.9b04768] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Detailed characterization
of complex biological surfaces by matrix-assisted
laser desorption/ionization (MALDI) mass spectrometry imaging (MSI)
requires instrumentation that is capable of high mass resolving power,
mass accuracy, and dynamic range. Fourier transform ion cyclotron
resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral
performance for MALDI MSI experiments, and often reveals molecular
features that are unresolved on lower performance instrumentation.
Higher magnetic field strength improves all performance characteristics
of FT-ICR; mass resolving power improves linearly, while mass accuracy
and dynamic range improve quadratically with magnetic field strength.
Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving
power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below
100 ppb, and dynamic range per pixel over 500:1 were obtained from
the direct analysis of biological tissue sections. Molecular features
with m/z differences as small as
1.79 mDa were resolved and identified with high mass accuracy. These
features allow for the separation and identification of lipids to
the underlying structures of tissues. The unique molecular detail,
accuracy, sensitivity, and dynamic range combined in a 21T MALDI FT-ICR
MSI experiment enable researchers to visualize molecular structures
in complex tissues that have remained hidden until now. The instrument
described allows for future innovative, such as high-end studies to
unravel the complexity of biological, geological, and engineered organic
material surfaces with an unsurpassed detail.
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Affiliation(s)
- Andrew P Bowman
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Greg T Blakney
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States.,Department of Chemistry and Biochemistry , Florida State University , 95 Chieftain Way , Tallahassee , Florida 32306 , United States
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Donald F Smith
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States
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89
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McDonough LK, O'Carroll DM, Meredith K, Andersen MS, Brügger C, Huang H, Rutlidge H, Behnke MI, Spencer RGM, McKenna A, Marjo CE, Oudone P, Baker A. Changes in groundwater dissolved organic matter character in a coastal sand aquifer due to rainfall recharge. WATER RESEARCH 2020; 169:115201. [PMID: 31675607 DOI: 10.1016/j.watres.2019.115201] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Dissolved organic matter (DOM) in groundwater is fundamentally important with respect to biogeochemical reactions, global carbon cycling, heavy metal transport, water treatability and potability. One source of DOM to groundwater is from the transport of organic matter from the vadose zone by rainfall recharge. Changes in precipitation patterns associated with natural climate variability and climate change are expected to alter the load and character of organic matter released from these areas, which ultimately impacts on groundwater quality and DOM treatability. In order to investigate potential changes in groundwater DOM character after rainfall recharge, we sampled shallow groundwater from a coastal peat-rich sand aquifer in New South Wales, Australia, during an extended period of low precipitation (average daily precipitation rate < 1.6 mm day-1 over the 8 months prior to sampling), and after two heavy precipitation events (84 mm day-1 and 98 mm day-1 respectively). We assess changes in DOM composition after correcting for dilution by a novel combination of two advanced analytical techniques: liquid chromatography organic carbon detection (LC-OCD) and negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). We also assess changes in water chemistry pre- and post-rainfall. Post-rainfall, we show that the dilution-corrected amount of highly aromatic DOM molecular formulae (i.e. those categorised into the groups polyphenolics and condensed aromatics) were 1.7 and 2.0 times higher respectively than in pre-rainfall samples. We attribute this to the flushing of peat-derived DOM from buried organic material into the groundwater. We also identify that periods of low precipitation can lead to low hydrophilic/HOC ratios in groundwater (median = 4.9, n = 14). Redundancy analysis (RDA) was used to compare the HOC fraction with FT-ICR MS compound groups. We show that HOC has a more aromatic character in pre-rainfall samples, and is less similar to the aromatic groups in post-rainfall samples. This suggests that the decline in water-borne hydrophobics observed post-rainfall could be associated with preferential adsorption of the hydrophobic aromatic DOM, making post-rainfall samples less treatable for potable water supply. Post-rainfall we also observe significant increases in arsenic (leading to concentrations greater than 3 times the World Health Organisation drinking water limit of 10 μg / L). Increases in coastal rainfall due to climate change may therefore alter the composition of groundwater DOM in coastal peatland areas in ways that may impact DOM bioavailability, and increase arsenic concentrations, reducing the ease of water treatment for human consumption. To the best of our knowledge, this is the first study to identify the chemical and molecular changes of shallow groundwater DOM pre-rainfall and post-rainfall in a sedimentary organic carbon rich environment through multiple analytical techniques.
