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Liu R, Lu G, Hu X, Li J, Zhang Z, Tang K. Capillary zone electrophoresis-tandem mass spectrometry for in-depth proteomics analysis via data-independent acquisition. Anal Bioanal Chem 2024:10.1007/s00216-024-05502-7. [PMID: 39196334 DOI: 10.1007/s00216-024-05502-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024]
Abstract
A capillary zone electrophoresis (CZE) system was coupled to an Orbitrap mass spectrometer operating in a data-independent acquisition (DIA) mode for in-depth proteomics analysis. The performance of this CZE-DIA-MS system was systemically evaluated and optimized under different operating conditions. The performance of the fully optimized CZE-DIA-MS system was subsequently compared to the one by using the same CZE-MS system operating in a data-dependent acquisition (DDA) mode. The experimental results show that the numbers of identified peptides and proteins acquired in the DIA mode are much higher than the ones acquired in the DDA mode, especially with the small sample loading amount. Specifically, the numbers of identified peptides and proteins acquired in the DIA mode are 1.8-fold and 2-fold higher than the ones acquired in the DDA mode by using 12.5 ng Hela digests. The proteins identified in the DIA mode also cover almost all the proteins identified in the DDA mode. In addition, a potential cancer biomarker protein, carbohydrate antigen 125, undetected in the DDA mode, can be easily identified in the DIA mode even with 12.5 ng Hela digests. The performance of the CZE-DIA-MS system for in-depth proteomics analysis with a limited sample amount has been fully demonstrated for the first time through this study.
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Affiliation(s)
- Rong Liu
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Gang Lu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, PR China
| | - Xiaozhong Hu
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Junhui Li
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Zhenbin Zhang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, PR China
| | - Keqi Tang
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China.
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China.
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
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2
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Nandy A, Mondal S, Koner D, Banerjee S. Heavy Water Microdroplet Surface Enriches the Lighter Isotopologue Impurities. J Am Chem Soc 2024; 146:19050-19058. [PMID: 38958201 DOI: 10.1021/jacs.4c03315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Water microdroplets promote unusual chemical reactions at the air-water interface. However, the interfacial structure of water microdroplets and its potential influence on chemical processes are still enigmatic. Here, we present evidence of in-droplet fractionation of water isotopologues. Employing a sonic spray, we atomized the heavy water (D2O, 99.9 atom % D) solution of three classes of organic compounds (basic, acidic, and neutral). The analytes were predominantly desorbed from the resulting droplet surface in protonated form rather than deuterated form, as detected by mass spectrometry. This result remained unaltered upon adding formic acid-d2 (DCOOD) to the droplet. Monitoring Dakin oxidation of benzaldehyde at the surface of binary microdroplets composed of 1:1 (v/v) D2O/H218O revealed the preferred formation of phenolate-16O over phenolate-18O. Atmospheric pressure chemical ionization mass spectrometric analysis of the vapor composition in the sprayed aerosol revealed the preferential evaporation of lighter water isotopologue impurities from the surface of heavy water microdroplets. These results indicate the enrichment of lighter water isotopologue impurities (HOD/H2O) on the surface of heavy water microdroplets, implying possible future developments for water isotopologue fractionation using microdroplets.
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Affiliation(s)
- Abhijit Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati 517507, India
| | - Supratim Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati 517507, India
| | - Debasish Koner
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502284, India
| | - Shibdas Banerjee
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati 517507, India
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3
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Harper CC, Jordan JS, Papanu S, Williams ER. Characterization of Mass, Diameter, Density, and Surface Properties of Colloidal Nanoparticles Enabled by Charge Detection Mass Spectrometry. ACS NANO 2024; 18:17806-17814. [PMID: 38913932 DOI: 10.1021/acsnano.4c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
A variety of scattering-based, microscopy-based, and mobility-based methods are frequently used to probe the size distributions of colloidal nanoparticles with transmission electron microscopy (TEM) often considered to be the "gold standard". Charge detection mass spectrometry (CDMS) is an alternative method for nanoparticle characterization that can rapidly measure the mass and charge of individual nanoparticle ions with high accuracy. Two low polydispersity, ∼100 nm diameter nanoparticle size standards with different compositions (polymethyl methacrylate/polystyrene copolymer and 100% polystyrene) were characterized using both TEM and CDMS to explore the merits and complementary aspects of both methods. Mass and diameter distributions are rapidly obtained from CDMS measurements of thousands of individual ions of known spherical shape, requiring less time than TEM sample preparation and image analysis. TEM image-to-image variations resulted in a ∼1-2 nm range in the determined mean diameters whereas the CDMS mass precision of ∼1% in these experiments leads to a diameter uncertainty of just 0.3 nm. For the 100% polystyrene nanoparticles with known density, the CDMS and TEM particle diameter distributions were in excellent agreement. For the copolymer nanoparticles with unknown density, the diameter from TEM measurements combined with the mass from CDMS measurements enabled an accurate measurement of nanoparticle density. Differing extents of charging for the two nanoparticle standards measured by CDMS show that charging is sensitive to nanoparticle surface properties. A mixture of the two samples was separated based on their different extents of charging despite having overlapping mass distributions centered at 341.5 and 331.0 MDa.
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Affiliation(s)
- Conner C Harper
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Steven Papanu
- Colloidal Metrics Corporation, 2520 Wyandotte Street Suite F, Mountain View, California 94083-2381, United States
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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4
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Graça AT, Lihavainen J, Hussein R, Schröder WP. Obscurity of chlorophyll tails - Is chlorophyll with farnesyl tail incorporated into PSII complexes? PHYSIOLOGIA PLANTARUM 2024; 176:e14428. [PMID: 38981693 DOI: 10.1111/ppl.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 07/11/2024]
Abstract
Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.
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Affiliation(s)
- André T Graça
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jenna Lihavainen
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, Sweden
| | - Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, Berlin, Germany
| | - Wolfgang P Schröder
- Department of Chemistry, Umeå University, Umeå, Sweden
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, Sweden
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5
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Ahmad S, Lohiya S, Taksande A, Meshram RJ, Varma A, Vagha K. A Comprehensive Review of Innovative Paradigms in Microbial Detection and Antimicrobial Resistance: Beyond Traditional Cultural Methods. Cureus 2024; 16:e61476. [PMID: 38952583 PMCID: PMC11216122 DOI: 10.7759/cureus.61476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/01/2024] [Indexed: 07/03/2024] Open
Abstract
Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the efficacy of antimicrobial agents. While foundational in microbial identification, traditional cultural methods are often laborious, time-consuming, and limited in their ability to detect AMR markers. In response to these challenges, innovative paradigms have emerged, leveraging advances in molecular biology, genomics, proteomics, nanotechnology, and bioinformatics. This comprehensive review provides an overview of innovative approaches beyond traditional cultural methods for microbial detection and AMR surveillance. Molecular-based techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer enhanced sensitivity and specificity, enabling the rapid identification of microbial pathogens and AMR determinants. Mass spectrometry-based methods provide rapid and accurate detection of microbial biomarkers, including matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and biosensor technologies. Nanotechnology approaches, such as nanoparticle-based assays and nanopore sequencing, offer novel platforms for sensitive and label-free detection of pathogens and AMR markers. Embracing these innovative paradigms holds immense promise for improving disease diagnosis, antibiotic stewardship, and AMR containment efforts. However, challenges such as cost, standardization, and integration with existing healthcare systems must be addressed to realize the full potential of these technologies. By fostering interdisciplinary collaboration and innovation, we can strengthen our ability to detect, monitor, and combat AMR, safeguarding public health for generations.
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Affiliation(s)
- Shahzad Ahmad
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Sham Lohiya
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
- Pediatrics, Acharya Vinoba Bhave Rural Hospital, Wardha, IND
| | - Amar Taksande
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Revat J Meshram
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Ashish Varma
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Keta Vagha
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
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6
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Spoorthi BK, Debnath K, Basuri P, Nagar A, Waghmare UV, Pradeep T. Spontaneous weathering of natural minerals in charged water microdroplets forms nanomaterials. Science 2024; 384:1012-1017. [PMID: 38815034 DOI: 10.1126/science.adl3364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/08/2024] [Indexed: 06/01/2024]
Abstract
In this work, we show that particles of common minerals break down spontaneously to form nanoparticles in charged water microdroplets within milliseconds. We transformed micron-sized natural minerals like quartz and ruby into 5- to 10-nanometer particles when integrated into aqueous microdroplets generated via electrospray. We deposited the droplets on a substrate, which allowed nanoparticle characterization. We determined through simulations that quartz undergoes proton-induced slip, especially when reduced in size and exposed to an electric field. This leads to particle scission and the formation of silicate fragments, which we confirmed with mass spectrometry. This rapid weathering process may be important for soil formation, given the prevalence of charged aerosols in the atmosphere.
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Affiliation(s)
- B K Spoorthi
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Koyendrila Debnath
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Pallab Basuri
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ankit Nagar
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Thalappil Pradeep
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
- International Centre for Clean Water, IIT Madras Research Park, Chennai 600113, India
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7
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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8
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Vikram HP, Kumar TP, Kumar G, Beeraka NM, Deka R, Suhail SM, Jat S, Bannimath N, Padmanabhan G, Chandan RS, Kumar P, Gurupadayya B. Nitrosamines crisis in pharmaceuticals - Insights on toxicological implications, root causes and risk assessment: A systematic review. J Pharm Anal 2024; 14:100919. [PMID: 38799236 PMCID: PMC11126534 DOI: 10.1016/j.jpha.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 05/29/2024] Open
Abstract
The presence of N-nitroso compounds, particularly N-nitrosamines, in pharmaceutical products has raised global safety concerns due to their significant genotoxic and mutagenic effects. This systematic review investigates their toxicity in active pharmaceutical ingredients (APIs), drug products, and pharmaceutical excipients, along with novel analytical strategies for detection, root cause analysis, reformulation strategies, and regulatory guidelines for nitrosamines. This review emphasizes the molecular toxicity of N-nitroso compounds, focusing on genotoxic, mutagenic, carcinogenic, and other physiological effects. Additionally, it addresses the ongoing nitrosamine crisis, the development of nitrosamine-free products, and the importance of sensitive detection methods and precise risk evaluation. This comprehensive overview will aid molecular biologists, analytical scientists, formulation scientists in research and development sector, and researchers involved in management of nitrosamine-induced toxicity and promoting safer pharmaceutical products.
