1
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Ning C, Gao Y, Sun S, Yang H, Tang W, Wang D. Size-Resolved Molecular Characterization of Water-Soluble Organic Matter in Atmospheric Particulate Matter from Northern China. ENVIRONMENTAL RESEARCH 2024; 258:119436. [PMID: 38897433 DOI: 10.1016/j.envres.2024.119436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
Atmospheric particulate matter (PM) affects visibility, climate, biogeochemical cycles and human health. Water-soluble organic matter (WSOM) is an important component of PM. In this study, PM samples with size-resolved measurements at aerodynamic cut-point diameters (Dp) of 0.01-18μm were collected in the rural area of Baoding and the urban area of Dalian, Northern China. Non-targeted analysis was adopted for the characterization of the molecule constitutes of WSOM in different sized particles using Fourier transform-ion cyclotron resonance mass spectrometry. Regardless of the location, the composition of WSOM in Aitken mode particles (aerodynamic diameter < 0.05 μm) was similar. The WSOM in accumulation mode particles (0.05-2 μm) in Baoding was predominantly composed of CHO compounds (84.9%), which were mainly recognized as lignins and lipids species. However, S-containing compounds (64.2%), especially protein and carbohydrates species, accounted for most of the WSOM in the accumulation mode particles in Dalian. The CHO compounds (67.6%-79.7%) contributed the most to the WSOM in coarse mode particles (> 2 μm) from both sites. Potential sources analysis indicated the WSOM in Baoding were mainly derived from biomass burning and oxidation reactions, while the WSOM in Dalian arose from coal combustion, oxidation reactions, and regional transport.
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Affiliation(s)
- Cuiping Ning
- School of Chemical Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Yuan Gao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Shuai Sun
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, China.
| | - Haiming Yang
- School of Chemical Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Wei Tang
- School of Chemical Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Dan Wang
- School of Chemical Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
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2
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Zhu Y, Liu Z, Liu J, Zhao H, Feng R, Shu K, Wang F, Chang C. Panda-UV Unlocks Deeper Protein Characterization with Internal Fragments in Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2024; 96:8474-8483. [PMID: 38739687 PMCID: PMC11140674 DOI: 10.1021/acs.analchem.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry unlocks insights into the protein structure and sequence through fragmentation patterns. While N- and C-terminal fragments are traditionally relied upon, this work highlights the critical role of internal fragments in achieving near-complete sequencing of protein. Previous limitations of internal fragment utilization, owing to their abundance and potential for random matching, are addressed here with the development of Panda-UV, a novel software tool combining spectral calibration, and Pearson correlation coefficient scoring for confident fragment assignment. Panda-UV showcases its power through comprehensive benchmarks on three model proteins. The inclusion of internal fragments boosts identified fragment numbers by 26% and enhances average protein sequence coverage to a remarkable 93% for intact proteins, unlocking the hidden region of the largest protein carbonic anhydrase II in model proteins. Notably, an average of 65% of internal fragments can be identified in multiple replicates, demonstrating the high confidence of the fragments Panda-UV provided. Finally, the sequence coverages of mAb subunits can be increased up to 86% and the complementary determining regions (CDRs) are nearly completely sequenced in a single experiment. The source codes of Panda-UV are available at https://github.com/PHOENIXcenter/Panda-UV.
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Affiliation(s)
- Yinlong Zhu
- Chongqing
Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
- State
Key Laboratory of Medical Proteomics, Beijing
Proteome Research Center, National Center for Protein Sciences (Beijing),
Beijing Institute of Lifeomics, Beijing 102206, China
- CAS
Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
| | - Zheyi Liu
- CAS
Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jialiang Liu
- CAS
Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- School of
Pharmacy, China Medical University, Shenyang 110122, China
| | - Heng Zhao
- CAS
Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Rui Feng
- State
Key Laboratory of Medical Proteomics, Beijing
Proteome Research Center, National Center for Protein Sciences (Beijing),
Beijing Institute of Lifeomics, Beijing 102206, China
| | - Kunxian Shu
- Chongqing
Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Fangjun Wang
- CAS
Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Chang
- State
Key Laboratory of Medical Proteomics, Beijing
Proteome Research Center, National Center for Protein Sciences (Beijing),
Beijing Institute of Lifeomics, Beijing 102206, China
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3
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Gosset-Erard C, Aubriet F, Leize-Wagner E, François YN, Chaimbault P. Hyphenation of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with separation methods: The art of compromises and the possible - A review. Talanta 2023; 257:124324. [PMID: 36780779 DOI: 10.1016/j.talanta.2023.124324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
This review provides an overview of the online hyphenation of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with separation methods to date. The online coupling between separation techniques (gas and liquid chromatography, capillary electrophoresis) and FT-ICR MS essentially raises questions of compromise and is not look as straightforward as hyphenation with other analyzers (QTOF-MS for instance). FT-ICR MS requires time to reach its highest resolving power and accuracy in mass measurement capabilities whereas chromatographic and electrophoretic peaks are transient. In many applications, the strengths and the weaknesses of each technique are balanced by their hyphenation. Untargeted "Omics" (e.g. proteomics, metabolomics, petroleomics, …) is one of the main areas of application for FT-ICR MS hyphenated to online separation techniques because of the complexity of the sample. FT-ICR MS achieves the required high mass measurement accuracy to determine accurate molecular formulae and resolution for isobar distinction. Meanwhile separation techniques highlight isomers and reduce the ion suppression effects extending the dynamic range. Even if the implementation of FT-ICR MS hyphenated with online separation methods is a little trickier (the art of compromise), this review shows that it provides unparalleled results to the scientific community (the art of the possible), along with raising the issue of its future in the field with the relentless technological progress.
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Affiliation(s)
- Clarisse Gosset-Erard
- Université de Lorraine, LCP-A2MC, F-57000, Metz, France; Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
| | | | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de, Strasbourg, France.
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4
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Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
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Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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5
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Kellie JF, Schneck NA, Causon JC, Baba T, Mehl JT, Pohl KI. Top-Down Characterization and Intact Mass Quantitation of a Monoclonal Antibody Drug from Serum by Use of a Quadrupole TOF MS System Equipped with Electron-Activated Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:17-26. [PMID: 36459688 DOI: 10.1021/jasms.2c00206] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Time-of-flight MS systems for biopharmaceutical and protein characterization applications may play an even more pivotal role in the future as biotherapeutics increase in drug pipelines and as top-down MS approaches increase in use. Here, a recently developed TOF MS system is examined for monoclonal antibody (mAb) characterization from serum samples. After immunocapture, purified drug material spiked into monkey serum or dosed for an in-life study is analyzed by top-down MS. While characterization aspects are a distinct advantage of the MS platform, MS system and software capabilities are also shown regarding intact protein quantitation. Such applications are demonstrated to help enable comprehensive protein molecule quantitation and characterization by use of TOF MS instrumentation.
