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Donndelinger DV, Yan T, Scoggins TR, Specker JT, Prentice BM. Sequencing of Phosphopeptides Using a Sequential Charge Inversion Ion/Ion Reaction and Electron Capture Dissociation Workflow. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1556-1566. [PMID: 38806410 DOI: 10.1021/jasms.4c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Protein phosphorylation, a common post-translational modification (PTM), is fundamental in a plethora of biological processes, most importantly in modulating cell signaling pathways. Matrix-assisted laser desorption/ionization (MALDI) coupled to tandem mass spectrometry (MS/MS) is an attractive method for phosphopeptide characterization due to its high speed, low limit of detection, and surface sampling capabilities. However, MALDI analysis of phosphopeptides is constrained by relatively low abundances in biological samples and poor relative ionization efficiencies in positive ion mode. Additionally, MALDI tends to produce singly charged ions, generally limiting the accessible MS/MS techniques that can be used for peptide sequencing. For example, collision induced dissociation (CID) is readily amendable to the analysis of singly charged ions, but results in facile loss of phosphoric acid, precluding the localization of the PTM. Electron-based dissociation methods (e.g., electron capture dissociation, ECD) are well suited for PTM localization, but require multiply charged peptide cations to avoid neutralization during ECD. Conversely, phosphopeptides are readily ionized using MALDI in negative ion mode. If the precursor ions are first formed in negative ion mode, a gas-phase charge inversion ion/ion reaction could then be used to transform the phosphopeptide anions produced via MALDI into multiply charged cations that are well-suited for ECD. Herein we demonstrate a multistep workflow combining a charge inversion ion/ion reaction that first transforms MALDI-generated phosphopeptide monoanions into multiply charged cations, and then subjects these multiply charged phosphopeptide cations to ECD for sequence determination and phosphate bond localization.
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Affiliation(s)
- David V Donndelinger
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Tingting Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Troy R Scoggins
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Jonathan T Specker
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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2
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Sasiene ZJ, Jackson GP. Installation protocol for charge transfer dissociation mass spectrometry on ion trapping mass spectrometers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9750. [PMID: 38616287 DOI: 10.1002/rcm.9750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/29/2024] [Accepted: 03/16/2024] [Indexed: 04/16/2024]
Abstract
RATIONALE Charge transfer dissociation (CTD) is a novel fragmentation technique that demonstrates enhanced structural characterization for a wide variety of molecules compared to standard fragmentation techniques like collision-induced dissociation (CID). Alternative fragmentation techniques, such as electron transfer dissociation, electron capture dissociation, and ultraviolet photodissociation, also overcome many of the shortfalls of CID, but none of them are a silver bullet that can adequately characterize a wide variety of structures and charge states of target compounds. Given the diversity of structural classes and their occasional obstinance towards certain activation techniques, alternative fragmentation techniques are required that rely on novel or alternative modes of activation. METHODS Herein, we present a step-by-step protocol for the installation of CTD on a quadrupole ion trap mass spectrometer and best practices for optimizing the signal-to-noise ratio and acquisition times for CTD mass spectra. RESULTS In addition to two CTD installations in the Jackson laboratory, CTD has also been installed, and is currently in operation, on two 3D ion trap mass spectrometers in France: one in the laboratory of Dr. David Ropartz and Dr. Hélène Rogneaux at INRAE in Nantes, and the other in the laboratory of Dr. Jean-Yves Salpin at Université d'Évry Val-d'Essonne, part of the Paris-Saclay University system. CONCLUSIONS Here, we provide a visual protocol to help others accomplish the instrument modification.