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Affiliation(s)
- Hemanth P.R. Vikram
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy Mysuru, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570015, India
- Xenone Healthcare Pvt. Ltd., New Delhi, 110076, India
| | - Tegginamath Pramod Kumar
- Department of Pharmaceutics, JSS College of Pharmacy Mysuru, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570015, India
| | - Gunjan Kumar
- Xenone Healthcare Pvt. Ltd., New Delhi, 110076, India
| | - Narasimha M. Beeraka
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russian Federation
- Department of Pharmacology, Raghavendra Institute of Pharmaceutical Education and Research (RIPER), Ananthapuramu, 515721, India
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Rajashree Deka
- Animal Physiology and Biochemistry Laboratory, Department of Zoology, Gauhati University, Guwahati, 781014, India
| | - Sheik Mohammed Suhail
- Department of Pharmacology, JSS College of Pharmacy Mysuru, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570015, India
| | - Sandeep Jat
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, 781101, India
| | - Namitha Bannimath
- Department of Pharmacology, University of Galway, Galway, H91 TK33, Ireland
| | - Gayatiri Padmanabhan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy Mysuru, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570015, India
| | - Ravandur S. Chandan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy Mysuru, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570015, India
| | - Pramod Kumar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, 781101, India
| | - Bannimath Gurupadayya
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy Mysuru, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, 570015, India
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9
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Wesdemiotis C, Williams-Pavlantos KN, Keating AR, McGee AS, Bochenek C. Mass spectrometry of polymers: A tutorial review. MASS SPECTROMETRY REVIEWS 2024; 43:427-476. [PMID: 37070280 DOI: 10.1002/mas.21844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Ever since the inception of synthetic polymeric materials in the late 19th century, the number of studies on polymers as well as the complexity of their structures have only increased. The development and commercialization of new polymers with properties fine-tuned for specific technological, environmental, consumer, or biomedical applications requires powerful analytical techniques that permit the in-depth characterization of these materials. One such method with the ability to provide chemical composition and structure information with high sensitivity, selectivity, specificity, and speed is mass spectrometry (MS). This tutorial review presents and exemplifies the various MS techniques available for the elucidation of specific structural features in a synthetic polymer, including compositional complexity, primary structure, architecture, topology, and surface properties. Key to every MS analysis is sample conversion to gas-phase ions. This review describes the fundamentals of the most suitable ionization methods for synthetic materials and provides relevant sample preparation protocols. Most importantly, structural characterizations via one-step as well as hyphenated or multidimensional approaches are introduced and demonstrated with specific applications, including surface sensitive and imaging techniques. The aim of this tutorial review is to illustrate the capabilities of MS for the characterization of large, complex polymers and emphasize its potential as a powerful compositional and structural elucidation tool in polymer chemistry.
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Affiliation(s)
| | | | - Addie R Keating
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Andrew S McGee
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Calum Bochenek
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
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10
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Liang X, Andrikopoulos N, Tang H, Wang Y, Ding F, Ke PC. Nanoplastic Stimulates the Amyloidogenesis of Parkinson's Alpha-Synuclein NACore. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308753. [PMID: 37988678 PMCID: PMC10994764 DOI: 10.1002/smll.202308753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Environmental plastic wastes are potential health hazards due to their prevalence as well as their versatility in initiating physical, chemical, and biological interactions and transformations. Indeed, recent research has implicated the adverse effects of micro- and nano-plastics, including their neurotoxicity, yet how plastic particulates may impact the aggregation pathway and toxicity of amyloid proteins pertinent to the pathologies of neurological diseases remains unknown. Here, electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS) is employed to reveal the polymorphic oligomerization of NACore, a surrogate of alpha-synuclein that is associated with the pathogenesis of Parkinson's disease. These data indicate that the production rate and population of the NACore oligomers are modulated by their exposure to a polystyrene nanoplastic, and these cellular assays further reveal an elevated NACore toxicity in microglial cells elicited by the nanoplastic. These simulations confirm that the nanoplastic-NACore association is promoted by their hydrophobic interactions. These findings are corroborated by an impairment in zebrafish hatching, survival, and development in vivo upon their embryonic exposure to the nanoplastic. Together, this study has uncovered the dynamics and mechanism of amyloidogenesis elevated by a nanoplastic trigger, shedding a new light on the neurological burden of plastic pollution.
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Affiliation(s)
- Xiufang Liang
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 510006, China
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
| | - Nicholas Andrikopoulos
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Huayuan Tang
- College of Mechanics and Materials, Hohai University, Nanjing, 211100, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Yue Wang
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 510006, China
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Pu Chun Ke
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
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11
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Maiti S, Singh A, Maji T, Saibo NV, De S. Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins. Curr Res Struct Biol 2024; 7:100138. [PMID: 38707546 PMCID: PMC11068507 DOI: 10.1016/j.crstbi.2024.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 05/07/2024] Open
Abstract
Eukaryotic proteins often feature long stretches of amino acids that lack a well-defined three-dimensional structure and are referred to as intrinsically disordered proteins (IDPs) or regions (IDRs). Although these proteins challenge conventional structure-function paradigms, they play vital roles in cellular processes. Recent progress in experimental techniques, such as NMR spectroscopy, single molecule FRET, high speed AFM and SAXS, have provided valuable insights into the biophysical basis of IDP function. This review discusses the advancements made in these techniques particularly for the study of disordered regions in proteins. In NMR spectroscopy new strategies such as 13C detection, non-uniform sampling, segmental isotope labeling, and rapid data acquisition methods address the challenges posed by spectral overcrowding and low stability of IDPs. The importance of various NMR parameters, including chemical shifts, hydrogen exchange rates, and relaxation measurements, to reveal transient secondary structures within IDRs and IDPs are presented. Given the high flexibility of IDPs, the review outlines NMR methods for assessing their dynamics at both fast (ps-ns) and slow (μs-ms) timescales. IDPs exert their functions through interactions with other molecules such as proteins, DNA, or RNA. NMR-based titration experiments yield insights into the thermodynamics and kinetics of these interactions. Detailed study of IDPs requires multiple experimental techniques, and thus, several methods are described for studying disordered proteins, highlighting their respective advantages and limitations. The potential for integrating these complementary techniques, each offering unique perspectives, is explored to achieve a comprehensive understanding of IDPs.
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Affiliation(s)
| | - Aakanksha Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Tanisha Maji
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Nikita V. Saibo
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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12
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Cordes MS, Gallagher ES. Molecular Dynamics Simulations of Native Protein Charging via Proton Transfer during Electrospray Ionization with Grotthuss Diffuse H 3O . Anal Chem 2024; 96:4146-4153. [PMID: 38427846 PMCID: PMC11337394 DOI: 10.1021/acs.analchem.3c05089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Unraveling the mechanism by which native proteins are charged through electrospray ionization (ESI) has been the focus of considerable research because observable charge states can be correlated to biophysical characteristics, such as protein folding and, thus, solution conformation. Difficulties in characterizing electrosprayed droplets have catalyzed the use of molecular dynamics (MD) to provide insights into the mechanisms by which proteins are charged and transferred to the gas phase. However, prior MD studies have utilized metal ions, primarily Na+, as charge carriers, even though proteins are primarily detected as protonated ions in the mass spectra. Here, we propose a modified MD protocol for simulating discrete Grotthuss diffuse H3O+ that is capable of dynamically altering amino-acid protonation states to model electrospray charging and gaseous ion formation of model proteins, ubiquitin, and myoglobin. Application of the protocol to the evaporation of acidic droplets enables a molecular perspective of H3O+ coordination and proton transfer to/from proteins, which is unfeasible with the metal charge carriers used in previous MD studies of ESI. Our protocol recreates experimentally observed charge-state distributions and supports the charge residue model (CRM) as the dominant mechanism of native protein ionization during ESI. Additionally, our results suggest that protonation is highly specific to individual residues and is correlated to the formation of localized hydrated regions on the protein surface as droplets desolvate. Considering the use of discrete H3O+ instead of Na+, the developed protocol is a necessary step toward developing a more comprehensive model of protein ionization during ESI.
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Affiliation(s)
- Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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13
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Liu CY, Chen Y, Hu J. Identification of the Electrogenerated Hidden Nitrenium Ions by In Situ Mass Spectrometry. Anal Chem 2024; 96:3354-3361. [PMID: 38295431 DOI: 10.1021/acs.analchem.3c04315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The identification of the electrogenerated reactive intermediates is essential for an in-depth understanding of the electroredox processes. Although various short-lived intermediates are well characterized by coupling electrochemistry with mass spectrometry (EC/MS), many electrogenerated transient species (τ < 1 μs) are still rarely captured by the currently available EC/MS approaches. Here, we present a low-delay coupling device, which was constructed by decorating a microelectrode into the front tip of a microsized ion emitter. For the first time, the in situ detection of a previously hidden intermediate, i.e., the transient nitrenium ion of carbazole (τ = 333 ns), was achieved. The electrochemical generation of indole nitrenium ion, whose half-life is estimated to be shorter compared to the carbazole nitrenium ion due to less resonance stabilization, was also confirmed by direct observation. This clog-free microelectrode/ion emitter is cheap and easy to fabricate and offers a general and powerful approach to monitoring the fast reactions of electrogenerated reactive intermediates. We believe that our integrated EC/MS approach holds substantial potential for broad applicability, particularly in probing the intricate and ultrafast electroredox processes occurring at the electrode-solution interface.
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Affiliation(s)
- Chun-Yan Liu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, P. R. China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, P. R. China
| | - Jun Hu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, P. R. China
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, P. R. China
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14
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Shohel M, Bustos J, Roseborough A, Nyman M. Pertechnetate/perrhenate-capped Zr/Hf-Dihydroxide Dimers: Elucidating Zr-TcO 4 Co-Mobility in the Nuclear Fuel Cycle. Chemistry 2024; 30:e202303218. [PMID: 38109648 DOI: 10.1002/chem.202303218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/20/2023]
Abstract
Spent nuclear fuel contains heavy element fission products that must be separated for effective reprocessing for a safe and sustainable nuclear fuel cycle. 93 Zr and 99 Tc are high-yield fission products that co-transport in liquid-liquid extraction processes. Here we seek atomic-level information of this co-extraction process, as well as fundamental knowledge about ZrIV (and HfIV ) aqueous speciation in the presence of topology-directing ligands such as pertechnetate (TcO4 - ) and non-radioactive surrogate perrhenate (ReO4 - ). In this context, we show that the flat tetrameric oxyhydroxyl-cluster [MIV 4 (OH)8 (H2 O)16 ]8+ (and related polymers) is dissociated by perrhenate/pertechnetate to yield isostructural dimers, M2 (OH)2 (XO4 - )6 (H2 O)6 ⋅ 3H2 O (M=Zr/HfIV ; X=Re/TcVII ), elucidated by single-crystal X-ray diffraction. We used these model compounds to understand the pervasive 93 Zr-99 Tc coextraction with further speciation studies in water, nitric acid, and tetrabutylphosphate (TBP) -kerosene; where the latter two media are relevant to nuclear fuel reprocessing. SAXS (small angle X-ray scattering), compositional evaluation, and where experimentally feasible, ESI-MS (electrospray ionization mass spectrometry) showed that perrhenate/pertechnetate influence Zr/HfIV -speciation in water. In Zr-XO4 solvent extraction studies to simulate fuel reprocessing, we provide evidence that TcO4 - enhances extraction of ZrIV , and compositional analysis of the extracted metal-complexes (Zr-ReO4 study) is consistent with the crystallized ZrIV 2 (OH)2 (ReVII O4 - )6 (H2 O)6 ⋅dimer.