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Affiliation(s)
- John F Kellie
- GSK, Collegeville, Pennsylvania 19426, United States
| | | | | | | | - John T Mehl
- GSK, Collegeville, Pennsylvania 19426, United States
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6
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de Almeida C, Motta LC, Folli GS, Marcarini WD, Costa CA, Vilela ACS, Barauna VG, Martin FL, Singh MN, Campos LCG, Costa NL, Vassallo PF, Chaves AR, Endringer DC, Mill JG, Filgueiras PR, Romão W. MALDI(+) FT-ICR Mass Spectrometry (MS) Combined with Machine Learning toward Saliva-Based Diagnostic Screening for COVID-19. J Proteome Res 2022; 21:1868-1875. [PMID: 35880262 PMCID: PMC9344790 DOI: 10.1021/acs.jproteome.2c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Indexed: 11/28/2022]
Abstract
Rapid identification of existing respiratory viruses in biological samples is of utmost importance in strategies to combat pandemics. Inputting MALDI FT-ICR MS (matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry) data output into machine learning algorithms could hold promise in classifying positive samples for SARS-CoV-2. This study aimed to develop a fast and effective methodology to perform saliva-based screening of patients with suspected COVID-19, using the MALDI FT-ICR MS technique with a support vector machine (SVM). In the method optimization, the best sample preparation was obtained with the digestion of saliva in 10 μL of trypsin for 2 h and the MALDI analysis, which presented a satisfactory resolution for the analysis with 1 M. SVM models were created with data from the analysis of 97 samples that were designated as SARS-CoV-2 positives versus 52 negatives, confirmed by RT-PCR tests. SVM1 and SVM2 models showed the best results. The calibration group obtained 100% accuracy, and the test group 95.6% (SVM1) and 86.7% (SVM2). SVM1 selected 780 variables and has a false negative rate (FNR) of 0%, while SVM2 selected only two variables with a FNR of 3%. The proposed methodology suggests a promising tool to aid screening for COVID-19.
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Affiliation(s)
- Camila
M. de Almeida
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Larissa C. Motta
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Gabriely S. Folli
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Wena D. Marcarini
- Department
of Physiological Sciences, Federal University
of Espírito Santo, Vitória, ES 29040-090, Brazil
| | - Camila A. Costa
- School
of Dentistry, Department of Stomatology (Oral Pathology), Federal University of Goiás, Goiânia, GO 74000-000, Brazil
| | - Ana C. S. Vilela
- School
of Dentistry, Department of Stomatology (Oral Pathology), Federal University of Goiás, Goiânia, GO 74000-000, Brazil
| | - Valério G. Barauna
- Department
of Physiological Sciences, Federal University
of Espírito Santo, Vitória, ES 29040-090, Brazil
| | | | - Maneesh N. Singh
- Biocel
UK Ltd., 15 Riplingham
Road, West Ella, Hull HU10
6TS, U.K.
| | - Luciene C. G. Campos
- Department
of Biological Science, Santa Cruz State
University, Ilhéus, BA 45662-900, Brazil
| | - Nádia L. Costa
- School
of Dentistry, Department of Stomatology (Oral Pathology), Federal University of Goiás, Goiânia, GO 74000-000, Brazil
| | - Paula F. Vassallo
- Clinical
Hospital, Federal University of Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Andrea R. Chaves
- Chromatography
and Mass Spectrometry Laboratory, Institute of Chemistry, Federal University of Goiás, Goiânia, GO 74690-900, Brazil
| | - Denise C. Endringer
- Pharmaceutical
Science Graduate Program, Universidade Vila
Velha, Vila Velha, ES 29106-010, Brazil
| | - José G. Mill
- Department
of Physiological Sciences, Federal University
of Espírito Santo, Vitória, ES 29040-090, Brazil
| | - Paulo R. Filgueiras
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Wanderson Romão
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
- Science
Department, Federal Institute of Education,
Science, and Technology of Espírito Santo, Vila Velha, ES 29106-010, Brazil
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7
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Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
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8
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Kocheril PA, Moore SC, Lenz KD, Mukundan H, Lilley LM. Progress Toward a Multiomic Understanding of Traumatic Brain Injury: A Review. Biomark Insights 2022; 17:11772719221105145. [PMID: 35719705 PMCID: PMC9201320 DOI: 10.1177/11772719221105145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Traumatic brain injury (TBI) is not a single disease state but describes an array
of conditions associated with insult or injury to the brain. While some
individuals with TBI recover within a few days or months, others present with
persistent symptoms that can cause disability, neuropsychological trauma, and
even death. Understanding, diagnosing, and treating TBI is extremely complex for
many reasons, including the variable biomechanics of head impact, differences in
severity and location of injury, and individual patient characteristics. Because
of these confounding factors, the development of reliable diagnostics and
targeted treatments for brain injury remains elusive. We argue that the
development of effective diagnostic and therapeutic strategies for TBI requires
a deep understanding of human neurophysiology at the molecular level and that
the framework of multiomics may provide some effective solutions for the
diagnosis and treatment of this challenging condition. To this end, we present
here a comprehensive review of TBI biomarker candidates from across the
multiomic disciplines and compare them with known signatures associated with
other neuropsychological conditions, including Alzheimer’s disease and
Parkinson’s disease. We believe that this integrated view will facilitate a
deeper understanding of the pathophysiology of TBI and its potential links to
other neurological diseases.
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Affiliation(s)
- Philip A Kocheril
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shepard C Moore
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kiersten D Lenz
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Laura M Lilley
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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9
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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10
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Lebedev AT, Vasileva ID, Samgina TY. FT-MS in the de novo top-down sequencing of natural nontryptic peptides. MASS SPECTROMETRY REVIEWS 2022; 41:284-313. [PMID: 33347655 DOI: 10.1002/mas.21678] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.
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Affiliation(s)
- Albert T Lebedev
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Irina D Vasileva
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Y Samgina
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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11
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Lin Y, Agarwal AM, Marshall AG, Anderson LC. Characterization of Structural Hemoglobin Variants by Top-Down Mass Spectrometry and R Programming Tools for Rapid Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:123-130. [PMID: 34955023 DOI: 10.1021/jasms.1c00291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hemoglobinopathies are one of the most prevalent genetic disorders, affecting millions throughout the world. These are caused by pathogenic variants in genes that control the production of hemoglobin (Hb) subunits. As the number of known Hb variants has increased, it has become more challenging to obtain unambiguous results from routine chromatographic assays employed in the clinical laboratory. Top-down proteomic analysis of Hb by mass spectrometry is a definitive method to directly characterize the sequences of intact subunits. Here, we apply "chimeric ion loading" to characterize Hb β subunit variants. In this technique, product ions derived from complementary dissociation techniques are accumulated in a multipole storage device before delivery to a 21 T Fourier-transform ion cyclotron resonance mass spectrometer for simultaneous detection. To further improve the efficiency of identification of Hb variants and localization of the mutation site(s), we developed an R programming script, "Variants Identifier", to search top-down data against a database containing accurate intact mass differences and diagnostic ions from investigated Hb variants. A second R script, "PredictDiag", was developed and employed to determine relevant diagnostic ions for additional Hb variants with known sequences. These two R scripts were successfully applied to the identification of a Hb δ-β fusion protein and other Hb variants. The combination of chimeric ion loading and the above R scripts enables rapid and reliable interpretation of top-down mass spectrometry data, regardless of activation type, for Hb variant identification.