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Affiliation(s)
- Liza K McDonough
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW, 2052, Australia.
| | - Denis M O'Carroll
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Karina Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia
| | - Martin S Andersen
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Clément Brügger
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia
| | - Hanxue Huang
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Helen Rutlidge
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Civil and Environmental Engineering, UNSW Sydney, NSW, 2052, Australia
| | - Megan I Behnke
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Florida, 32310, USA
| | - Robert G M Spencer
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Florida, 32310, USA
| | - Amy McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310-4005, USA
| | - Christopher E Marjo
- Mark Wainwright Analytical Centre, UNSW Sydney, NSW, 2052, Sydney, Australia
| | - Phetdala Oudone
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Andy Baker
- Connected Waters Initiative Research Centre, UNSW Sydney, NSW, 2052, Australia; School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW, 2052, Australia
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90
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Sanders JD, Mullen C, Watts E, Holden DD, Syka JEP, Schwartz JC, Brodbelt JS. Enhanced Sequence Coverage of Large Proteins by Combining Ultraviolet Photodissociation with Proton Transfer Reactions. Anal Chem 2019; 92:1041-1049. [DOI: 10.1021/acs.analchem.9b04026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dustin D. Holden
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - John E. P. Syka
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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91
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Historical, current and future developments of travelling wave ion mobility mass spectrometry: A personal perspective. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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92
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Prokai L. Rapid and accurate diagnosis of hemoglobinopathy and β-thalassemia by ultrahigh-resolution mass spectrometry and tandem mass spectrometry from blood: review of a benchmark study. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S227. [PMID: 31656806 DOI: 10.21037/atm.2019.08.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Laszlo Prokai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
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93
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Kim JS, Kim HS. Diagnosis of hemoglobinopathy and β-thalassemia by 21-Tesla Fourier transform ion cyclotron resonance mass spectrometry. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S239. [PMID: 31656818 DOI: 10.21037/atm.2019.07.97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Hyun Sik Kim
- Division of Mass Spectrometry & Advanced Instrumentation Research Group, Korea Basic Science Institute, Cheongju, Chungbuk, Korea
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94
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Schaffer LV, Tucholski T, Shortreed MR, Ge Y, Smith LM. Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms. Anal Chem 2019; 91:10937-10942. [PMID: 31393705 DOI: 10.1021/acs.analchem.9b02343] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteoforms, the primary effectors of biological processes, are the different forms of proteins that arise from molecular processing events such as alternative splicing and post-translational modifications. Heart diseases exhibit changes in proteoform levels, motivating the development of a deeper understanding of the heart proteoform landscape. Our recently developed two-dimensional top-down proteomics platform coupling serial size exclusion chromatography (sSEC) to reversed-phase chromatography (RPC) expanded coverage of the human heart proteome and allowed observation of high-molecular weight proteoforms. However, most of these observed proteoforms were not identified due to the difficulty in obtaining quality tandem mass spectrometry (MS2) fragmentation data for large proteoforms from complex biological mixtures on a chromatographic time scale. Herein, we sought to identify human heart proteoforms in this data set using an enhanced version of Proteoform Suite, which identifies proteoforms by intact mass alone. Specifically, we added a new feature to Proteoform Suite to determine candidate identifications for isotopically unresolved proteoforms larger than 50 kDa, enabling subsequent MS2 identification of important high-molecular weight human heart proteoforms such as lamin A (72 kDa) and trifunctional enzyme subunit α (79 kDa). With this new workflow for large proteoform identification, endogenous human cardiac myosin binding protein C (140 kDa) was identified for the first time. This study demonstrates the integration of our sSEC-RPC-MS proteomics platform with intact-mass analysis through Proteoform Suite to create a catalog of human heart proteoforms and facilitate the identification of large proteoforms in complex systems.