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Affiliation(s)
- Mohammad Shohel
- Department of Chemistry, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Jenna Bustos
- Department of Chemistry, Oregon State University, Corvallis, Oregon, 97331, USA
| | | | - May Nyman
- Department of Chemistry, Oregon State University, Corvallis, Oregon, 97331, USA
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15
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Dong J, Chen J, Wang W, Wei Z, Tian ZQ, Fan FR. Charged Microdroplets as Microelectrochemical Cells for CO 2 Reduction and C-C Coupling. J Am Chem Soc 2024; 146:2227-2236. [PMID: 38224553 DOI: 10.1021/jacs.3c12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Charged microdroplets offer novel electrochemical environments, distinct from traditional solid-liquid or solid-liquid-gas interfaces, due to the intense electric fields at liquid-gas interfaces. In this study, we propose that charged microdroplets serve as microelectrochemical cells (MECs), enabling unique electrochemical reactions at the gas-liquid interface. Using electrospray-generated microdroplets, we achieved multielectron CO2 reduction and C-C coupling to synthesize ethanol using molecular catalysts. These catalysts effectively harness and relay electrons, enhancing the longevity of solvated electrons and enabling multielectron reactions. Importantly, we revealed the intrinsic relationship between the size and charge density of a MEC and its reaction selectivity. Employing in situ mass spectrometry, we identified reaction intermediates (molecular catalyst adducts with HCOO) and oxidation products, elucidating the CO2 reduction mechanism and the comprehensive reaction procedure. Our research underscores the promising role of charged microdroplets in pioneering new electrochemical systems.
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Affiliation(s)
- Jianing Dong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jianxiong Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Wenxin Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhenwei Wei
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Feng Ru Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
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16
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Wang Y, Dong J, Song X, Luo K, Nan ZA, Fan FR, Tian ZQ. Utilization of charged microdroplets for the controlled rapid synthesis of hollow sodium chloride single crystals. Chem Commun (Camb) 2024; 60:980-983. [PMID: 38165770 DOI: 10.1039/d3cc05640f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Charged microdroplets are favored in microfluidic control, biomedicine, chemistry and materials processing due to their unique physicochemical environment, including interface double layers, high electric fields, surface concentration enrichment, and more. Herein, we investigated the crystallization of charged sodium chloride microdroplets and achieved the formation of hollow single crystals in a single-step process lasting only a few seconds, without the use of templates. Additionally, we discussed the plausible crystal growth mechanism, which appears to be an unconventional outward-inward growth process.
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Affiliation(s)
- Yanjie Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
| | - Jianing Dong
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
| | - Xianmeng Song
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
| | - Kai Luo
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
| | - Zi-Ang Nan
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
| | - Feng Ru Fan
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
| | - Zhong-Qun Tian
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
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17
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Chua ZQ, Prabhu GRD, Wang YW, Raju CM, Buchowiecki K, Ochirov O, Elpa DP, Urban PL. Moderate Signal Enhancement in Electrospray Ionization Mass Spectrometry by Focusing Electrospray Plume with a Dielectric Layer around the Mass Spectrometer's Orifice. Molecules 2024; 29:316. [PMID: 38257229 PMCID: PMC10821223 DOI: 10.3390/molecules29020316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Electrospray ionization (ESI) is among the commonly used atmospheric pressure ionization techniques in mass spectrometry (MS). One of the drawbacks of ESI is the formation of divergent plumes composed of polydisperse microdroplets, which lead to low transmission efficiency. Here, we propose a new method to potentially improve the transmission efficiency of ESI, which does not require additional electrical components and complex interface modification. A dielectric plate-made of ceramic-was used in place of a regular metallic sampling cone. Due to the charge accumulation on the dielectric surface, the dielectric layer around the MS orifice distorts the electric field, focusing the charged electrospray cloud towards the MS inlet. The concept was first verified using charge measurement on the dielectric material surface and computational simulation; then, online experiments were carried out to demonstrate the potential of this method in MS applications. In the online experiment, signal enhancements were observed for dielectric plates with different geometries, distances of the electrospray needle axis from the MS inlet, and various compounds. For example, in the case of acetaminophen (15 μM), the signal enhancement was up to 1.82 times (plate B) using the default distance of the electrospray needle axis from the MS inlet (d = 1.5 mm) and 12.18 times (plate C) using a longer distance (d = 7 mm).
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Affiliation(s)
- Zi Qing Chua
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
| | - Gurpur Rakesh D. Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
| | - Yi-Wun Wang
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
| | - Chamarthi Maheswar Raju
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
| | - Krzysztof Buchowiecki
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
| | - Ochir Ochirov
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
| | - Decibel P. Elpa
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
| | - Pawel L. Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan (Y.-W.W.); (C.M.R.); (K.B.); (O.O.); (D.P.E.)
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan
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18
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Xu A, Tang LC, Jovanovic M, Regev O. Uncovering Distinct Peptide Charging Behaviors in Electrospray Ionization Mass Spectrometry Using a Large-Scale Dataset. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:90-99. [PMID: 38095561 PMCID: PMC10767741 DOI: 10.1021/jasms.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023]
Abstract
Electrospray ionization is a powerful and prevalent technique used to ionize analytes in mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important consideration for interpreting mass spectra. However, due to an incomplete understanding of the ionization mechanism, the analyte properties that influence CSDs are not fully understood. Here, we employ a machine learning-based approach and analyze CSDs of hundreds of thousands of peptides. Interestingly, half of the peptides exhibit charges that differ from what one would naively expect (the number of basic sites). We find that these peptides can be classified into two regimes (undercharging and overcharging) and that these two regimes display markedly different charging characteristics. Notably, peptides in the overcharging regime show minimal dependence on basic site count, and more generally, the two regimes exhibit distinct sequence determinants. These findings highlight the rich ionization behavior of peptides and the potential of CSDs for enhancing peptide identification.
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Affiliation(s)
- Allyn
M. Xu
- Department
of Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Lauren C. Tang
- Department
of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Marko Jovanovic
- Department
of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Oded Regev
- Computer
Science Department, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
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19
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Kumar BS. Recent developments and applications of ambient mass spectrometry imaging in pharmaceutical research: an overview. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 16:8-32. [PMID: 38088775 DOI: 10.1039/d3ay01267k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The application of ambient mass spectrometry imaging "MSI" is expanding in the areas of fundamental research on drug delivery and multiple phases of the process of identifying and developing drugs. Precise monitoring of a drug's pharmacological workflows, such as intake, distribution, metabolism, and discharge, is made easier by MSI's ability to determine the concentrations of the initiating drug and its metabolites across dosed samples without losing spatial data. Lipids, glycans, and proteins are just a few of the many phenotypes that MSI may be used to concurrently examine. Each of these substances has a particular distribution pattern and biological function throughout the body. MSI offers the perfect analytical tool for examining a drug's pharmacological features, especially in vitro and in vivo effectiveness, security, probable toxic effects, and putative molecular pathways, because of its high responsiveness in chemical and physical environments. The utilization of MSI in the field of pharmacy has further extended from the traditional tissue examination to the early stages of drug discovery and development, including examining the structure-function connection, high-throughput capabilities in vitro examination, and ex vivo research on individual cells or tumor spheroids. Additionally, an enormous array of endogenous substances that may function as tissue diagnostics can be scanned simultaneously, giving the specimen a highly thorough characterization. Ambient MSI techniques are soft enough to allow for easy examination of the native sample to gather data on exterior chemical compositions. This paper provides a scientific and methodological overview of ambient MSI utilization in research on pharmaceuticals.
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Affiliation(s)
- Bharath Sampath Kumar
- Independent researcher, 21, B2, 27th Street, Lakshmi Flats, Nanganallur, Chennai 600061, India.
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20
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Song JG, Baral KC, Kim GL, Park JW, Seo SH, Kim DH, Jung DH, Ifekpolugo NL, Han HK. Quantitative analysis of therapeutic proteins in biological fluids: recent advancement in analytical techniques. Drug Deliv 2023; 30:2183816. [PMID: 36880122 PMCID: PMC10003146 DOI: 10.1080/10717544.2023.2183816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Pharmaceutical application of therapeutic proteins has been continuously expanded for the treatment of various diseases. Efficient and reliable bioanalytical methods are essential to expedite the identification and successful clinical development of therapeutic proteins. In particular, selective quantitative assays in a high-throughput format are critical for the pharmacokinetic and pharmacodynamic evaluation of protein drugs and to meet the regulatory requirements for new drug approval. However, the inherent complexity of proteins and many interfering substances presented in biological matrices have a great impact on the specificity, sensitivity, accuracy, and robustness of analytical assays, thereby hindering the quantification of proteins. To overcome these issues, various protein assays and sample preparation methods are currently available in a medium- or high-throughput format. While there is no standard or universal approach suitable for all circumstances, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay often becomes a method of choice for the identification and quantitative analysis of therapeutic proteins in complex biological samples, owing to its high sensitivity, specificity, and throughput. Accordingly, its application as an essential analytical tool is continuously expanded in pharmaceutical R&D processes. Proper sample preparation is also important since clean samples can minimize the interference from co-existing substances and improve the specificity and sensitivity of LC-MS/MS assays. A combination of different methods can be utilized to improve bioanalytical performance and ensure more accurate quantification. This review provides an overview of various protein assays and sample preparation methods, with particular emphasis on quantitative protein analysis by LC-MS/MS.