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Affiliation(s)
- Yuan Lin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32308, United States
| | - Archana M Agarwal
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, United States
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32308, United States
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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12
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Segl M, Stutz H. Bottom-Up Analysis of Proteins by Peptide Mass Fingerprinting with tCITP-CZE-ESI-TOF MS After Tryptic Digest. Methods Mol Biol 2022; 2531:93-106. [PMID: 35941481 DOI: 10.1007/978-1-0716-2493-7_7] [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] [Indexed: 06/15/2023]
Abstract
The identification of proteins in samples of moderate to complex composition is primarily done by bottom-up approaches. Therefore, proteins are enzymatically digested, mostly by trypsin, and the resulting peptides are then separated prior to their transfer to a mass spectrometer. The following protocol portrays a bottom-up method, which was optimized for the application of CZE-ESI-TOF MS. Protein denaturation is achieved by addition of 2,2,2-trifluoroethanol (TFE) and heat treatment. Afterwards, disulfide bonds are reduced with tris-(2-carboxyethyl)phosphine (TCEP) and subsequently alkylated with iodoacetamide (IAA). The tryptic digest is performed in an ammonium bicarbonate buffer at pH 8.0. The digested protein sample is then concentrated in-capillary by transient capillary isotachophoresis (tCITP) with subsequent CZE separation of tryptic peptides in an acidic background electrolyte. Hyphenation to a time-of-flight (TOF) mass spectrometer is carried out by a triple-tube coaxial sheath flow interface, which uses electrospray ionization (ESI). Peptide identification is done by peptide mass fingerprinting (PMF). The protocol is outlined exemplarily for a model protein, i.e., bovine β-lactoglobulin A.
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Affiliation(s)
- Marius Segl
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Salzburg, Austria
| | - Hanno Stutz
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Salzburg, Austria.
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13
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Li C, Chu S, Tan S, Yin X, Jiang Y, Dai X, Gong X, Fang X, Tian D. Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers. Front Chem 2021; 9:813359. [PMID: 34993180 PMCID: PMC8724130 DOI: 10.3389/fchem.2021.813359] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/06/2021] [Indexed: 01/12/2023] Open
Abstract
Mass spectrometry (MS) is one of the most widely used analytical techniques in many fields. Recent developments in chemical and biological researches have drawn much attention to the measurement of substances with low abundances in samples. Continuous efforts have been made consequently to further improve the sensitivity of MS. Modifications on the mass analyzers of mass spectrometers offer a direct, universal and practical way to obtain higher sensitivity. This review provides a comprehensive overview of the latest developments in mass analyzers for the improvement of mass spectrometers' sensitivity, including quadrupole, ion trap, time-of-flight (TOF) and Fourier transform ion cyclotron (FT-ICR), as well as different combinations of these mass analyzers. The advantages and limitations of different mass analyzers and their combinations are compared and discussed. This review provides guidance to the selection of suitable mass spectrometers in chemical and biological analytical applications. It is also beneficial to the development of novel mass spectrometers.
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Affiliation(s)
- Chang Li
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
| | - Shiying Chu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Di Tian
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
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14
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Diving Deep into the Data: A Review of Deep Learning Approaches and Potential Applications in Foodomics. Foods 2021; 10:foods10081803. [PMID: 34441579 PMCID: PMC8392494 DOI: 10.3390/foods10081803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/18/2023] Open
Abstract
Deep learning is a trending field in bioinformatics; so far, mostly known for image processing and speech recognition, but it also shows promising possibilities for data processing in food analysis, especially, foodomics. Thus, more and more deep learning approaches are used. This review presents an introduction into deep learning in the context of metabolomics and proteomics, focusing on the prediction of shelf-life, food authenticity, and food quality. Apart from the direct food-related applications, this review summarizes deep learning for peptide sequencing and its context to food analysis. The review’s focus further lays on MS (mass spectrometry)-based approaches. As a result of the constant development and improvement of analytical devices, as well as more complex holistic research questions, especially with the diverse and complex matrix food, there is a need for more effective methods for data processing. Deep learning might offer meeting this need and gives prospect to deal with the vast amount and complexity of data.
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15
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Shi RL, Xiao G, Dillon TM, Ricci MS, Bondarenko PV. Characterization of therapeutic proteins by cation exchange chromatography-mass spectrometry and top-down analysis. MAbs 2021; 12:1739825. [PMID: 32292112 PMCID: PMC7188404 DOI: 10.1080/19420862.2020.1739825] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recently, cation exchange chromatography (CEX) using aqueous volatile buffers was directly coupled with mass spectrometry (MS) and applied for intact analysis of therapeutic proteins and antibodies. In our study, chemical modifications responsible for charge variants were identified by CEX-UV-MS for a monoclonal antibody (mAb), a bispecific antibody, and an Fc-fusion protein. We also report post-CEX column addition of organic solvent and acid followed by mixing at elevated temperatures, which unfolded proteins, increased ion intensity (sensitivity) and facilitated top-down analysis. mAb stressed by hydrogen peroxide oxidation was used as a model system, which produced additional CEX peaks. The on-line CEX-UV-MS top-down analysis produced gas-phase fragments containing one or two methionine residues. Oxidation of some methionine residues contributed to earlier (acidic), some to later (basic) eluting peaks, while oxidation of other residues did not change CEX elution. The abundance of the oxidized and non-oxidized fragment ions also allowed estimation of the oxidation percentage of different methionine residues in stressed mAb. CEX-UV-MS measurement revealed a new intact antibody proteoform at 5% that eluted as a basic peak and included paired modifications: high-mannose glycosylation and remaining C-terminal lysine residue (M5/M5 + K). This finding was confirmed by peptide mapping and on-column disulfide reduction coupled with reversed-phase liquid chromatography – top-down MS analysis of the collected basic peak. Overall, our results demonstrate the utility of the on-line method in providing site-specific structural information of charge modifications without fraction collection and laborious peptide mapping.
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Affiliation(s)
- Rachel Liuqing Shi
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Gang Xiao
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Thomas M Dillon
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Margaret S Ricci
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Pavel V Bondarenko
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
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16
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Bothen J, Wallschläger D. The identification of selenopolythionates in aqueous solutions by electrospray ionization-Fourier transform-ion cyclotron resonance-mass spectrometry. Talanta 2021; 223:121770. [PMID: 33298279 DOI: 10.1016/j.talanta.2020.121770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 11/17/2022]
Abstract
Selenosulfate (SeSO32-) has been shown to occur in certain industrial process waters, and selenopolythionates (SenSxO62-) can be suspected to form from SeSO32- via oxidative or addition reactions. We report here the first observation of selenopolythionates in waters by mass spectrometry. The high mass accuracy and ultra-high resolution of Fourier transform-ion cyclotron resonance-mass Spectrometry with electrospray ionization (ESI-FT-ICR-MS) were used to analyze the isotope patterns of selenium (Se), sulfur (S), and oxygen (O) satellites, in order to provide unequivocal determination of the molecular sum formula of three different selenopolythionates. An aged aqueous solution of SeSO32- was shown to contain the sodium adducts of selenotrithionate (NaSeS2O6-), diselenotetrathionate (NaSe2S2O6-), and triselenopentathionate (NaSe3S2O6-). The identity of these ions was confirmed by accurate mass determination (Δ m/z < 3 ppm error) and by isotopic intensity ratio analysis of the [MIS+2] satellites. Furthermore, Collision Induced Dissociation (CID) was applied to selenotrithionate to distinguish between isomers, and the fragmentation mass spectrum reveals that the Se atom in NaSeS2O6- is located in the middle of the chalcogen chain. Ion chromatographic analysis of the analyzed selenosulfate solutions indicates that selenopolythionates are not suitable for determination by common separations employed for Se speciation analysis, which emphasizes the value of ESI-FT-ICR-MS for complete qualitative characterization of trace element speciation in solution.