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Affiliation(s)
- Zachary J Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Glen P Jackson
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, West Virginia, USA
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
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3
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Wang N, Dixit SM, Lee T, DeFiglia SA, Ruotolo BT, Håkansson K. Salt-Bridged Peptide Anion Gaseous Structures Enable Efficient Negative Ion Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:784-792. [PMID: 38489759 DOI: 10.1021/jasms.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
We previously discovered that electron attachment to gaseous peptide anions can occur within a relatively narrow electron energy range. The resulting charge-increased radical ions undergo dissociation analogous to conventional cation electron capture/transfer dissociation (ECD/ETD), thus enabling a novel tandem mass spectrometry (MS/MS) technique that we termed negative ion electron capture dissociation (niECD). We proposed that gaseous zwitterionic structures are required for niECD with electron capture either occurring at or being directed by a positively charged site. Here, we further evaluate this zwitterion mechanism by performing niECD of peptides derivatized to alter their ability to form zwitterionic gaseous structures. Introduction of a fixed positive charge tag, a highly basic guanidino group, or a highly acidic sulfonate group to promote zwitterionic structures in singly charged anions, rescued the niECD ability of a peptide refractory to niECD in its unmodified form. We also performed a systematic study of five sets of synthetic peptides with decreasing zwitterion propensity and found that niECD efficiency decreased accordingly, further supporting the zwitterion mechanism. However, traveling-wave ion mobility-mass spectrometry experiments, performed to gain further insight into the gas-phase structures of peptides showing high niECD efficiency, exhibited an inverse correlation between the orientationally averaged collision cross sections and niECD efficiency. These results indicate that compact salt-bridged structures are also a requirement for effective niECD.
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Affiliation(s)
- Ning Wang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Teresa Lee
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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5
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Agostini M, Traldi P, Hamdan M. Mass Spectrometry Investigation of Some ATP-Binding Cassette (ABC) Proteins. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:200. [PMID: 38399488 PMCID: PMC10890348 DOI: 10.3390/medicina60020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
Drug resistance remains one of the main causes of poor outcome in cancer therapy. It is also becoming evident that drug resistance to both chemotherapy and to antibiotics is driven by more than one mechanism. So far, there are at least eight recognized mechanisms behind such resistance. In this review, we choose to discuss one of these mechanisms, which is known to be partially driven by a class of transmembrane proteins known as ATP-binding cassette (ABC) transporters. In normal tissues, ABC transporters protect the cells from the toxic effects of xenobiotics, whereas in tumor cells, they reduce the intracellular concentrations of anticancer drugs, which ultimately leads to the emergence of multidrug resistance (MDR). A deeper understanding of the structures and the biology of these proteins is central to current efforts to circumvent resistance to both chemotherapy, targeted therapy, and antibiotics. Understanding the biology and the function of these proteins requires detailed structural and conformational information for this class of membrane proteins. For many years, such structural information has been mainly provided by X-ray crystallography and cryo-electron microscopy. More recently, mass spectrometry-based methods assumed an important role in the area of structural and conformational characterization of this class of proteins. The contribution of this technique to structural biology has been enhanced by its combination with liquid chromatography and ion mobility, as well as more refined labelling protocols and the use of more efficient fragmentation methods, which allow the detection and localization of labile post-translational modifications. In this review, we discuss the contribution of mass spectrometry to efforts to characterize some members of the ATP-binding cassette (ABC) proteins and why such a contribution is relevant to efforts to clarify the link between the overexpression of these proteins and the most widespread mechanism of chemoresistance.
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Affiliation(s)
| | - Pietro Traldi
- Corso Stati Uniti 4, Istituto di Ricerca Pediatrica Città della Speranza, 35100 Padova, Italy; (M.A.)
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Taha HB, Chawla E, Bitan G. IM-MS and ECD-MS/MS Provide Insight into Modulation of Amyloid Proteins Self-Assembly by Peptides and Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2066-2086. [PMID: 37607351 DOI: 10.1021/jasms.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Neurodegenerative proteinopathies are characterized by formation and deposition of misfolded, aggregated proteins in the nervous system leading to neuronal dysfunction and death. It is widely believed that metastable oligomers of the offending proteins, preceding the fibrillar aggregates found in the tissue, are the proximal neurotoxins. There are currently almost no disease-modifying therapies for these diseases despite an active pipeline of preclinical development and clinical trials for over two decades, largely because studying the metastable oligomers and their interaction with potential therapeutics is notoriously difficult. Mass spectrometry (MS) is a powerful analytical tool for structural investigation of proteins, including protein-protein and protein-ligand interactions. Specific MS tools have been useful in determining the composition and conformation of abnormal protein oligomers involved in proteinopathies and the way they interact with drug candidates. Here, we analyze critically the utilization of ion-mobility spectroscopy-MS (IM-MS) and electron-capture dissociation (ECD) MS/MS for analyzing the oligomerization and conformation of multiple amyloidogenic proteins. We also discuss IM-MS investigation of their interaction with two classes of compounds developed by our group over the last two decades: C-terminal fragments derived from the 42-residue form of amyloid β-protein (Aβ42) and molecular tweezers. Finally, we review the utilization of ECD-MS/MS for elucidating the binding sites of the ligands on multiple proteins. These approaches are readily applicable to future studies addressing similar questions and hold promise for facilitating the development of successful disease-modifying drugs against neurodegenerative proteinopathies.