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Affiliation(s)
- Jae Geun Song
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Kshitis Chandra Baral
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Gyu-Lin Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Ji-Won Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Soo-Hwa Seo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Da-Hyun Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Dong Hoon Jung
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Nonye Linda Ifekpolugo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Hyo-Kyung Han
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
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21
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Williams ML, Olomukoro AA, Emmons RV, Godage NH, Gionfriddo E. Matrix effects demystified: Strategies for resolving challenges in analytical separations of complex samples. J Sep Sci 2023; 46:e2300571. [PMID: 37897324 DOI: 10.1002/jssc.202300571] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
Matrix effects can significantly impede the accuracy, sensitivity, and reliability of separation techniques presenting a formidable challenge to the analytical process. It is crucial to address matrix effects to achieve accurate and precise measurements in complex matrices. The multifaceted nature of matrix effects which can be influenced by factors such as target analyte, sample preparation protocol, composition, and choice of instrument necessitates a pragmatic approach when analyzing complex matrices. This review aims to highlight common challenges associated with matrix effects throughout the entire analytical process with emphasis on gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, and sample preparation techniques. These techniques are susceptible to matrix effects that could lead to ion suppression/enhancement or impact the analyte signal at various stages of the analytical workflow. The assessment, quantification, and mitigation of matrix effects are necessary in developing any analytical method. Strategies can be implemented to reduce or eliminate the matrix effect by changing the type of ionization, improving extraction and clean-up methods, optimization of chromatography conditions, and corrective calibration methods. While development of an effective strategy to completely mitigate matrix effects remains elusive, an integrated approach that combines sample preparation, analytical extraction, and effective instrumental analysis remains the most promising avenue for identifying and resolving matrix effects.
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Affiliation(s)
- Madison L Williams
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, Ohio, USA
- Dr. Nina McClelland Laboratory for Water Chemistry and Environmental Analysis, The University of Toledo, Toledo, Ohio, USA
| | - Aghogho Abigail Olomukoro
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, Ohio, USA
- Dr. Nina McClelland Laboratory for Water Chemistry and Environmental Analysis, The University of Toledo, Toledo, Ohio, USA
| | - Ronald V Emmons
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, Ohio, USA
- Dr. Nina McClelland Laboratory for Water Chemistry and Environmental Analysis, The University of Toledo, Toledo, Ohio, USA
| | - Nipunika H Godage
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, Ohio, USA
- Dr. Nina McClelland Laboratory for Water Chemistry and Environmental Analysis, The University of Toledo, Toledo, Ohio, USA
| | - Emanuela Gionfriddo
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, Ohio, USA
- Dr. Nina McClelland Laboratory for Water Chemistry and Environmental Analysis, The University of Toledo, Toledo, Ohio, USA
- School of Green Chemistry and Engineering, The University of Toledo, Toledo, Ohio, USA
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22
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Wang T, Li Z, Gao H, Hu J, Chen HY, Xu JJ. Ultrafast C-C and C-N bond formation reactions in water microdroplets facilitated by the spontaneous generation of carbocations. Chem Sci 2023; 14:11515-11520. [PMID: 37886101 PMCID: PMC10599473 DOI: 10.1039/d3sc03870j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/24/2023] [Indexed: 10/28/2023] Open
Abstract
Carbocations are important electrophilic intermediates in organic chemistry, but their formation typically requires harsh conditions such as extremely low pH, elevated temperature, strong oxidants and/or expensive noble-metal catalysts. Herein, we report the spontaneous generation of highly reactive carbocations in water microdroplets by simply spraying a diarylmethanol aqueous solution. The formation of transient carbocations as well as their ultrafast in-droplet transformations through carbocation-involved C-C and C-N bond formation reactions are directly characterized by mass spectrometry. The intriguing formation and stabilization of carbocations are attributed to the super acidity of the positively charged water microdroplets as well as the high electric fields at the water-air interfaces. Without the utilization of external acids as catalysts, we believe that these microdroplet reactions would pose a new and sustainable way for the construction of aryl-substituted compounds.
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Affiliation(s)
- Ting Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Zheng Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Hang Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Jun Hu
- School of Life Sciences and Health Engineering, Jiangnan University Wuxi 214122 China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
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23
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Chung SH, Yoo D, Ahn TB, Lee W, Hong J. Profiling Analysis of Tryptophan Metabolites in the Urine of Patients with Parkinson's Disease Using LC-MS/MS. Pharmaceuticals (Basel) 2023; 16:1495. [PMID: 37895965 PMCID: PMC10610059 DOI: 10.3390/ph16101495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Although Parkinson's disease (PD) is a representative neurodegenerative disorder and shows characteristic motor impediments, the pathophysiological mechanisms and treatment targets for PD have not yet been clearly identified. Since several tryptophan metabolites produced by gut microbiota could pass the blood-brain barrier and, furthermore, might influence the central nervous system, tryptophan metabolites within the indole, kynurenine, and serotonin metabolic pathways might be the most potent targets for PD development. Furthermore, most metabolites are circulated via the blood, play roles in and/or are metabolized via the host organs, and finally are excreted into the urine. Therefore, profiling the overall tryptophan metabolic pathways in urine samples of patients with PD is important to understanding the pathological mechanisms, finding biomarkers, and discovering therapeutic targets for PD. However, the development of profiling analysis based on tryptophan metabolism pathways in human urine samples is still challenging due to the wide physiological ranges, the varied signal response, and the structural diversity of tryptophan metabolites in complicated urine matrices. In this study, an LC-MS/MS method was developed to profile 21 tryptophan metabolites within the indole, kynurenine, and serotonin metabolic pathways in human urine samples using ion-pairing chromatography and multiple reaction monitoring determination. The developed method was successfully applied to urine samples of PD patients (n = 41) and controls (n = 20). Further, we investigated aberrant metabolites to find biomarkers for PD development and therapeutic targets based on the quantitative results. Unfortunately, most tryptophan metabolites in the urine samples did not present significant differences between control and PD patients, except for indole-3-acetic acid. Nonetheless, indole-3-acetic acid was reported for the first time for its aberrant urinary levels in PD patients and tentatively selected as a potential biomarker for PD. This study provides accurate quantitative results for 21 tryptophan metabolites in biological samples and will be helpful in revealing the pathological mechanisms of PD development, discovering biomarkers for PD, and further providing therapeutic targets for various PD symptoms. In the near future, to further investigate the relationship between gut microbial metabolites and PD, we will employ studies on microbial metabolites using plasma and stool samples from control and PD patients.
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Affiliation(s)
- So Hyeon Chung
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea;
| | - Dallah Yoo
- Department of Neurology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (D.Y.); (T.-B.A.)
| | - Tae-Beom Ahn
- Department of Neurology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (D.Y.); (T.-B.A.)
| | - Wonwoong Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju 55338, Republic of Korea
| | - Jongki Hong
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea;
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Koy C, Glocker UM, Danquah BD, Glocker MO. Native and compactly folded in-solution conformers of pepsin are revealed and distinguished by mass spectrometric ITEM-TWO analyses of gas-phase pepstatin A - pepsin complex binding strength differences. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:303-312. [PMID: 37259551 DOI: 10.1177/14690667231178999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pepsin, because of its optimal activity at low acidic pH, has gained importance in mass spectrometric proteome research as a readily available and easy-to-handle protease. Pepsin has also been study object of protein higher-order structure analyses, but questions about how to best investigate pepsin in-solution conformers still remain. We first determined dependencies of pepsin ion charge structures on solvent pH which indicated the in-solution existence of (a) natively folded pepsin (N) which by nanoESI-MS analysis gave rise to a narrow charge state distribution with an 11-fold protonated most intense ion signal, (b) unfolded pepsin (U) with a rather broad ion charge state distribution whose highest ion signal carried 25 protons, and (c) a compactly folded pepsin conformer (C) with a narrow charge structure and a 12-fold protonated ion signal in the center of its charge state envelope. Because pepsin is a protease, unfolded pepsin became its own substrate in solution at pH 6.6 since at this pH some portion of pepsin maintained a compact/native fold which displayed enzymatic activity. Subsequent mass spectrometric ITEM-TWO analyses of pepstatin A - pepsin complex dissociation reactions in the gas phase confirmed a very strong binding of pepstatin A by natively folded pepsin (N). ITEM-TWO further revealed the existence of two compactly folded in-solution pepsin conformers (Ca and Cb) which also were able to bind pepstatin A. Binding strengths of the respective compactly folded pepsin conformer-containing complexes could be determined and apparent gas phase complex dissociation constants and reaction enthalpies differentiated these from each other and from the pepstatin A - pepsin complex which had been formed from natively folded pepsin. Thus, ITEM-TWO turned out to be well suited to pinpoint in-solution pepsin conformers by interrogating quantitative traits of pepstatin A - pepsin complexes in the gas phase.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Ursula M Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
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25
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Kumar BS. Recent Advances and Applications of Ambient Mass Spectrometry Imaging in Cancer Research: An Overview. Mass Spectrom (Tokyo) 2023; 12:A0129. [PMID: 37789912 PMCID: PMC10542858 DOI: 10.5702/massspectrometry.a0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/25/2023] [Indexed: 10/05/2023] Open
Abstract
Cancer metabolic variability has a significant impact on both diagnosis and treatment outcomes. The discovery of novel biological indicators and metabolic dysregulation, can significantly rely on comprehension of the modified metabolism in cancer, is a research focus. Tissue histology is a critical feature in the diagnostic testing of many ailments, such as cancer. To assess the surgical margin of the tumour on patients, frozen section histology is a tedious, laborious, and typically arbitrary method. Concurrent monitoring of ion images in tissues facilitated by the latest advancements in mass spectrometry imaging (MSI) is far more efficient than optical tissue image analysis utilized in conventional histopathology examination. This article focuses on the "desorption electrospray ionization (DESI)-MSI" technique's most recent advancements and uses in cancer research. DESI-MSI can provide wealthy information based on the variances in metabolites and lipids in normal and cancerous tissues by acquiring ion images of the lipid and metabolite variances on biopsy samples. As opposed to a systematic review, this article offers a synopsis of the most widely employed cutting-edge DESI-MSI techniques in cancer research.