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Affiliation(s)
- Jacob Bothen
- Department of Chemistry, Trent University, 1600 West Bank Drive, Peterborough, Ontario, K9L 0G2, Canada.
| | - Dirk Wallschläger
- Department of Chemistry, Trent University, 1600 West Bank Drive, Peterborough, Ontario, K9L 0G2, Canada; School of the Environment, Trent University, 1600 West Bank Drive, Peterborough, Ontario, K9L 0G2, Canada
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17
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Mass Spectrometry-based Metabolomics in Translational Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1310:509-531. [PMID: 33834448 DOI: 10.1007/978-981-33-6064-8_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Metabolomics is the systematic study of metabolite profiles of complex biological systems, and involves the systematic identification and quantification of metabolites. Metabolism is integrated with all biochemical reactions in biological systems; thus metabolite profiles provide collective information on biochemical processes induced by genetic or environmental perturbations. Transcriptomes or proteomes may not be functionally active and not always reflect phenotypic variations. The metabolome, however, consists of the biomolecules closest to the phenotype of living organisms, and is often called the molecular phenotype of biological systems. Thus, metabolome alterations can easily result in disease states, providing important clues to understand pathophysiological mechanisms contributing to various biomedical symptoms. The metabolome and metabolomics have been emphasized in translational research related to biomarker discovery, drug target discovery, drug responses, and disease mechanisms. This review describes the basic concepts, workflows, and applications of mass spectrometry-based metabolomics in translational research.
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18
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Devitt NM, Davis JM, Schure MR. Estimation of low-level components lost through chromatographic separations with finite detection limits. J Chromatogr A 2020; 1626:461266. [PMID: 32797862 DOI: 10.1016/j.chroma.2020.461266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 12/29/2022]
Abstract
The search for biomarkers allowing the assessment of disease by early diagnosis is facilitated by liquid chromatography. However, it is not clear how many components are lost due to being present in concentrations below the detection limit and/or being obscured by chromatographic peak overlap. First, we extend the study of missing components undertaken by Enke and Nagels, who employed the log-normal probability density function (pdf) for the distribution of signal intensities (and concentrations) of three mixtures. The Weibull and exponential pdfs, which have a higher probability of small-concentration components than the log-normal pdf, are also investigated. Results show that assessments of the loss of low-intensity signals by curve fitting are ambiguous. Next, we simulate synthetic chromatograms to compare the loss of peaks from superposition (overlap) with neighboring peaks to the loss arising from lying below the limit of detection (LOD) imposed by a finite signal-to-noise ratio (SNR). The simulations are made using amplitude pdfs based on the Enke-Nagels data as functions of relative column efficiency, i.e., saturation, and SNR. Results show that at the highest efficiencies, the lowest-amplitude peaks are lost below the LOD. However, at small and medium efficiencies, peak overlap is the dominant loss mechanism, suggesting that low-level components will not be found easily in liquid chromatography with single channel detectors regardless of SNR. A simple treatment shows that a multichannel detector, e.g., a mass spectrometer, is necessary to expose more low-level components.
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Affiliation(s)
- Nicole M Devitt
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716 USA
| | - Joe M Davis
- Department of Chemistry and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901-4409 USA.
| | - Mark R Schure
- Theoretical Separation Science Laboratory, Kroungold Analytical, Inc., 1299 Butler Pike, Blue Bell, Pennsylvania 19422 USA.
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19
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Esteves CV, Campos WGD, Souza MMD, Lourenço SV, Siqueira WL, Lemos-Júnior CA. Diagnostic potential of saliva proteome analysis: a review and guide to clinical practice. Braz Oral Res 2019; 33:e043. [PMID: 31508727 DOI: 10.1590/1807-3107bor-2019.vol33.0043] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/25/2019] [Indexed: 01/26/2023] Open
Abstract
Proteomic techniques have become popular in medicine and dentistry because of their widespread use in analyzing bodily fluids such as blood, saliva, urine, and gingival crevicular fluids as well as hard tissues such as enamel, dentine, and cementum. This review is a guide to proteomic techniques in general dentistry, summarizing techniques and their clinical application in understanding and diagnosing diseases and their use in identifying biomarkers of various diseases.
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Affiliation(s)
- Camilla Vieira Esteves
- Department of Stomatology, School of Dentistry, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Silvia Vanessa Lourenço
- Department of General Pathology, School of Dentistry, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Walter Luiz Siqueira
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
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20
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Lisitsa AV, Petushkova NA, Levitsky LI, Zgoda VG, Larina OV, Kisrieva YS, Frankevich VE, Gamidov SI. Comparative Analysis of the Performаnce of Mascot and IdentiPy Algorithms on a Benchmark Dataset Obtained by Tandem Mass Spectrometry Analysis of Testicular Biopsies. Mol Biol 2019. [DOI: 10.1134/s0026893319010096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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van der Burgt YEM, Kilgour DPA, Tsybin YO, Srzentić K, Fornelli L, Beck A, Wuhrer M, Nicolardi S. Structural Analysis of Monoclonal Antibodies by Ultrahigh Resolution MALDI In-Source Decay FT-ICR Mass Spectrometry. Anal Chem 2019; 91:2079-2085. [PMID: 30571088 PMCID: PMC6365908 DOI: 10.1021/acs.analchem.8b04515] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The
emergence of complex protein therapeutics in general and monoclonal
antibodies (mAbs) in particular have stimulated analytical chemists
to develop new methods and strategies for their structural characterization.
Mass spectrometry plays a key role in providing information on the
primary amino acid sequence, post-translational modifications, and
other structure characteristics that must be monitored during the
manufacturing process and subsequent quality control assessment. In
this study, we present a novel method that allows structural characterization
of mAbs based on MALDI in-source decay (ISD) fragmentation, coupled
with Fourier transform ion cyclotron resonance (FT-ICR) MS. The method
benefits from higher resolution of absorption mode FT mass spectra,
compared to magnitude mode, which enables simultaneous identification
of ISD fragments from both the heavy and light chains with a higher
confidence in a wide mass range up to m/z 13 500. This method was applied to two standard mAbs, namely
NIST mAb and trastuzumab, in preparation for method application in
an interlaboratory study on mAbs structural analysis coordinated by
the Consortium for Top-Down Proteomics. Extensive sequence coverage
was obtained from the middle-down analysis (IdeS- and GingisKHAN-digested
mAbs) that complemented the top-down analysis of intact mAbs. In addition,
MALDI FT-ICR MS of IdeS-digested mAbs allowed isotopic-level profiling
of proteoforms with regard to heavy chain N-glycosylation.