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Affiliation(s)
- Hash Brown Taha
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Integrative Biology & Physiology, University of California Los Angeles, California 90095, United States
| | - Esha Chawla
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Brain Research Institute, University of California Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California Los Angeles, California 90095, United States
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7
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Deschamps E, Calabrese V, Schmitz I, Hubert-Roux M, Castagnos D, Afonso C. Advances in Ultra-High-Resolution Mass Spectrometry for Pharmaceutical Analysis. Molecules 2023; 28:molecules28052061. [PMID: 36903305 PMCID: PMC10003995 DOI: 10.3390/molecules28052061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Pharmaceutical analysis refers to an area of analytical chemistry that deals with active compounds either by themselves (drug substance) or when formulated with excipients (drug product). In a less simplistic way, it can be defined as a complex science involving various disciplines, e.g., drug development, pharmacokinetics, drug metabolism, tissue distribution studies, and environmental contamination analyses. As such, the pharmaceutical analysis covers drug development to its impact on health and the environment. Moreover, due to the need for safe and effective medications, the pharmaceutical industry is one of the most heavily regulated sectors of the global economy. For this reason, powerful analytical instrumentation and efficient methods are required. In the last decades, mass spectrometry has been increasingly used in pharmaceutical analysis both for research aims and routine quality controls. Among different instrumental setups, ultra-high-resolution mass spectrometry with Fourier transform instruments, i.e., Fourier transform ion cyclotron resonance (FTICR) and Orbitrap, gives access to valuable molecular information for pharmaceutical analysis. In fact, thanks to their high resolving power, mass accuracy, and dynamic range, reliable molecular formula assignments or trace analysis in complex mixtures can be obtained. This review summarizes the principles of the two main types of Fourier transform mass spectrometers, and it highlights applications, developments, and future perspectives in pharmaceutical analysis.
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Affiliation(s)
- Estelle Deschamps
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Valentina Calabrese
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100 Villeurbanne, France
| | - Isabelle Schmitz
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Marie Hubert-Roux
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Denis Castagnos
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- Correspondence:
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8
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Song Y, Song Q, Liu W, Li J, Tu P. High-confidence structural identification of metabolites relying on tandem mass spectrometry through isomeric identification: A tutorial. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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9
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Lignieres L, Legros V, Khelil M, Senecaut N, Lauber MA, Camadro JM, Chevreux G. Capillary liquid chromatography coupled with mass spectrometry for analysis of nanogram protein quantities on a wide-pore superficially porous particle column in top-down proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1214:123566. [PMID: 36516651 DOI: 10.1016/j.jchromb.2022.123566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
In top-down proteomics experiments, intact protein ions are subjected to gas-phase fragmentation for MS analysis without prior digestion. This approach is used to characterize post-translational modifications and clipped forms of proteins, avoids several "inference" problems associated with bottom-up proteomics, and is well suited to the study of proteoforms. In the past decade, top-down proteomics has progressed rapidly, taking advantage of MS instrumentation improvements and the efforts of pioneering groups working to improve sample handling and data processing. The potential of this technology has been established through its successful use in a number of important biological studies. However, many challenges remain to be addressed like improving protein separation capabilities such that it might become possible to expand the dynamic range of whole proteome analysis, address co-elution and convoluted mass spectral data, and aid final data processing from peak identification to quantification. In this study, we investigated the use of a wide-pore silica-based superficially porous media with a high coverage phenyl bonding, commercially packed into customized capillary columns for the purpose of top-down proteomics. Protein samples of increasing complexity were tested, namely subunit digests of a monoclonal antibody, components of purified histones and proteins extracted from eukaryotic ribosomes. High quality mass spectra were obtained from only 100 ng of protein sample while using difluoroacetic acid as an ion pairing agent to improve peak shape and chromatographic resolution. A peak width at half height of about 15 s for a 45 min gradient time was observed on a complex mixture giving an estimated peak capacity close to 100. Most importantly, efficient separations were obtained for highly diverse proteins and there was no need to make method specific adjustments, suggesting this is a highly versatile and easy-to-use setup for top-down proteomics.