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Affiliation(s)
- Bharath S. Kumar
- Correspondence to: Bharath S. Kumar, 21, B2, 27th Street, Nanganallur, Chennai, India, e-mail:
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26
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Lacson MLB, Arbotante CA, Magdayao MJTE, Bundalian RD, Anas ARJ. Ultra-high-performance liquid chromatography-tandem high-resolution elevated mass spectrometry profiling of anti-methicillin-resistant Staphylococcus aureus metabolites from the endophytic bacteria collected from the weeds of a previous dumpsite. J Chromatogr A 2023; 1706:464228. [PMID: 37556933 DOI: 10.1016/j.chroma.2023.464228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/08/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023]
Abstract
The culturable endophytic bacteria from the weeds Cleome rutidosperma of the family Cleomaceae and Digitaria sanguinalis of the family Poaceae obtained from a previous dumpsite in Pampanga, Philippines have been assessed for their anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and the analytes with such activity should be identified. However, due to the limited amounts collected from the isolation process, 1.8 mg yield of compound 1 from the endophyte of C. rutidosperma and 1.2 mg of a mixture from the endophyte of D. sanguinalis were selected for LC-MSE analysis. The production of compounds from the culturable endophytic bacteria Pseudomonas aeruginosa- determined by gene-sequencing, an untargeted and data-independent analysis (DIA) by ultra-high performance liquid chromatography-high resolution-elevated energy mass spectrometry (UHPLC-HR-MSE) technique was employed to profile the metabolites present in the two high-performance liquid chromatography (HPLC) fractions. The analytes present from P. aeruginosa detected by UHPLC-HR-MSE isolated from C. rutidosperma was phenazine-1-carboxylic acid (1), and for D. sanguinalis were chamigrenal (2), dialkyl resorcinol (3), and a pyoverdine elicitor (4). This study proves that UHPLC-HR-MSE could identify the anti-MRSA constituents in P. aeruginosa from commensal weeds C. rutidosperma and D. sanguinalis. The UHPLC-HR-MSE could help strengthen metabolomics antibacterial research and its related applications from a future perspective. Application of metabolomics research using UHPLC-HR-MSE could enhance the rehabilitation of dumpsites by the microbial community present.
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Affiliation(s)
- Mona Lisa B Lacson
- Center for Advanced Research and Innovation, Office of the Vice President for Research and Innovation, Angeles University Foundation, Pampanga 2009 Philippines; College of Allied Medical Professions, Angeles University Foundation, Pampanga 2009 Philippines.
| | - Carolyn A Arbotante
- College of Arts and Sciences, Angeles University Foundation, Pampanga 2009 Philippines
| | - Ma Jamaica Trexy E Magdayao
- Applied Chemistry Laboratory Regional Research Center, University of the Philippines Visayas, Miag-ao, Iloilo 5023 Philippines
| | - Reynaldo Dl Bundalian
- Center for Advanced Research and Innovation, Office of the Vice President for Research and Innovation, Angeles University Foundation, Pampanga 2009 Philippines.
| | - Andrea Roxanne J Anas
- Department of Brain Function, Division of Stress Adaptation and Protection, Research Institute of Environmental Medicine, Nagoya University, Chikusa-Ku, Nagoya 464-8601, Japan; Department of Molecular Pharmacokinetics, Division of Clinical Pharmacology, Graduate School of Medicine Nagoya University, Chikusa-Ku, Nagoya 464-8601, Japan.
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27
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Ju Y, He Y, Kan G, Yu K, Jiang J, Wang X, Zhang H. Reaction acceleration in microdroplet mass spectrometry: Inlet capillary and solvent composition effects. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37 Suppl 1:e9498. [PMID: 36852554 DOI: 10.1002/rcm.9498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
RATIONALE Microdroplet chemistry has attracted tremendous interest in recent years. We have previously reported that microdroplet mass spectrometry (MS) achieves reaction acceleration. Here we systematically investigated the effect of capillary heating of MS inlet and solvent polarity of microdroplets on the conversion ratios of dehydration and phosphorylation reactions. METHODS The micron-sized droplets generated by high-speed gas encapsulated the compounds. The conversion ratios of dehydration and phosphorylation reactions were investigated at different capillary temperatures of MS inlet between 30°C and 300°C. Subsequently, the effects of solvent polarity of different microdroplets (acetonitrile, acetonitrile/water [v/v: 9:1], and water) on microdroplet reactions were investigated. RESULTS The microdroplets could be used as reaction vessels for rapid dehydration and phosphorylation reactions. Microdroplet MS is characterized by the completion of the reaction in microseconds. The increase in capillary temperature increased the conversion ratio of dehydration reactions but had little effect on phosphorylation reactions. The stability of compounds supports this phenomenon. In addition, the increase in solvent polarity in microdroplets promoted the dehydration reaction but inhibited the nucleophilic substitution reaction (phosphorylation reaction). CONCLUSIONS Microdroplet MS achieved an acceleration of the reaction, which was attributed to capillary temperature, microdroplet solvents, and the stability of reaction products. This finding suggested that the inlet capillary and solvent system should be considered in the study and interpretation of microdroplet MS.
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Affiliation(s)
- Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong, 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Yuwei He
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong, 264209, China
| | - Guangfeng Kan
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong, 264209, China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong, 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong, 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong, 264209, China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong, 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
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28
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Jin Y, Chi J, LoMonaco K, Boon A, Gu H. Recent Review on Selected Xenobiotics and Their Impacts on Gut Microbiome and Metabolome. Trends Analyt Chem 2023; 166:117155. [PMID: 37484879 PMCID: PMC10361410 DOI: 10.1016/j.trac.2023.117155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
As it is well known, the gut is one of the primary sites in any host for xenobiotics, and the many microbial metabolites responsible for the interactions between the gut microbiome and the host. However, there is a growing concern about the negative impacts on human health induced by toxic xenobiotics. Metabolomics, broadly including lipidomics, is an emerging approach to studying thousands of metabolites in parallel. In this review, we summarized recent advancements in mass spectrometry (MS) technologies in metabolomics. In addition, we reviewed recent applications of MS-based metabolomics for the investigation of toxic effects of xenobiotics on microbial and host metabolism. It was demonstrated that metabolomics, gut microbiome profiling, and their combination have a high potential to identify metabolic and microbial markers of xenobiotic exposure and determine its mechanism. Further, there is increasing evidence supporting that reprogramming the gut microbiome could be a promising approach to the intervention of xenobiotic toxicity.
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Affiliation(s)
- Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jinhua Chi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Kaelene LoMonaco
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
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29
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Kumar BS. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) in disease diagnosis: an overview. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:3768-3784. [PMID: 37503728 DOI: 10.1039/d3ay00867c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tissue analysis, which is essential to histology and is considered the benchmark for the diagnosis and prognosis of many illnesses, including cancer, is significant. During surgery, the surgical margin of the tumor is assessed using the labor-intensive, challenging, and commonly subjective technique known as frozen section histopathology. In the biopsy section, large numbers of molecules can now be visualized at once (ion images) following recent developments in [MSI] mass spectrometry imaging under atmospheric conditions. This is vastly superior to and different from the single optical tissue image processing used in traditional histopathology. This review article will focus on the advancement of desorption electrospray ionization mass spectrometry imaging [DESI-MSI] technique, which is label-free and requires little to no sample preparation. Since the proportion of molecular species in normal and abnormal tissues is different, DESI-MSI can capture ion images of the distributions of lipids and metabolites on biopsy sections, which can provide rich diagnostic information. This is not a systematic review but a summary of well-known, cutting-edge and recent DESI-MSI applications in cancer research between 2018 and 2023.
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Affiliation(s)
- Bharath Sampath Kumar
- Independent Researcher, 21, B2, 27th Street, Nanganallur, Chennai 61, TamilNadu, India.
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30
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Geri A, Massai L, Messori L. Protein Metalation by Medicinal Gold Compounds: Identification of the Main Features of the Metalation Process through ESI MS Experiments. Molecules 2023; 28:5196. [PMID: 37446857 DOI: 10.3390/molecules28135196] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Gold compounds form a new class of promising anticancer agents with innovative modes of action. It is generally believed that anticancer gold compounds, at variance with clinically established platinum drugs, preferentially target proteins rather than nucleic acids. The reactions of several gold compounds with a few model proteins have been systematically explored in recent years through ESI MS measurements to reveal adduct formation and identify the main features of those reactions. Here, we focus our attention on a group of five gold compounds of remarkable medicinal interest, i.e., Auranofin, Au(NHC)Cl, [Au(NHC)2]PF6, Aubipyc, and Auoxo6, and on their reactions with four different biomolecular targets, i.e., the proteins HEWL, hCA I, HSA and the C-terminal dodecapeptide of the enzyme thioredoxin reductase. Complete ESI MS data are available for those reactions due to previous experimental work conducted in our laboratory. From the comparative analysis of the ESI MS reaction profiles, some characteristic trends in the metallodrug-protein reactivity may be identified as detailed below. The main features are described and analyzed in this review. Overall, all these observations are broadly consistent with the concept that cytotoxic gold drugs preferentially target cancer cell proteins, with a remarkable selectivity for the cysteine and selenocysteine proteome. These interactions typically result in severe damage to cancer cell metabolism and profound alterations in the redox state, leading to eventual cancer cell death.
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Affiliation(s)
- Andrea Geri
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Florence, Italy
| | - Lara Massai
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Florence, Italy
| | - Luigi Messori
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Florence, Italy
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31
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Fernandes AS, Obeid G, Laureno TJN, Correra TC. Protonated and Sodiated Cyclophosphamide Fragmentation Pathways Evaluation by Infrared Multiple Photon Dissociation Spectroscopy. J Phys Chem A 2023. [PMID: 37285455 DOI: 10.1021/acs.jpca.3c01323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cyclophosphamide (CP or CTX) is a widely used antineoplastic agent, and the evaluation of its efficacy and its impacts on the environment are dependent on tandem mass spectrometry (MSn) techniques. Because there is no dedicated experimental study to characterize the actual molecular nature of the CP fragments upon collision-induced dissociation, this work evaluated the chemical structure of the fragments of protonated and sodiated CP and CP protonation sites by infrared multiple photon dissociation spectroscopy supported by density functional theory calculations. This study allowed us to propose a new fragment structure and confirm the nature of multiple fragments, including those relevant for transitions used for CP quantitative and qualitative analyses. Our results also show that there is no spectroscopic evidence that can rule out the existence of aziridinium fragments, making it clear that further studies on the nature of iminium/aziridinium fragments in the gas phase are necessary.