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Affiliation(s)
- Yuri E M van der Burgt
- Center for Proteomics and Metabolomics , Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC , Leiden , The Netherlands
| | - David P A Kilgour
- Department of Chemistry , Nottingham Trent University , Nottingham , NG11 0JN , U.K
| | - Yury O Tsybin
- Spectroswiss , EPFL Innovation Park , 1015 Lausanne , Switzerland
| | - Kristina Srzentić
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 N. Sheridan Road , Evanston , Illinois 60208 , United States
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 N. Sheridan Road , Evanston , Illinois 60208 , United States
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre , 74160 St. Julien-en-Genevois , France
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics , Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC , Leiden , The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics , Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC , Leiden , The Netherlands
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22
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Zhao X, Shen Y, Tong W, Wang G, Chen DDY. Deducing disulfide patterns of cysteine-rich proteins using signature fragments produced by top-down mass spectrometry. Analyst 2019; 143:817-823. [PMID: 29362732 DOI: 10.1039/c7an01625e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct mapping of protein disulfide patterns using top-down mass spectrometry (MS) is often hampered by inadequate fragmentation at the disulfide-enclosing region, and insufficient structural information provided by the fragments. Here we used electron-transfer/high energy collision dissociation (EThcD) to improve the fragmentation efficiency, and developed strategies that minimize the false positive identification of fragments and deconvolute the signals representing specific modifications made to the disulfide-cleavage-induced fragments. We observed clear correlations between unique modification (attachment or removal of H or SH) patterns and the number of disulfide bonds that enclose the corresponding region. Using the characteristic signature fragments, we in part localized the Cys-bridging sites in disulfide-scrambled lysozymes, and reduced the number of putative disulfide patterns from 104 to 6. The results demonstrated the feasibility of direct analysis of complex disulfide patterns using top-down MS.
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Affiliation(s)
- Xiuxiu Zhao
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, and School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
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23
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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24
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Proteomics: Tools of the Trade. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:1-22. [DOI: 10.1007/978-3-030-12298-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Sekera ER, Wood TD. Sequencing Proteins from Bottom to Top: Combining Techniques for Full Sequence Analysis of Glucokinase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:111-119. [DOI: 10.1007/978-3-030-15950-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Perez JJ, Chen CY. Implementation of normalized retention time (iRT) for bottom-up proteomic analysis of the aminoglycoside phosphotransferase enzyme facilitating method distribution. Anal Bioanal Chem 2018; 411:4701-4708. [DOI: 10.1007/s00216-018-1377-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2018] [Accepted: 09/13/2018] [Indexed: 01/05/2023]
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27
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Calvete JJ. Snake venomics – from low-resolution toxin-pattern recognition to toxin-resolved venom proteomes with absolute quantification. Expert Rev Proteomics 2018; 15:555-568. [DOI: 10.1080/14789450.2018.1500904] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Juan J. Calvete
- Evolutionary and Translational Venomics Laboratory, CSIC, Valencia, Spain
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28
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Proteoform Analysis to Fulfill Unmet Clinical Needs and Reach Global Standardization of Protein Measurands in Clinical Chemistry Proteomics. Clin Lab Med 2018; 38:487-497. [PMID: 30115393 DOI: 10.1016/j.cll.2018.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In clinical testing of protein markers, structure variants of the measurand are often not taken into account. This heterogeneous character of protein measurands in immunoassays often renders test standardization impossible. Consequently, test results from different methods can lead to underdiagnosis or overdiagnosis and, thus, undertreatment or overtreatment of patients. The systematic structural analysis of protein isoforms has been coined proteoform profiling and is performed through mass spectrometry-based proteomics strategies. Knowledge on proteoforms allows refining existing uni-marker tests and moreover has great potential to contribute to the urgent need for new tests to predict prognosis and severity of diseases.
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29
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Top-down characterization of chicken core histones. J Proteomics 2018; 184:34-38. [PMID: 29935335 DOI: 10.1016/j.jprot.2018.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022]
Abstract
Core histones and their PTMs play important roles in regulating gene transcription and other DNA-related processes. The study of core histones PTMs, their cross-talk and functional roles is not only of broad biological significance but also of wide pathological and clinical relevance. Having the strength of comprehensive proteoform identification with 100% amino acid sequence coverage and combinatorial PTMs, top-down proteomics has become the state-of-the-art analytical tool for combinatorial PTM characterization of core histones. In this study, we report our top-down characterization of chicken (Gallus gallus domesticus) core histones, which have been widely used as models for chromosome re-construction among others because of easy availability and not-so-dense PTMs. With nanoRPLC-MS/MS analysis and ProteinGoggle database search, a total of 58 proteoforms were identified for the core histone families of H4, H2B, H2A, and H3.
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30
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Floris F, Chiron L, Lynch AM, Barrow MP, Delsuc MA, O’Connor PB. Top-Down Deep Sequencing of Ubiquitin Using Two-Dimensional Mass Spectrometry. Anal Chem 2018; 90:7302-7309. [DOI: 10.1021/acs.analchem.8b00500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Federico Floris
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Lionel Chiron
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
| | - Alice M. Lynch
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Mark P. Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Marc-André Delsuc
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
- Institut de Génétique
et de Biologie Moléculaire et Cellulaire, Institut National
de la Santé et de la Recherche, U596; Centre National de la
Recherche Scientifique, Unité Mixte de Recherche 7104; Université
de Strasbourg, 67404, Illkirch-Graffenstaden, France
| | - Peter B. O’Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
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31
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Wang Z, Ma H, Smith K, Wu S. Two-Dimensional Separation Using High-pH and Low-pH Reversed Phase Liquid Chromatography for Top-down Proteomics. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:43-51. [PMID: 31097918 PMCID: PMC6516780 DOI: 10.1016/j.ijms.2017.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Advancements in chromatographic separation are critical to in-depth top-down proteomics of complex intact protein samples. Reversed-phase liquid chromatography is the most prevalent technique for top-down proteomics. However, in cases of high complexities and large dynamic ranges, 1D-RPLC may not provide sufficient coverage of the proteome. To address these challenges, orthogonal separation techniques are often combined to improve the coverage and the dynamic range of detection. In this study, a "salt-free" high-pH RPLC was evaluated as an orthogonal dimension of separation to conventional low-pH RPLC with top-down MS. The RPLC separations with low-pH conditions (pH=2) and high-pH conditions (pH=10) were compared to confirm the good orthogonality between high-pH and low-pH RPLC's. The offline 2D RPLC-RPLC-MS/MS analyses of intact E. coli samples were evaluated for the improvement of intact protein identifications as well as intact proteoform characterizations. Compared to the 163 proteins and 328 proteoforms identified using a 1D RPLC-MS approach, 365 proteins and 886 proteoforms were identified using the 2D RPLC-RPLC top-down MS approach. Our results demonstrate that the 2D RPLC-RPLC top-down approach holds great potential for in-depth top-down proteomics studies by utilizing the high resolving power of RPLC separations and by using mass spectrometry compatible buffers for easy sample handling for online MS analysis.