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Affiliation(s)
- Laurent Lignieres
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Véronique Legros
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Manel Khelil
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Nicolas Senecaut
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Matthew A Lauber
- Waters Corporation, 34, Maple Street, Milford, MA 01757-3696, United States
| | | | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France.
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Qi Y, Fu P, Volmer DA. Analysis of natural organic matter via fourier transform ion cyclotron resonance mass spectrometry: an overview of recent non-petroleum applications. MASS SPECTROMETRY REVIEWS 2022; 41:647-661. [PMID: 32412674 DOI: 10.1002/mas.21634] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/22/2019] [Indexed: 06/11/2023]
Abstract
Among the different techniques for mass analysis, ultra-high-resolution Fourier transform ion cyclotron resonance (FTICR) is the method of choice for highly complex samples, as it offers unrivaled mass accuracy and resolving power, combined with a high degree of flexibility in hybrid instruments as well as for ion activation techniques. FTICR instruments are readily embraced by the biological and biomedical research communities and applied over a wide range of applications for the analysis of biomolecules such as carbohydrates, lipids, nucleic acids, and proteins. In the field of natural organic matter (NOM) analysis, petroleum-related studies currently dominate FTICR-MS applications. Recently, however, there is a growing interest in developing high-performance MS methods for the characterization of NOM samples from natural aquatic and terrestrial environments. Here, we present an overview of FTICR-MS techniques for complex, non-petroleum NOM samples, including data analysis and novel tandem mass spectrometry (MS/MS) methods for structural classifications. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd.
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Affiliation(s)
- Yulin Qi
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Pingqing Fu
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Dietrich A Volmer
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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12
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Mase C, Maillard JF, Paupy B, Hubert-Roux M, Afonso C, Giusti P. Speciation and Semiquantification of Nitrogen-Containing Species in Complex Mixtures: Application to Plastic Pyrolysis Oil. ACS OMEGA 2022; 7:19428-19436. [PMID: 35721918 PMCID: PMC9202011 DOI: 10.1021/acsomega.2c01114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Plastic pyrolysis oil is of particular interest for waste management in the current context of a circular economy. Due to their uncontrolled origin, these oils may contain significant amount of unwanted compounds such as nitrogen-containing species. These compounds are known to be catalyst poisons during refining processes. Therefore, the removal of these species is crucial, and their characterization from structural and quantification points of view is essential for this purpose. This study presents a method to specify and quantify nitrogen-containing classes in a plastic pyrolysis oil by direct infusion mass spectrometry. Two steps were used, namely structural characterization to select suitable standards and semiquantification. The structural speciation of nitrogen-containing compounds was first performed by electrospray ionization Fourier transform mass spectrometry, followed by tandem mass spectrometry using high-resolution mass isolation and infrared multiphoton dissociation fragmentation. A semiquantification is then performed by the standard addition method, which is very appropriate for such complex matrices. Aromatic cores such as quinoline and quinoxaline were evidenced for both N1 and N2 classes, allowing 2-methylquinoxaline and 2-butylquinoline to be proposed as standards for the semiquantification of N2- and N1-containing compounds, respectively. The amount of nitrogen detected from the sum of the individual species was consistent with the bulk analysis. The reported methodology can be applied to numerous other families of compounds in various other complex matrices.