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Affiliation(s)
- André S Fernandes
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
| | - Guilherme Obeid
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
| | - Tiago J N Laureno
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
| | - Thiago C Correra
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
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32
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Hatvany JB, Gallagher ES. Hydrogen/deuterium exchange for the analysis of carbohydrates. Carbohydr Res 2023; 530:108859. [PMID: 37290371 DOI: 10.1016/j.carres.2023.108859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Carbohydrates and glycans are integral to many biological processes, including cell-cell recognition and energy storage. However, carbohydrates are often difficult to analyze due to the high degree of isomerism present. One method being developed to distinguish these isomeric species is hydrogen/deuterium exchange-mass spectrometry (HDX-MS). In HDX-MS, carbohydrates are exposed to a deuterated reagent and the functional groups with labile hydrogen atoms, including hydroxyls and amides, exchange with the 1 amu heavier isotope, deuterium. These labels can then be detected by MS, which monitors the mass increase with the addition of D-labels. The observed rate of exchange is dependent on the exchanging functional group, the accessibility of the exchanging functional group, and the presence of hydrogen bonds. Herein, we discuss how HDX has been applied in the solution-phase, gas-phase, and during MS ionization to label carbohydrates and glycans. Additionally, we compare differences in the conformations that are labeled, the labeling timeframes, and applications of each of these methods. Finally, we comment on future opportunities for development and use of HDX-MS to analyze glycans and glycoconjugates.
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Affiliation(s)
- Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA.
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Hilal I, Khourcha S, Safi A, Hmyene A, Asnawi S, Othman I, Stöcklin R, Oukkache N. Comparative Proteomic Analysis of the Venoms from the Most Dangerous Scorpions in Morocco: Androctonus mauritanicus and Buthus occitanus. Life (Basel) 2023; 13:life13051133. [PMID: 37240778 DOI: 10.3390/life13051133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Morocco is known to harbor two of the world's most dangerous scorpion species: the black Androctonus mauritanicus (Am) and the yellow Buthus occitanus (Bo), responsible for 83% and 14% of severe envenomation cases, respectively. Scorpion venom is a mixture of biological molecules of variable structures and activities, most of which are proteins of low molecular weights referred to as toxins. In addition to toxins, scorpion venoms also contain biogenic amines, polyamines, and enzymes. With the aim of investigating the composition of the Am and Bo venoms, we conducted an analysis of the venoms by mass spectrometry (ESI-MS) after separation by reversed-phase HPLC chromatography. Results from a total of 19 fractions obtained for the Am venom versus 22 fractions for the Bo venom allowed the identification of approximately 410 and 252 molecular masses, respectively. In both venoms, the most abundant toxins were found to range between 2-5 kDa and 6-8 kDa. This proteomic analysis not only allowed the drawing of an extensive mass fingerprint of the Androctonus mauritanicus and Buthus occitanus venoms but also provided a better insight into the nature of their toxins.
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Affiliation(s)
- Ines Hilal
- Laboratory of Venoms and Toxins, Pasteur Institute of Morocco, Casablanca 20360, Morocco
- Laboratory of Biochemistry, Environment and Food Technology, Faculty of Sciences and Techniques of Mohammedia, Mohammedia 20650, Morocco
| | - Soukaina Khourcha
- Laboratory of Venoms and Toxins, Pasteur Institute of Morocco, Casablanca 20360, Morocco
- Laboratory of Biochemistry, Environment and Food Technology, Faculty of Sciences and Techniques of Mohammedia, Mohammedia 20650, Morocco
| | - Amal Safi
- Laboratory of Biochemistry, Environment and Food Technology, Faculty of Sciences and Techniques of Mohammedia, Mohammedia 20650, Morocco
| | - Abdelaziz Hmyene
- Laboratory of Biochemistry, Environment and Food Technology, Faculty of Sciences and Techniques of Mohammedia, Mohammedia 20650, Morocco
| | - Syafiq Asnawi
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Reto Stöcklin
- Atheris Laboratories, Case Postale 314, CH-1233 Bernex, Geneva, Switzerland
| | - Naoual Oukkache
- Laboratory of Venoms and Toxins, Pasteur Institute of Morocco, Casablanca 20360, Morocco
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Ventouri IK, Chang W, Meier F, Drexel R, Somsen GW, Schoenmakers PJ, de Spiegeleer B, Haselberg R, Astefanei A. Characterizing Non-covalent Protein Complexes Using Asymmetrical Flow Field-Flow Fractionation On-Line Coupled to Native Mass Spectrometry. Anal Chem 2023; 95:7487-7494. [PMID: 37146101 DOI: 10.1021/acs.analchem.2c05049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We report an online analytical platform based on the coupling of asymmetrical flow field-flow fractionation (AF4) and native mass spectrometry (nMS) in parallel with UV-absorbance, multi-angle light scattering (MALS), and differential-refractive-index (UV-MALS-dRI) detectors to elucidate labile higher-order structures (HOS) of protein biotherapeutics. The technical aspects of coupling AF4 with nMS and the UV-MALS-dRI multi-detection system are discussed. The "slot-outlet" technique was used to reduce sample dilution and split the AF4 effluent between the MS and UV-MALS-dRI detectors. The stability, HOS, and dissociation pathways of the tetrameric biotherapeutic enzyme (anticancer agent) l-asparaginase (ASNase) were studied. ASNase is a 140 kDa homo-tetramer, but the presence of intact octamers and degradation products with lower molecular weights was indicated by AF4-MALS/nMS. Exposing ASNase to 10 mM NaOH disturbed the equilibrium between the different non-covalent species and led to HOS dissociation. Correlation of the information obtained by AF4-MALS (liquid phase) and AF4-nMS (gas phase) revealed the formation of monomeric, tetrameric, and pentameric species. High-resolution MS revealed deamidation of the main intact tetramer upon exposure of ASNase to high pH (NaOH and ammonium bicarbonate). The particular information retrieved from ASNase with the developed platform in a single run demonstrates that the newly developed platform can be highly useful for aggregation and stability studies of protein biopharmaceuticals.
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Affiliation(s)
- Iro Konstantina Ventouri
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Wayne Chang
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Florian Meier
- Postnova Analytics GmbH, Rankinestraße 1, 86899 Landsberg, Germany
| | - Roland Drexel
- Postnova Analytics GmbH, Rankinestraße 1, 86899 Landsberg, Germany
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Peter J Schoenmakers
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Bart de Spiegeleer
- Drug Quality and Registration (DruQuaR) Group, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Rob Haselberg
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Alina Astefanei
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
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35
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Keating AR, Wesdemiotis C. Rapid and simple determination of average molecular weight and composition of synthetic polymers via electrospray ionization-mass spectrometry and a Bayesian universal charge deconvolution. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9478. [PMID: 36669764 DOI: 10.1002/rcm.9478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
RATIONALE Simple, affordable, and rapid methods for identifying the molecular weight (MW) distribution and macromolecular composition of polymeric materials are limited. Current tools require extensive solvent consumption, linear calibrations, and expensive consumables. A simple method for the determination of average MW (Mn , Mw ) and chain end groups is demonstrated for synthetic homopolymer standards using direct injection electrospray ionization-mass spectrometry (ESI-MS) and an open-sourced charge deconvolution (CDC) algorithm. METHODS Five homopolymer standards in the 1-7 kDa MW range were analyzed using direct-injection ESI-MS on a quadrupole/time-of-flight mass spectrometer. The samples investigated, viz. two poly(ethylene oxide) (PEO) and two poly(styrene sulfonic acid) (PSS) standards with narrow polydispersity and one poly(d,l-alanine) (pAla) standard with undefined polydispersity, were chosen to illustrate challenges with ESI-MS quantitation. Using the UniDec program, weight average MWs (Mw ) obtained from the charge-deconvoluted spectra were compared to the reported Mw data of the standards from size exclusion chromatography (SEC) measurements. RESULTS The MW data derived for the PSS, PEO, and pAla standards agreed well with the corresponding reported Mw or MW range values. The method was able to provide MW, degree of polymerization (DP), and polydispersity index (PDI) information for polymers with narrow (PSS, PEO) as well as broader (pAla) molecular weight distribution; this feature provides an advantage over MW analysis via matrix-assisted laser desorption/ionization (MALDI) for ESI-compatible materials. PSS standards differing in average MW by only a few repeat units could be confidently distinguished. Additionally, the oligomeric resolution observed for all samples studied unveiled chain-end information not available through chromatographic analysis. CONCLUSIONS Overall, the free and easy-to-use UniDec CDC algorithm provides a simple, alternative method to measuring MW and DP for polymeric materials without high solvent consumption, expensive ionization sources, or calibration curves. Information about the masses of individual oligomers and the possibility to further characterize these oligomers using tandem mass spectrometry and/or ion mobility techniques constitutes additional benefits of this approach vis-à-vis traditional MW and PDI elucidation through SEC.
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Affiliation(s)
- Addie R Keating
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Chrys Wesdemiotis
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio, USA
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36
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Fabijanczuk KC, Hager JW, McLuckey SA. Separation and Simultaneous Trapping of Multiply Charged and Singly Charged Ions for Mass Spectrometry: Application to Lipid Mixtures. Anal Chem 2023; 95:6115-6121. [PMID: 37000630 PMCID: PMC10129443 DOI: 10.1021/acs.analchem.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Conventional electrospray ionization (ESI) of mixtures can give rise to singly and multiply charged analyte species that overlap in mass-to-charge (m/z) ratios, which can complicate the analysis of individual components. The overlap in m/z for ions of different mass and charge is particularly problematic when ions of low relative abundance are of interest. For example, cardiolipins (CLs) are structurally complex phospholipids present in low relative abundance in the lipidome but play crucial roles in mitochondrial metabolism and various regulatory processes. ESI of CLs in negative ion mode shows abundant doubly deprotonated ions and minor singly deprotonated ions. In the ESI of lipid extracts, highly abundant singly charged phospholipids extensively overlap in m/z space with CL dianions of much lesser abundance, thereby complicating the study of the CLs. To address this challenge, we employed a gas-phase approach to separate singly charged ions from a population of ions of mixed charge states while allowing for the storage of one or both of the separated ion populations. Herein, we describe the considerations for applying enhanced singly charged (ESC) and enhanced multiply charged (EMC) scans to perform a gas-phase separation of singly charged lipids from doubly charged lipids in an Escherichia coli extract. This method allows for improved signal-to-noise (S/N) ratio of low abundance ions with minimal overall signal loss, removal of "chemical noise" arising from singly charged ions, and allows for retention of spatially separated ions within a mass spectrometer.