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Affiliation(s)
- Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
| | - Hongyan Ma
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
| | - Kenneth Smith
- Arthritis & Clinical Immunology Research Program, Oklahoma
Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
- To whom correspondence should be addressed: Si
Wu, Ph.D., Department of Chemistry and Biochemistry, 101 Stephenson
Parkway, Room 2210, Norman, Oklahoma 73019-5251, United States, Phone: (405)
325-6931, , Fax: (405) 325-6111
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32
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
| | - Gege Xu
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Qiongyu Li
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elisha Goonatilleke
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Carlito B Lebrilla
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States.,Department of Biochemistry and Molecular Medicine , University of California, Davis , Davis , California 95616 , United States.,Foods for Health Institute , University of California, Davis , Davis , California 95616 , United States
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33
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Xu C, Wu F, Ding L, Ding CF. An Orbital Trap Mass Analyzer Using a Hybrid Magnetic-Electric Field: A Simulation Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:613-622. [PMID: 29372554 DOI: 10.1007/s13361-017-1868-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/03/2017] [Accepted: 12/07/2017] [Indexed: 06/07/2023]
Abstract
An orbital ion trap mass analyzer employing hybrid magnetic-electric field was designed and simulated. The trap has a rotational symmetrical structure and the hybrid trapping field was created in a toroidal space between 12 pairs of sector detection electrodes. Ion injection and ion orbital motion inside the trap were simulated using SIMION 8.1 with a user Lua program, and the required electric and magnetic field were investigated. The image charge signal can be picked up by the 12 pairs of detection electrodes and the mass resolution was evaluated using FFT. The simulated resolving power for the optimized configuration over 79,000 FWHM was obtained at the magnetic induction intensity of 0.5 Tesla in the simulation. Graphical Abstract ᅟ.
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Affiliation(s)
- Chongsheng Xu
- Department of Chemistry and Laser Chemistry Institute, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Fangling Wu
- Department of Chemistry and Laser Chemistry Institute, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Li Ding
- Shimadzu Research Laboratory (Europe) Ltd., Wharfside, Trafford Wharf Road, Manchester, M17 1GP, UK.
| | - Chuan-Fan Ding
- Department of Chemistry and Laser Chemistry Institute, Fudan University, 220 Handan Road, Shanghai, 200433, China.
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34
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Chetwynd AJ, Guggenheim EJ, Briffa SM, Thorn JA, Lynch I, Valsami-Jones E. Current Application of Capillary Electrophoresis in Nanomaterial Characterisation and Its Potential to Characterise the Protein and Small Molecule Corona. NANOMATERIALS (BASEL, SWITZERLAND) 2018; 8:E99. [PMID: 29439415 PMCID: PMC5853730 DOI: 10.3390/nano8020099] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/22/2018] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
Due to the increasing use and production of nanomaterials (NMs), the ability to characterise their physical/chemical properties quickly and reliably has never been so important. Proper characterisation allows a thorough understanding of the material and its stability, and is critical to establishing dose-response curves to ascertain risks to human and environmental health. Traditionally, methods such as Transmission Electron Microscopy (TEM), Field Flow Fractionation (FFF) and Dynamic Light Scattering (DLS) have been favoured for size characterisation, due to their wide-availability and well-established protocols. Capillary Electrophoresis (CE) offers a faster and more cost-effective solution for complex dispersions including polydisperse or non-spherical NMs. CE has been used to rapidly separate NMs of varying sizes, shapes, surface modifications and compositions. This review will discuss the literature surrounding the CE separation techniques, detection and NM characteristics used for the analysis of a wide range of NMs. The potential of combining CE with mass spectrometry (CE-MS) will also be explored to further expand the characterisation of NMs, including the layer of biomolecules adsorbed to the surface of NMs in biological or environmental compartments, termed the acquired biomolecule corona. CE offers the opportunity to uncover new/poorly characterised low abundance and polar protein classes due to the high ionisation efficiency of CE-MS. Furthermore, the possibility of using CE-MS to characterise the poorly researched small molecule interactions within the NM corona is discussed.
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Affiliation(s)
- Andrew J. Chetwynd
- AB Sciex UK Ltd., Phoenix House, Lakeside Drive, Warrington, Cheshire WA1 1RX, UK;
| | - Emily J. Guggenheim
- School of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (E.J.G.); (S.M.B.); (E.V.-J.)
| | - Sophie M. Briffa
- School of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (E.J.G.); (S.M.B.); (E.V.-J.)
| | - James A. Thorn
- AB Sciex UK Ltd., Phoenix House, Lakeside Drive, Warrington, Cheshire WA1 1RX, UK;
| | - Iseult Lynch
- School of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (E.J.G.); (S.M.B.); (E.V.-J.)
| | - Eugenia Valsami-Jones
- School of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (E.J.G.); (S.M.B.); (E.V.-J.)
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35
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Zhang D, Zhang Q, Bai L, Han D, Liu H, Yan H. Fabrication of an ionic-liquid-based polymer monolithic column and its application in the fractionation of proteins from complex biosamples. J Sep Sci 2018; 41:1923-1929. [PMID: 29368444 DOI: 10.1002/jssc.201701369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 12/28/2022]
Abstract
An ionic-liquid-based polymer monolithic column was synthesized by free radical polymerization within the confines of a stainless-steel column (50 mm × 4.6 mm id). In the processes, ionic liquid and stearyl methacrylate were used as dual monomers, ethylene glycol dimethacrylate as the cross-linking agent, and polyethylene glycol 200 and isopropanol as co-porogens. Effects of the prepolymerization solution components on the properties of the resulting monoliths were studied in detail. Scanning electron microscopy, nitrogen adsorption-desorption measurements, and mercury intrusion porosimetry were used to investigate the morphology and pore size distribution of the prepared monoliths, which showed that the homemade ionic-liquid-based monolith column possessed a relatively uniform macropore structure with a total macropore specific surface area of 44.72 m2 /g. Compared to a non-ionic-liquid-based monolith prepared under the same conditions, the ionic-liquid-based monolith exhibited excellent selectivity and high performance for separating proteins from complex biosamples, such as egg white, snailase, bovine serum albumin digest solution, human plasma, etc., indicating promising applications in the fractionation and analysis of proteins from the complex biosamples in proteomics research.
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Affiliation(s)
- Doudou Zhang
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, P. R. China
| | - Qian Zhang
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
| | - Ligai Bai
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, P. R. China
| | - Dandan Han
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
| | - Haiyan Liu
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, P. R. China
| | - Hongyuan Yan
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
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36
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Schmidt EM, Pudenzi MA, Santos JM, Angolini CFF, Pereira RCL, Rocha YS, Denisov E, Damoc E, Makarov A, Eberlin MN. Petroleomics via Orbitrap mass spectrometry with resolving power above 1 000 000 at m/z 200. RSC Adv 2018; 8:6183-6191. [PMID: 35539593 PMCID: PMC9078259 DOI: 10.1039/c7ra12509g] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/27/2018] [Indexed: 12/18/2022] Open
Abstract
The performance of the high-field MegaOrbitrap Fourier transform mass spectrometer (FT-MS) with electrospray ionization (ESI) was evaluated to perform petroleum sample characterization via classical petroleomics approaches. Pertinent parameters that underpin the main figures of merit, that is, signal to noise ratios, dynamic range, spectral error, scan speed, mass accuracy and mass resolving power = Rp, and provide subsidies to develop these analyzers were tested. Comparisons are made with data obtained using the most common petroleomics instrument, which is a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), that has been used in the last decade in our laboratory for crude oil analysis providing Rp of 340 000 at m/z 400 with transients of 3 s duration, and has been extensively demonstrated to fulfill all major requirements for precise petroleomics investigations. The high-field compact MegaOrbitrap mass analyzer, when operated at an Rp = 840 000 at m/z 400 (Rp > 1 000 000 at m/z 200) with a detection time of 3 s, was found to be well suited for adequate characterization of crude oil. Accurate class classification and mass accuracy below 1 ppm was obtained leading to proper, comprehensive petroleomics characterization. The performance of the high-field MegaOrbitrap Fourier transform mass spectrometer (FT-MS) with electrospray ionization (ESI) was evaluated to perform petroleum sample characterization via classical petroleomics approaches.![]()
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Affiliation(s)
- Eduardo M. Schmidt
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Marcos A. Pudenzi
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Jandyson M. Santos
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Celio F. F. Angolini
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | | | | | | | | | | | - Marcos N. Eberlin
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
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37
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Pettit ME, Brantley MR, Donnarumma F, Murray KK, Solouki T. Broadband ion mobility deconvolution for rapid analysis of complex mixtures. Analyst 2018; 143:2574-2586. [DOI: 10.1039/c8an00193f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Broadband IM-MS deconvolution allows generation of IM and MS data for species that are UPLC-IM-MS unresolved.