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Affiliation(s)
- Charlotte Mase
- UMR
6014 et FR 3038, COBRA, INSA de Rouen, IRCOF, Université de
Rouen, Normandie Université, CNRS, Mont-Saint-Aignan, Rouen 76130, France
- TotalEnergies
OneTech, TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
- International
Joint Laboratory − iC2MC: Complex Matrices Molecular Characterization,
TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
| | - Julien Florent Maillard
- UMR
6014 et FR 3038, COBRA, INSA de Rouen, IRCOF, Université de
Rouen, Normandie Université, CNRS, Mont-Saint-Aignan, Rouen 76130, France
- International
Joint Laboratory − iC2MC: Complex Matrices Molecular Characterization,
TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
| | - Benoit Paupy
- TotalEnergies
OneTech, TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
- International
Joint Laboratory − iC2MC: Complex Matrices Molecular Characterization,
TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
| | - Marie Hubert-Roux
- UMR
6014 et FR 3038, COBRA, INSA de Rouen, IRCOF, Université de
Rouen, Normandie Université, CNRS, Mont-Saint-Aignan, Rouen 76130, France
- International
Joint Laboratory − iC2MC: Complex Matrices Molecular Characterization,
TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
| | - Carlos Afonso
- UMR
6014 et FR 3038, COBRA, INSA de Rouen, IRCOF, Université de
Rouen, Normandie Université, CNRS, Mont-Saint-Aignan, Rouen 76130, France
- International
Joint Laboratory − iC2MC: Complex Matrices Molecular Characterization,
TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
| | - Pierre Giusti
- UMR
6014 et FR 3038, COBRA, INSA de Rouen, IRCOF, Université de
Rouen, Normandie Université, CNRS, Mont-Saint-Aignan, Rouen 76130, France
- TotalEnergies
OneTech, TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
- International
Joint Laboratory − iC2MC: Complex Matrices Molecular Characterization,
TotalEnergies Research and Technology Gonfreville, BP 27, Harfleur 76700, France
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13
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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14
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Liu FC, Ridgeway ME, Winfred JSRV, Polfer NC, Lee J, Theisen A, Wootton CA, Park MA, Bleiholder C. Tandem-trapped ion mobility spectrometry/mass spectrometry coupled with ultraviolet photodissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9192. [PMID: 34498312 PMCID: PMC9195479 DOI: 10.1002/rcm.9192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 05/05/2023]
Abstract
RATIONALE Tandem-ion mobility spectrometry/mass spectrometry methods have recently gained traction for the structural characterization of proteins and protein complexes. However, ion activation techniques currently coupled with tandem-ion mobility spectrometry/mass spectrometry methods are limited in their ability to characterize structures of proteins and protein complexes. METHODS Here, we describe the coupling of the separation capabilities of tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS) with the dissociation capabilities of ultraviolet photodissociation (UVPD) for protein structure analysis. RESULTS We establish the feasibility of dissociating intact proteins by UV irradiation at 213 nm between the two TIMS devices in tTIMS/MS and at pressure conditions compatible with ion mobility spectrometry (2-3 mbar). We validate that the fragments produced by UVPD under these conditions result from a radical-based mechanism in accordance with prior literature on UVPD. The data suggest stabilization of fragment ions produced from UVPD by collisional cooling due to the elevated pressures used here ("UVnoD2"), which otherwise do not survive to detection. The data account for a sequence coverage for the protein ubiquitin comparable to recent reports, demonstrating the analytical utility of our instrument in mobility-separating fragment ions produced from UVPD. CONCLUSIONS The data demonstrate that UVPD carried out at elevated pressures of 2-3 mbar yields extensive fragment ions rich in information about the protein and that their exhaustive analysis requires IMS separation post-UVPD. Therefore, because UVPD and tTIMS/MS each have been shown to be valuable techniques on their own merit in proteomics, our contribution here underscores the potential of combining tTIMS/MS with UVPD for structural proteomics.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4389, USA
| | - Mark E. Ridgeway
- Bruker Daltonics, Inc., 40 Manning Rd., Billerica, MA 01821, USA
| | | | - Nicolas C. Polfer
- Athénée de Luxembourg, 24 boulevard Pierre Dupont, L-1430 Luxembourg, Grand-Duchy of Luxembourg
| | - Jusung Lee
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4389, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., 40 Manning Rd., Billerica, MA 01821, USA
- Correspondence to: ,
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4389, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4389, USA
- Correspondence to: ,
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15