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Affiliation(s)
- Leah V Schaffer
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Trisha Tucholski
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Michael R Shortreed
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Lloyd M Smith
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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95
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Tucker LH, Hamm GR, Sargeant RJE, Goodwin RJA, Mackay CL, Campbell CJ, Clarke DJ. Untargeted Metabolite Mapping in 3D Cell Culture Models Using High Spectral Resolution FT-ICR Mass Spectrometry Imaging. Anal Chem 2019; 91:9522-9529. [DOI: 10.1021/acs.analchem.9b00661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lulu H. Tucker
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Gregory R. Hamm
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Rebecca J. E. Sargeant
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Richard J. A. Goodwin
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - C. Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Colin J. Campbell
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - David J. Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
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96
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Drake TW, Van Oost K, Barthel M, Bauters M, Hoyt AM, Podgorski DC, Six J, Boeckx P, Trumbore SE, Ntaboba LC, Spencer RGM. Mobilization of aged and biolabile soil carbon by tropical deforestation. NATURE GEOSCIENCE 2019; 12:541-546. [PMID: 31338120 PMCID: PMC6650295 DOI: 10.1038/s41561-019-0384-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In the mostly pristine Congo Basin, agricultural land-use change has intensified in recent years. One potential and understudied consequence of this deforestation and conversion to agriculture is the mobilization and loss of organic matter from soils to rivers as dissolved organic matter. Here, we quantify and characterize dissolved organic matter sampled from 19 catchments of varying deforestation extent near Lake Kivu over a two-week period during the wet season. Dissolved organic carbon from deforested, agriculturally-dominated catchments was older (14C age: ~1.5kyr) and more biolabile than from pristine forest catchments. Ultrahigh-resolution mass spectrometry revealed that this aged organic matter from deforested catchments was energy-rich and chemodiverse, with higher proportions of nitrogen- and sulfur-containing formulae. Given the molecular composition and biolability, we suggest that organic matter from deforested landscapes is preferentially respired upon disturbance, resulting in elevated in-stream concentrations of carbon dioxide. We estimate that while deforestation reduces the overall flux of dissolved organic carbon by ~56%, it does not significantly change the yield of biolabile dissolved organic carbon. Ultimately, the exposure of deeper soil horizons through deforestation and agricultural expansion releases old, previously stable, and biolabile soil organic carbon into the modern carbon cycle via the aquatic pathway.
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Affiliation(s)
- Travis W. Drake
- Department of Earth, Ocean, and Atmospheric Science, Florida State
University, Tallahassee, FL, USA
- National High Magnetic Field Laboratory Geochemistry Group,
Tallahassee, FL, USA
- Corresponding author. tel.: +1-503-806-0727; Requests for
materials should be addressed to T.W.D.
()
| | - Kristof Van Oost
- Earth and Life Institute, Université Catholique de Louvain,
Louvain-la-Neuve, Belgium
| | - Matti Barthel
- Department of Environmental Systems Science, ETH Zurich,
Switzerland
| | - Marijn Bauters
- Isotope Bioscience Laboratory, Department of Green Chemistry and
Technology, Ghent University, 9000 Gent, Belgium
- Computational & Applied Vegetation Ecology Lab, Department of
Environment, Ghent University, 9000 Gent, Belgium
| | - Alison M. Hoyt
- Max Planck Institute for Biogeochemistry, 07745 Jena, Germany
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - David C. Podgorski
- Department of Earth, Ocean, and Atmospheric Science, Florida State
University, Tallahassee, FL, USA
- National High Magnetic Field Laboratory Geochemistry Group,
Tallahassee, FL, USA
| | - Johan Six
- Department of Environmental Systems Science, ETH Zurich,
Switzerland
| | - Pascal Boeckx
- Isotope Bioscience Laboratory, Department of Green Chemistry and
Technology, Ghent University, 9000 Gent, Belgium
| | - Susan E. Trumbore
- Max Planck Institute for Biogeochemistry, 07745 Jena, Germany
- Earth System Science, University of California, Irvine, CA,
USA
| | - Landry Cizungu Ntaboba
- Faculty of Agronomy, Université Catholique de Bukavu, BP 285
Bukavu, Democratic Republic of Congo
| | - Robert G. M. Spencer
- Department of Earth, Ocean, and Atmospheric Science, Florida State
University, Tallahassee, FL, USA
- National High Magnetic Field Laboratory Geochemistry Group,
Tallahassee, FL, USA
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97
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Lioznov A, Baykut G, Nikolaev E. Analytical Solution for the Electric Field Inside Dynamically Harmonized FT-ICR Cell. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:778-786. [PMID: 30825130 DOI: 10.1007/s13361-018-2121-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
Dynamically harmonized FT-ICR cell has a saddle-like hyperbolic field distribution inside when averaged over a cyclotron trajectory around the axis of the cell. Such a field distribution makes the motion along the magnetic field independent of the motion in the x,y-plane, as well as the cyclotron motion independent of the magnetron motion and prevents any disintegration of excited coherent ion clouds, which is ruining the resolution in the other types of FT-ICR cells providing by this ideal phasing of single-m/z ion clouds in the entire volume of the cell. FT-ICR instruments with such a cell show resolutions of more than ten million at m/z 1000 at relatively small magnetic fields like 7 Tesla in quadrupole detection mode, what is not reachable by any other type of modern mass spectrometers. We have found that for such ion traps, it is possible to find the analytical solution in the working volume of the trap without any averaging. The potential distribution for the almost whole volume of such a cell can be presented in the form ϕ(x, y, z) = αz2 + f2D(x, y), where f2D(x, y) is the solution of 2D Poisson equation, which could be found by the method of conformal transformation. This solution is applicable in the practical case and can serve as a base for an analytical theory of signal detection using such cells and as a standard for solutions obtained by numerical simulations of the cell field.