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Affiliation(s)
| | - James W. Hager
- Sciex, 71 Four Valley Road, Concord, ON, L4K 4V8, Canada
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
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Xu AM, Tang LC, Jovanovic M, Regev O. A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535171. [PMID: 37066236 PMCID: PMC10103939 DOI: 10.1101/2023.03.31.535171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Electrospray ionization is a powerful and prevalent technique used to ionize analytes in mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important consideration for interpreting mass spectra. However, due to an incomplete understanding of the ionization mechanism, the analyte properties that influence CSDs are not fully understood. Here, we employ a machine learning-based high-throughput approach and analyze CSDs of hundreds of thousands of peptides. Interestingly, half of the peptides exhibit charges that differ from what one would naively expect (number of basic sites). We find that these peptides can be classified into two regimes-undercharging and overcharging-and that these two regimes display markedly different charging characteristics. Strikingly, peptides in the overcharging regime show minimal dependence on basic site count, and more generally, the two regimes exhibit distinct sequence determinants. These findings highlight the rich ionization behavior of peptides and the potential of CSDs for enhancing peptide identification.
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Affiliation(s)
- Allyn M. Xu
- Department of Mathematics, Courant Institute of Mathematical Sciences, New York University, NY, USA
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Oded Regev
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, NY, USA
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38
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Jurina T, Sokač Cvetnić T, Šalić A, Benković M, Valinger D, Gajdoš Kljusurić J, Zelić B, Jurinjak Tušek A. Application of Spectroscopy Techniques for Monitoring (Bio)Catalytic Processes in Continuously Operated Microreactor Systems. Catalysts 2023. [DOI: 10.3390/catal13040690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
In the last twenty years, the application of microreactors in chemical and biochemical industrial processes has increased significantly. The use of microreactor systems ensures efficient process intensification due to the excellent heat and mass transfer within the microchannels. Monitoring the concentrations in the microchannels is critical for a better understanding of the physical and chemical processes occurring in micromixers and microreactors. Therefore, there is a growing interest in performing in-line and on-line analyses of chemical and/or biochemical processes. This creates tremendous opportunities for the incorporation of spectroscopic detection techniques into production and processing lines in various industries. In this work, an overview of current applications of ultraviolet–visible, infrared, Raman spectroscopy, NMR, MALDI-TOF-MS, and ESI-MS for monitoring (bio)catalytic processes in continuously operated microreactor systems is presented. The manuscript includes a description of the advantages and disadvantages of the analytical methods listed, with particular emphasis on the chemometric methods used for spectroscopic data analysis.
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Affiliation(s)
- Tamara Jurina
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Tea Sokač Cvetnić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Anita Šalić
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10 000 Zagreb, Croatia
| | - Maja Benković
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Davor Valinger
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Jasenka Gajdoš Kljusurić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
| | - Bruno Zelić
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10 000 Zagreb, Croatia
- Department for Packaging, Recycling and Environmental Protection, University North, Trg dr. Žarka Dolinara 1, 48 000 Koprivnica, Croatia
| | - Ana Jurinjak Tušek
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva ul. 6, 10 000 Zagreb, Croatia
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39
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Gawor A, Bulska E. A Standardized Protocol for Assuring the Validity of Proteomics Results from Liquid Chromatography-High-Resolution Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24076129. [PMID: 37047102 PMCID: PMC10093877 DOI: 10.3390/ijms24076129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Significant advances in the technological development of mass spectrometry in the field of proteomics and the generation of extremely large amounts of data require a very critical approach to assure the validity of results. Commonly used procedures involved liquid chromatography followed by high-resolution mass spectrometry measurements. Proteomics analysis is used in many fields including the investigation of the metabolism of biologically active substances in organisms. Thus, there is a need to care about the validity of the obtained results. In this work, we proposed a standardized protocol for proteomic analysis using liquid chromatography-high-resolution mass spectrometry, which covers all of these analytical steps to ensure the validity of the results. For this purpose, we explored the requirements of the ISO/IEC 17025:2017 standard as a reference document for quality control in biochemistry research-based mass spectrometry.
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Affiliation(s)
- Andrzej Gawor
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Ewa Bulska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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40
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Cronin SP, Dulovic S, Lawrence JA, Filsinger KA, Hernandez-Gonzalez AP, Evans R, Stiles JW, Morris J, Pelczer I, Bocarsly AB. Direct Synthesis of 1-Butanol with High Faradaic Efficiency from CO 2 Utilizing Cascade Catalysis at a Ni-Enhanced (Cr 2O 3) 3Ga 2O 3 Electrocatalyst. J Am Chem Soc 2023; 145:6762-6772. [PMID: 36922736 DOI: 10.1021/jacs.2c12251] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Electrochemical transformation of CO2 into energy-dense liquid fuels provides a viable solution to challenges regarding climate change and nonrenewable resource dependence. Here, we report on the modification of a Cr-Ga oxide electrocatalyst through the introduction of nickel to generate a catalyst that generates 1-butanol at unprecedented faradaic efficiencies (ξ = 42%). This faradaic efficiency occurs at -1.48 V vs Ag/AgCl, with 1-butanol production commencing at an overpotential of 320 mV. At this potential, minor products include formate, methanol, acetic acid, acetone, and 3-hydroxybutanal. At -1.0 and -1.4 V, 3-hydroxybutanal becomes the primary product. This is in contrast to the nickel-free (Cr2O3)3(Ga2O3) system, where neither 3-hydroxybutanal nor 1-butanol was detected. Mechanistic studies show that formate is the initial CO2 reduction product and identify acetaldehyde as the key intermediate. Nickel is found responsible for the coupling and reduction of acetaldehyde to generate the higher molecular weight carbon products observed. To the best of our knowledge, this is the first electrocatalyst to generate 1-butanol with high faradaic efficiency.
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Affiliation(s)
- Steve P Cronin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Stephanie Dulovic
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Josef A Lawrence
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kai A Filsinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | | | - Rebecca Evans
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Joseph W Stiles
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jalah Morris
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - István Pelczer
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Andrew B Bocarsly
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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41
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Advances in Mass Spectrometry-Based Single Cell Analysis. BIOLOGY 2023; 12:biology12030395. [PMID: 36979087 PMCID: PMC10045136 DOI: 10.3390/biology12030395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.
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42
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Tigineh GT, Abiye M, Melese A, Abebe A. Synthesis, structural investigations, and in vitro biological activity of Co(II) and Fe(III) mixed ligand complexes of 1,10-phenanthroline and 2,2'-bipyridine. Chem Biol Drug Des 2023; 101:479-488. [PMID: 34605176 DOI: 10.1111/cbdd.13967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/30/2021] [Accepted: 09/26/2021] [Indexed: 12/01/2022]
Abstract
Herein, we report, four new mixed ligand complexes of Cobalt(II) and Iron(III), viz., [Co(L1 )(L2 )(H2 O)2 ]Cl2 (1), [Co(L1 )(L2 )(L3 )(H2 O)]Cl2 (2), [Fe(L1 )(L2 )(H2 O)2 ]Cl3 (3), and [Fe(L1 )(L2 )(L3 )(H2 O)]Cl3 (4), where L1 = 1,10-phenanthroline (C12 H8 N2 ), L2 = 2,2'-bipyridine (C10 H8 N2 ), and L3 = acetamide (C2 H5 NO)). They were synthesized and characterized using spectroscopic analysis (ESI-MS, ICP-OES, FT-IR, and UV-Vis), elemental analysis, melting point determination, and conductance measurement. The in vitro antibacterial activity was tested on two Gram-positive Staphylococcus aureus (S. aureus) and Streptococcus pyogenes (S. pyogenes) and two Gram-negative Escherichia coli (E. Coli)and Klebsiella pneumoniae (K. pneumoniae) bacteria using the disc diffusion method. Based on the analytical and spectroscopic data, octahedral geometries are assigned to the complexes. Co(II) complexes were found more active against K. pneumoniae than the corresponding Fe(III) complexes which indicated that antibacterial activities of metal complexes have tuned with the nature of the metal. The results provide an insight to design and readily prepare task-specific metal-based drugs for interaction with particular bacterial strains.
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Affiliation(s)
| | - Melese Abiye
- Department of Chemistry, College of Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Aklilu Melese
- Department of Chemistry, College of Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Atakilt Abebe
- Department of Chemistry, College of Sciences, Bahir Dar University, Bahir Dar, Ethiopia
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43
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Sadek M, Moore BN, Yu C, Ruppe N, Abdun-Nabi A, Hao Z, Alvarez M, Dahotre S, Deperalta G. A Robust Purity Method for Biotherapeutics Using New Peak Detection in an LC-MS-Based Multi-Attribute Method. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:484-492. [PMID: 36802331 DOI: 10.1021/jasms.2c00355] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
New peak detection (NPD), as part of the LC-MS-based multi-attribute method (MAM), allows for sensitive and unbiased detection of new or changing site-specific attributes between a sample and reference that is not possible with conventional UV or fluorescence detection-based methods. MAM with NPD can serve as a purity test that can establish whether a sample and the reference are similar. The broad implementation of NPD in the biopharmaceutical industry has been limited by the potential presence of false positives or artifacts, which increase the analysis time and can trigger unnecessary investigations of product quality. Our novel contributions to the success of NPD are the curation of false positives, use of the known peak list concept, pairwise analysis approach, and the development of a NPD system suitability control strategy. In this report, we also introduce a unique experimental design utilizing sequence variant co-mixes to measure NPD performance. We show that NPD has superior performance relative to conventional control system methods in the detection of an unexpected change as compared with the reference. NPD is a new frontier in purity testing that reduces subjectivity, need for analyst intervention, and potential for missing unexpected product quality changes.
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Affiliation(s)
- Monica Sadek
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Benjamin Nathan Moore
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher Yu
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Ruppe
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Austin Abdun-Nabi
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Zhiqi Hao
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Melissa Alvarez
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Sanket Dahotre
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Galahad Deperalta
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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44
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Wichitnithad W, Nantaphol S, Noppakhunsomboon K, Thitikornpong W, Rojsitthisak P. Current status and prospects of development of analytical methods for determining nitrosamine and N-nitroso impurities in pharmaceuticals. Talanta 2023; 254:124102. [PMID: 36470020 DOI: 10.1016/j.talanta.2022.124102] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Nitrosamine impurities in pharmaceuticals have recently been concerned for several national regulatory agencies to avoid carcinogenic and mutagenic effects in patients. The demand for highly sensitive and specific analytical methods with LOQs in the ppb and sub-ppb ranges is among the most significant challenges facing analytical scientists. In addition, artifactual nitrosamine formation during sample preparation and injection leading to overestimation of nitrosamines has received considerable attention. Numerous analytical methodologies have been reported for quantifying nitrosamine impurities in active pharmaceutical ingredients and medicinal products at the interim limit criteria as preventive measures. In this review, we meticulously discuss those reported gas and liquid chromatographic methods for nitrosamine determination in pharmaceuticals in aspects of chromatographic conditions and sensitivity of detection. We also introduce the potential of novel fluorescence-based methods recently developed to rapidly screen nitrosamine impurities. In addition, the review assesses the nitrosation assay procedure (NAP test), which is expected to be a future preventive measure for screening potential nitrosation and identifying suspected contamination with N-nitroso or other potential mutagenic impurities during the drug development process.