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Affiliation(s)
| | | | | | | | - Touradj Solouki
- Department of Chemistry and Biochemistry
- Baylor University
- Waco
- USA
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38
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Driver JA, Nagornov KO, Kozhinov AN, Tsybin YO, Kharchenko A, Amster IJ. Multiparticle Simulations of Quadrupolar Ion Detection in an Ion Cyclotron Resonance Cell with Four Narrow Aperture Detection Electrodes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:51-62. [PMID: 29038997 DOI: 10.1007/s13361-017-1817-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/13/2017] [Accepted: 09/17/2017] [Indexed: 06/07/2023]
Abstract
The current paradigm in FT-ICR cell design is to approximate the ideal three-dimensional quadratic trapping potential as closely as possible to maintain ion cloud spatial coherence and achieve long transients, either with hyperbolically shaped electrodes, shimming electrodes, or by dynamic harmonization. In sharp contrast, the FT-ICR analyzer cell with four narrow aperture detection electrodes (NADEL) introduces significant anharmonic terms to the trapping potential. This analyzer cell is capable of quadrupolar detection by which one can measure a signal that is close to the unperturbed cyclotron frequency. This is far less sensitive to trapping potential and space charge shifts than the reduced cyclotron frequency measured in conventional ICR cells. The quadrupolar mode of ion detection in NADEL cells has been examined previously by SIMION simulations of ion clouds with up to 500 ions per simulation. Here, the behavior of the NADEL analyzer cell is examined through particle-in-cell (PIC) simulations, which allows us to examine the behavior of large populations (tens of thousands) of ions with space charge considerations, and to calculate the induced charge on the NADEL detection electrodes, and thus the transient signal. PIC simulations confirm a unique spatial distribution of the ions, with a coherent motion that results in long transient signals. Dependence of the ion cloud and image current signal on cell design, ion energy, and magnetron radius are examined. Coalescence effects are compared with those found in a dynamically harmonized cell. The insensitivity of the measured cyclotron frequency to space-charge is demonstrated both with simulations and experimentally. Graphical Abstract ᅟ.
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Affiliation(s)
- Joshua A Driver
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | | | - Anton N Kozhinov
- Spectroswiss Sàrl, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Yury O Tsybin
- Spectroswiss Sàrl, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Andriy Kharchenko
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
- NAS Institute of Cybernetics, Kyiv, Ukraine
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
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39
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Soboleva A, Schmidt R, Vikhnina M, Grishina T, Frolov A. Maillard Proteomics: Opening New Pages. Int J Mol Sci 2017; 18:E2677. [PMID: 29231845 PMCID: PMC5751279 DOI: 10.3390/ijms18122677] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/29/2017] [Accepted: 12/05/2017] [Indexed: 12/12/2022] Open
Abstract
Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs) represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer's disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus), proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.
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Affiliation(s)
- Alena Soboleva
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Rico Schmidt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther Universität Halle-Wittenberg, 06108 Halle, Germany.
| | - Maria Vikhnina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Tatiana Grishina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
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40
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Chang HY, Chen CT, Ko CL, Chen YJ, Chen YJ, Hsu WL, Juo CG, Sung TY. iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm. Anal Chem 2017; 89:13128-13136. [DOI: 10.1021/acs.analchem.7b02343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hui-Yin Chang
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Ching-Tai Chen
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chu-Ling Ko
- Department
of Computer Science, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chiun-Gung Juo
- Molecular
Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- PharmaEssentia Corp., Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
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41
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Lu M, Faull KF, Whitelegge JP, He J, Shen D, Saxton RE, Chang HR. Proteomics and Mass Spectrometry for Cancer Biomarker Discovery. Biomark Insights 2017. [DOI: 10.1177/117727190700200005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Proteomics is a rapidly advancing field not only in the field of biology but also in translational cancer research. In recent years, mass spectrometry and associated technologies have been explored to identify proteins or a set of proteins specific to a given disease, for the purpose of disease detection and diagnosis. Such biomarkers are being investigated in samples including cells, tissues, serum/plasma, and other types of body fluids. When sufficiently refined, proteomic technologies may pave the way for early detection of cancer or individualized therapy for cancer. Mass spectrometry approaches coupled with bioinformatic tools are being developed for biomarker discovery and validation. Understanding basic concepts and application of such technology by investigators in the field may accelerate the clinical application of protein biomarkers in disease management.
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Affiliation(s)
- Ming Lu
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Kym F. Faull
- The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry & Biobehavioral and the Neuropsychiatric Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry & Biobehavioral and the Neuropsychiatric Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Jianbo He
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Dejun Shen
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Romaine E. Saxton
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, Los Angeles, California
| | - Helena R. Chang
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, Los Angeles, California
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42
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Melani RD, Nogueira FCS, Domont GB. It is time for top-down venomics. J Venom Anim Toxins Incl Trop Dis 2017; 23:44. [PMID: 29075288 PMCID: PMC5648493 DOI: 10.1186/s40409-017-0135-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/21/2017] [Indexed: 12/19/2022] Open
Abstract
The protein composition of animal venoms is usually determined by peptide-centric proteomics approaches (bottom-up proteomics). However, this technique cannot, in most cases, distinguish among toxin proteoforms, herein called toxiforms, because of the protein inference problem. Top-down proteomics (TDP) analyzes intact proteins without digestion and provides high quality data to identify and characterize toxiforms. Denaturing top-down proteomics is the most disseminated subarea of TDP, which performs qualitative and quantitative analyzes of proteoforms up to ~30 kDa in high-throughput and automated fashion. On the other hand, native top-down proteomics provides access to information on large proteins (> 50 kDA) and protein interactions preserving non-covalent bonds and physiological complex stoichiometry. The use of native and denaturing top-down venomics introduced novel and useful techniques to toxinology, allowing an unprecedented characterization of venom proteins and protein complexes at the toxiform level. The collected data contribute to a deep understanding of venom natural history, open new possibilities to study the toxin evolution, and help in the development of better biotherapeutics.