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Affiliation(s)
- Anton Lioznov
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Evgeny Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, Russia.
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98
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He L, Rockwood AL, Agarwal AM, Anderson LC, Weisbrod CR, Hendrickson CL, Marshall AG. Diagnosis of Hemoglobinopathy and β-Thalassemia by 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry of Hemoglobin from Blood. Clin Chem 2019; 65:986-994. [PMID: 31040099 DOI: 10.1373/clinchem.2018.295766] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 03/28/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Hemoglobinopathies and thalassemias are the most common genetically determined disorders. Current screening methods include cation-exchange HPLC and electrophoresis, the results of which can be ambiguous because of limited resolving power. Subsequently, laborious genetic testing is required for confirmation. METHODS We performed a top-down tandem mass spectrometry (MS/MS) approach with a fast data acquisition (3 min), ultrahigh mass accuracy, and extensive residue cleavage by use of positive electrospray ionization 21 Tesla Fourier transform ion cyclotron resonance-tandem mass spectrometry (21 T FT-ICR MS/MS) for hemoglobin (Hb) variant de novo sequencing and β-thalassemia diagnosis. RESULTS We correctly identified all Hb variants in blind analysis of 18 samples, including the first characterization of homozygous Hb Himeji variant. In addition, an Hb heterozygous variant with isotopologue mass spacing as small as 0.0194 Da (Hb AD) was resolved in both precursor ion mass spectrum (MS1) and product ion mass spectrum (MS2). In blind analysis, we also observed that the abundance ratio between intact δ and β subunits (δ/β) or the abundance ratio between intact δ and α subunits (δ/α) could serve to diagnose β-thalassemia trait caused by a mutation in 1 HBB gene. CONCLUSIONS We found that 21 T FT-ICR MS/MS provides a benchmark for top-down MS/MS analysis of blood Hb. The present method has the potential to be translated to lower resolving power mass spectrometers (lower field FT-ICR mass spectrometry and Orbitrap) for Hb variant analysis (by MS1 and MS2) and β-thalassemia diagnosis (MS1).
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Affiliation(s)
- Lidong He
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL
| | - Alan L Rockwood
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL.,Rockwood Scientific Consulting, Salt Lake City, UT.,University of Utah Health, Salt Lake City, UT
| | - Archana M Agarwal
- University of Utah Health, Salt Lake City, UT.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL
| | - Christopher L Hendrickson
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL; .,National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL
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99
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Stopka SA, Samarah LZ, Shaw JB, Liyu AV, Veličković D, Agtuca BJ, Kukolj C, Koppenaal DW, Stacey G, Paša-Tolić L, Anderton CR, Vertes A. Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution Using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry. Anal Chem 2019; 91:5028-5035. [PMID: 30821434 DOI: 10.1021/acs.analchem.8b05084] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS) is an indispensable analytical tool to capture the array of metabolites within complex biological systems. However, conventional MS-based metabolomic workflows require extensive sample processing and separation resulting in limited throughput and potential alteration of the native molecular states in these systems. Ambient ionization methods, capable of sampling directly from tissues, circumvent some of these issues but require high-performance MS to resolve the molecular complexity within these samples. Here, we demonstrate a unique combination of laser ablation electrospray ionization (LAESI) coupled with a 21 tesla Fourier transform ion cyclotron resonance (21T-FTICR) for direct MS analysis and imaging applications. This analytical platform provides isotopic fine structure information directly from biological tissues, enabling the rapid assignment of molecular formulas and delivering a higher degree of confidence for molecular identification.
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Affiliation(s)
- Sylwia A Stopka
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Laith Z Samarah
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Caroline Kukolj
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Akos Vertes
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
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100
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He L, Anderson LC, Barnidge DR, Murray DL, Dasari S, Dispenzieri A, Hendrickson CL, Marshall AG. Classification of Plasma Cell Disorders by 21 Tesla Fourier Transform Ion Cyclotron Resonance Top-Down and Middle-Down MS/MS Analysis of Monoclonal Immunoglobulin Light Chains in Human Serum. Anal Chem 2019; 91:3263-3269. [DOI: 10.1021/acs.analchem.8b03294] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Lidong He
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32310, United States
| | - Lissa C. Anderson
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | | | | | | | | | - Christopher L. Hendrickson
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32310, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32310, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
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