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Affiliation(s)
- Wisut Wichitnithad
- Department of Analytical Development, Pharma Nueva Co., Ltd., Bangkok, 10900, Thailand; Department of Clinical Development, Pharma Nueva Co., Ltd., Bangkok, 10900, Thailand
| | - Siriwan Nantaphol
- Department of Clinical Development, Pharma Nueva Co., Ltd., Bangkok, 10900, Thailand
| | | | - Worathat Thitikornpong
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand; Center of Excellence in Natural Products for Ageing and Chronic Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Rojsitthisak
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand; Center of Excellence in Natural Products for Ageing and Chronic Diseases, Chulalongkorn University, Bangkok 10330, Thailand.
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45
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Gomes PWP, de Tralia Medeiros TC, Maimone NM, Leão TF, de Moraes LAB, Bauermeister A. Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:225-248. [PMID: 37843811 DOI: 10.1007/978-3-031-41741-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Since the discovery of penicillin, microbial metabolites have been extensively investigated for drug discovery purposes. In the last decades, microbial derived compounds have gained increasing attention in different fields from pharmacognosy to industry and agriculture. Microbial metabolites in microbiomes present specific functions and can be associated with the maintenance of the natural ecosystems. These metabolites may exhibit a broad range of biological activities of great interest to human purposes. Samples from either microbial isolated cultures or microbiomes consist of complex mixtures of metabolites and their analysis are not a simple process. Mass spectrometry-based metabolomics encompass a set of analytical methods that have brought several improvements to the microbial natural products field. This analytical tool allows the comprehensively detection of metabolites, and therefore, the access of the chemical profile from those biological samples. These analyses generate thousands of mass spectra which is challenging to analyse. In this context, bioinformatic metabolomics tools have been successfully employed to accelerate and facilitate the investigation of specialized microbial metabolites. Herein, we describe metabolomics tools used to provide chemical information for the metabolites, and furthermore, we discuss how they can improve investigation of microbial cultures and interactions.
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Affiliation(s)
- Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Talita Carla de Tralia Medeiros
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Naydja Moralles Maimone
- Departamento de Ciências Exatas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Tiago F Leão
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Luiz Alberto Beraldo de Moraes
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.
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46
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Rimayi C, Park JH. Adjustment of Matrix Effects in Analysis of 36 Secondary Metabolites of Microbial and Plant Origin in Indoor Floor Dust Using Liquid Chromatography-Tandem Mass Spectrometry. BUILDINGS (BASEL, SWITZERLAND) 2023; 13:10.3390/buildings13051112. [PMID: 38650616 PMCID: PMC11034732 DOI: 10.3390/buildings13051112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Exposure to microbial agents in water-damaged buildings is a major public health concern. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become a primary tool for testing environmental samples for microbial secondary metabolites (SMs); however, matrix effects can lead to inaccurate results in exposure assessment. Applying a universal internal standard (ISTD) and a matrix-matched calibration can adjust for matrix effects, as shown by our previous study. However, there are only few isotope-labeled internal standards for SMs available on the market. In this study, we determined the best-performing ISTDs among ten candidates (nine 13C-labeled isotopes and one unlabeled analogue) for each of 36 SMs. We analyzed school floor dust spiked with the 36 SMs to identify the best-performing ISTDs (initial experiment) and examined reproducibility with the selected ISTDs and the same spiked dust (validation 1). We also tested applicability for the selected ISTDs using spiked dust collected from different schools (validation 2). The three experiments showed that 26, 17, and 19 SMs had recoveries within the range 100 ± 40%. 13C-ochratoxin A and 13C-citrinin were most frequently selected as the best ISTDs for the 36 SMs, followed by deepoxy-deoxynivalenol, 13C-sterigmatocystin, and 13C-deoxynivalenol. Our study shows that using the identified, best-performing analogous ISTDs for those metabolites may improve testing accuracy for indoor dust and help better estimate exposure effects on potential health.
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Affiliation(s)
- Cornelius Rimayi
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV 26505, USA
| | - Ju-Hyeong Park
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV 26505, USA
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47
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From protein biomarkers to proteomics in dementia with Lewy Bodies. Ageing Res Rev 2023; 83:101771. [PMID: 36328346 DOI: 10.1016/j.arr.2022.101771] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/15/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative dementia. Despite considerable research progress, there remain gaps in our understanding of the pathophysiology and there is no disease-modifying treatment. Proteomics is a powerful tool to elucidate complex biological pathways across heterogenous conditions. This review summarizes the widely used proteomic methods and presents evidence for protein dysregulation in the brain and peripheral tissues in DLB. Proteomics of post-mortem brain tissue shows that DLB shares common features with other dementias, such as synaptic dysfunction, but retains a unique protein signature. Promising diagnostic biomarkers are being identified in cerebrospinal fluid (CSF), blood, and peripheral tissues, such as serum Heart-type fatty acid binding protein. Research is needed to track these changes from the prodromal stage to established dementia, with standardized workflows to ensure replicability. Identifying novel protein targets in causative biological pathways could lead to the development of new targeted therapeutics or the stratification of participants for clinical trials.
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Koopman J, Grimme S. Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2226-2242. [PMID: 36343304 DOI: 10.1021/jasms.2c00209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed. It enables fully automatic calculations of electron ionization (EI) and positive ion collision-induced dissociation (CID) mass spectra of singly charged molecular ions. In this work, the extension to negative and multiple ion charge for the CID run mode is presented. QCxMS is now capable of calculating structures carrying any charge, without the need for pretabulated fragmentation pathways or machine learning of database spectra. Mass spectra of four single negatively charged and two multiple positively charged organic ions with molecular sizes from 12 to 92 atoms were computed and compared to reference spectra. The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the semiempirical quantum mechanical GFN2-xTB method, while for some small molecules, ab initio DFT-based MD simulations were performed. Detailed insights into the fragmentation pathways were gained, and the effects of the computed charge assignments on the resulting spectrum are discussed. Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial. Doubly charged fragments could successfully be calculated fully automatically for the first time, while higher charged structures introduced severe assignment problems. Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation.
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Affiliation(s)
- Jeroen Koopman
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115Bonn, Germany
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Philliber M, Baxter ET, Johnson GE. Synthesis and Stability of Mixed-Diphosphine Ligated Gold Clusters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2138-2146. [PMID: 36166416 DOI: 10.1021/jasms.2c00217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Sub-nanometer gold clusters are promising size- and composition-tunable materials that may be used for advanced technological applications such as catalysis, energy generation, and microelectronics. Synthesis and characterization of phosphine ligated gold clusters containing different ligands provide insight into how steric and electronic effects resulting from changes in chemical functionality influence cluster size, stability, and formation in solution. Herein, we demonstrate that synthesizing gold clusters using two different diphosphines in solution at the same time results in a broad distribution of novel mixed-ligand clusters. In comparison, adding a second diphosphine to a solution of gold clusters presynthesized with another diphosphine does not result in extensive formation of mixed-ligand species. Utilizing high-mass resolution electrospray ionization mass spectrometry, we determined novel cluster compositions and observed size-dependent trends in gold clusters that undergo ligand exchange forming mixed diphosphine species. Adjacent peaks in the mass spectra, separated by characteristic mass-to-charge ratios, provide evidence for multiple 1,3-bis(diphenylphosphino)propane (L3) and 1,5-bis(diphenylphosphino)pentane (L5) ligands on cationic clusters containing 8, 10, 11, and 22 gold atoms. Energy-resolved collision-induced dissociation experiments provide qualitative insight into how different diphosphine ligands affect the relative stability of specific size gold clusters. Our results indicate that mixed-ligand clusters containing both L3 and L5 are generally more stable than their single ligand counterparts containing either L3 or L5. These molecular-level insights will facilitate the rational and scalable synthesis of gold clusters for targeted applications.
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Affiliation(s)
- Mallory Philliber
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemistry, University of Utah, 315 S 1400 E, Room 2020, Salt Lake City, Utah 84112, United States
| | - Eric T Baxter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Grant E Johnson
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Okoye CO, Nyaruaba R, Ita RE, Okon SU, Addey CI, Ebido CC, Opabunmi AO, Okeke ES, Chukwudozie KI. Antibiotic resistance in the aquatic environment: Analytical techniques and interactive impact of emerging contaminants. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 96:103995. [PMID: 36210048 DOI: 10.1016/j.etap.2022.103995] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/19/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic pollution is becoming an increasingly severe threat globally. Antibiotics have emerged as a new class of environmental pollutants due to their expanding usage and indiscriminate application in animal husbandry as growth boosters. Contamination of aquatic ecosystems by antibiotics can have a variety of negative impacts on the microbial flora of these water bodies, as well as lead to the development and spread of antibiotic-resistant genes. Various strategies for removing antibiotics from aqueous systems and environments have been developed. Many of these approaches, however, are constrained by their high operating costs and the generation of secondary pollutants. This review aims to summarize research on the distribution and effects of antibiotics in aquatic environments, their interaction with other emerging contaminants, and their remediation strategy. The ecological risks associated with antibiotics in aquatic ecosystems and the need for more effective monitoring and detection system are also highlighted.
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Affiliation(s)
- Charles Obinwanne Okoye
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya
| | - Raphael Nyaruaba
- Center for Biosafety Megascience, Wuhan Institute of Virology, CAS, Wuhan, PR China; Organization of African Academic Doctor, Nairobi, Kenya
| | - Richard Ekeng Ita
- Department of Biological Sciences Ritman University, Ikot Ekpene, Akwa Ibom State, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya
| | - Samuel Ukpong Okon
- Department of Marine Science, Akwa Ibom State University, Mkpat Enin, P.M.B. 1167, Nigeria; Department of Ocean Engineering, Ocean College, Zhejiang University, Zhoushan 316021, PR China; Organization of African Academic Doctor, Nairobi, Kenya
| | - Charles Izuma Addey
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China; Organization of African Academic Doctor, Nairobi, Kenya
| | - Chike C Ebido
- Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya
| | | | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, 212013, PR China; Organization of African Academic Doctor, Nairobi, Kenya.
| | - Kingsley Ikechukwu Chukwudozie
- Department of Microbiology, University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya; Department of Clinical Medicine, School of Medicine, Jiangsu University 212013, PR China.
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