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Affiliation(s)
- Rafael D. Melani
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Fabio C. S. Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Gilberto B. Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
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43
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Takemori N, Takemori A, Wongkongkathep P, Nshanian M, Loo RRO, Lermyte F, Loo JA. Top-down/Bottom-up Mass Spectrometry Workflow Using Dissolvable Polyacrylamide Gels. Anal Chem 2017; 89:8244-8250. [PMID: 28723075 DOI: 10.1021/acs.analchem.7b00357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Biologists' preeminent toolbox for separating, analyzing, and visualizing proteins is SDS-PAGE, yet recovering the proteins embedded in these polyacrylamide media as intact species is a long-standing challenge for mass spectrometry. In conventional workflows, protein mixtures from crude biological samples are electrophoretically separated at high-resolution within N,N'-methylene-bis-acrylamide cross-linked polyacrylamide gels to reduce sample complexity and facilitate sensitive characterization. However, low protein recoveries, especially for high molecular weight proteins, often hinder characterization by mass spectrometry. We describe a workflow for top-down/bottom-up mass spectrometric analyses of proteins in polyacrylamide slab gels using dissolvable, bis-acryloylcystamine-cross-linked polyacrylamide, enabling high-resolution protein separations while recovering intact proteins over a broad size range efficiently. The inferior electrophoretic resolution long associated with reducible gels has been overcome, as demonstrated by SDS-PAGE of crude tissue extracts. This workflow elutes intact proteins efficiently, supporting MS and MS/MS from proteins resolved on biologists' preferred separation platform.
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Affiliation(s)
- Nobuaki Takemori
- Proteo-Science Center, Division of Proteomics Research, Ehime University , Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Ayako Takemori
- Proteo-Science Center, Division of Proteomics Research, Ehime University , Shitsukawa, Toon, Ehime, 791-0295, Japan.,The United Graduate School of Agricultural Sciences, Ehime University , Matsuyama, Ehime, 790-8566, Japan
| | - Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California-Los Angeles , Los Angeles, California 90095, United States
| | - Michael Nshanian
- Department of Chemistry and Biochemistry, University of California-Los Angeles , Los Angeles, California 90095, United States
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles , Los Angeles, California 90095, United States
| | - Frederik Lermyte
- Department of Chemistry, University of Antwerp , Universiteitsplein 1, B-2610 Wilrijk-Antwerp, Belgium
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles , Los Angeles, California 90095, United States.,Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles , Los Angeles, California 90095, United States
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Zhdanova E, Kostyukevich Y, Nikolaev E. Static harmonization of dynamically harmonized Fourier transform ion cyclotron resonance cell. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:197-201. [PMID: 29028404 DOI: 10.1177/1469066717718369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Static harmonization in the Fourier transform ion cyclotron resonance cell improves the resolving power of the cell and prevents dephasing of the ion cloud in the case of any trajectory of the charged particle, not necessarily axisymmetric cyclotron (as opposed to dynamic harmonization). We reveal that the Fourier transform ion cyclotron resonance cell with dynamic harmonization (paracell) is proved to be statically harmonized. The volume of the statically harmonized potential distribution increases with an increase in the number of trap segments.
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Affiliation(s)
- Ekaterina Zhdanova
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Yury Kostyukevich
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Eugene Nikolaev
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Russia
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Duran-Ortiz S, Brittain AL, Kopchick JJ. The impact of growth hormone on proteomic profiles: a review of mouse and adult human studies. Clin Proteomics 2017; 14:24. [PMID: 28670222 PMCID: PMC5492507 DOI: 10.1186/s12014-017-9160-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
Growth hormone (GH) is a protein that is known to stimulate postnatal growth, counter regulate insulin's action and induce expression of insulin-like growth factor-1. GH exerts anabolic or catabolic effects depending upon on the targeted tissue. For instance, GH increases skeletal muscle and decreases adipose tissue mass. Our laboratory has spent the past two decades studying these effects, including the effects of GH excess and depletion, on the proteome of several mouse and human tissues. This review first discusses proteomic techniques that are commonly used for these types of studies. We then examine the proteomic differences found in mice with excess circulating GH (bGH mice) or mice with disruption of the GH receptor gene (GHR-/-). We also describe the effects of increased and decreased GH action on the proteome of adult patients with either acromegaly, GH deficiency or patients after short-term GH treatment. Finally, we explain how these proteomic studies resulted in the discovery of potential biomarkers for GH action, particularly those related with the effects of GH on aging, glucose metabolism and body composition.
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Affiliation(s)
- Silvana Duran-Ortiz
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA
| | - Alison L Brittain
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
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Top-down HPLC-ESI-MS proteomic analysis of saliva of edentulous subjects evidenced high levels of cystatin A, cystatin B and SPRR3. Arch Oral Biol 2017; 77:68-74. [PMID: 28178587 DOI: 10.1016/j.archoralbio.2017.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 01/23/2017] [Accepted: 01/29/2017] [Indexed: 01/20/2023]
Abstract
OBJECTIVE This study aims to analyze the salivary peptidome/proteome of edentulous subject with respect to dentate control subjects. DESIGN Unstimulated whole saliva, collected from 11 edentulous subjects (age 60-76 years) and 11 dentate age-matched control subjects, was immediately treated with 0.2% aqueous trifluoroacetic acid and the acidic soluble fraction analyzed by High Performace Liquid Chromatography-Mass Spectrometry. The relative abundance of the salivary peptides/proteins was determined by measuring the area of the High Performace Liquid Chromatography-Mass Spectrometry eXtracted Ion Current peaks which is linearly proportional to peptide/protein concentration under identical experimental conditions. Levels of salivary peptides/proteins in the two groups were compared by the nonparametric Mann-Whitney test to evidence statistically significant differences. RESULTS Levels of cystatin A, S-glutathionylated, S-cystenylated, S-S dimer derivatives of cystatin B and S-glutathionylated derivative of SPRR3, were found significantly higher in edentulous subjects with respect to dentate controls. The major peptides and proteins typically deriving from salivary glands did not show any statistically significant differences. CONCLUSIONS Cystatin A, S-glutathionylated, S-cystenylated, S-S dimer derivatives of cystatin B and S-glutathionylated derivative of SPRR3, which are mainly of intracellular origin and represent the major constituents of the cornified cell envelope are a clue of inflammation of mucosal epithelia.
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Santos IC, Hildenbrand ZL, Schug KA. Mass Spectrometry for the Study of Microbial Communities in Environmental Waters. ADVANCES IN CHEMICAL POLLUTION, ENVIRONMENTAL MANAGEMENT AND PROTECTION 2017. [DOI: 10.1016/bs.apmp.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Top-Down Proteomics and Farm Animal and Aquatic Sciences. Proteomes 2016; 4:proteomes4040038. [PMID: 28248248 PMCID: PMC5260971 DOI: 10.3390/proteomes4040038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/16/2023] Open
Abstract
Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.
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Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016; 35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.
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Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
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50
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Ruhaak LR, van der Burgt YE, Cobbaert CM. Prospective applications of ultrahigh resolution proteomics in clinical mass spectrometry. Expert Rev Proteomics 2016; 13:1063-1071. [DOI: 10.1080/14789450.2016.1253477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Yuri E.M. van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
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