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Baba T, Ryumin P, Duchoslav E, Chen K, Chelur A, Loyd B, Chernushevich I. Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1964-1975. [PMID: 34080873 DOI: 10.1021/jasms.0c00425] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report the progress on an electron-activated dissociation (EAD) device coupled to a quadrupole TOF mass spectrometer (QqTOF MS) developed in our group. This device features a new electron beam optics design allowing up to 100 times stronger electron currents in the reaction cell. The electron beam current reached the space-charge limit of 0.5 μA at near-zero electron kinetic energies. These advances enable fast and efficient dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. Tunable electron energy provides access to different fragmentation regimes: ECD, hot ECD, and electron-impact excitation of ions from organics (EIEIO). The efficiency of the device was tested on a wide range of precursor charge states. The EAD device was installed in a QqTOF MS employing a novel trap-and-release strategy facilitating spatial mass focusing of ions at the center of the TOF accelerator. This technique increased the sensitivity 6-10 times and allows for the first time comprehensive structural lipidomics on an LC time scale. The system was evaluated for other compound classes such as intact proteins and glycopeptides. Application of hot ECD for the analysis of glycopeptides resulted in rich fragmentation with predominantly peptide backbone fragments; however, glycan fragments attributed to the ECD process were also observed. A standard small protein ubiquitin (8.6 kDa) was sequenced with 90% cleavage coverage at spectrum accumulation times of 100 ms and 98% at 800 ms. Comparable cleavage coverage for a medium-size protein (carbonic anhydrase: 29 kDa) could be achieved, albeit with longer accumulation times.
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Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Pavel Ryumin
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Eva Duchoslav
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Keqin Chen
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Anjali Chelur
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Bill Loyd
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
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16
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Improved metabolite characterization by liquid chromatography – Tandem mass spectrometry through electron impact type fragments from adduct ions. Anal Chim Acta 2021; 1150:338207. [DOI: 10.1016/j.aca.2021.338207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 11/20/2022]
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17
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Banstola B, Murray KK. A nanoparticle co-matrix for multiple charging in matrix-assisted laser desorption ionization imaging of tissue. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35 Suppl 1:e8424. [PMID: 30822818 DOI: 10.1002/rcm.8424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/07/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE A two-component matrix of 2-nitrophloroglucinol (2-NPG) and silica nanoparticles was used for matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging of high-charge-state biomolecules in tissue. Potential advantages include increased effective mass range and efficiency of fragmentation. METHODS A mixture of 2-NPG matrix and silica nanoparticles was applied to cyrosectioned 10 μm thick mouse brain tissue. The mixture was pipetted onto the tissue for profiling and sprayed for tissue imaging. MALDI images were obtained under high vacuum in a commercial time-of-flight mass spectrometer. RESULTS The combined 2-NPG and nanoparticle matrix produced highly charged ions from tissue with high-vacuum MALDI. Nanoparticles of 20, 70, 400, and 1000 nm in diameter were tested, the 20 nm particles producing the highest charge states. Images of mouse brain tissue obtained from highly charged ions show similar spatial localization. CONCLUSIONS The combined 2-NPG and nanoparticle matrix produces highly charged ions from tissue through a mechanism that may rely on the high surface area of the particles which can dry the tissue, and their ability to bind analyte molecules thereby assisting in crystal formation and production of multiply charged ions on laser irradiation.
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Affiliation(s)
- Bijay Banstola
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
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18
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Barrientos RC, Zhang Q. Recent advances in the mass spectrometric analysis of glycosphingolipidome - A review. Anal Chim Acta 2020; 1132:134-155. [PMID: 32980104 PMCID: PMC7525043 DOI: 10.1016/j.aca.2020.05.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022]
Abstract
Aberrant expression of glycosphingolipids has been implicated in a myriad of diseases, but our understanding of the strucural diversity, spatial distribution, and biological function of this class of biomolecules remains limited. These challenges partly stem from a lack of sensitive tools that can detect, identify, and quantify glycosphingolipids at the molecular level. Mass spectrometry has emerged as a powerful tool poised to address most of these challenges. Here, we review the recent developments in analytical glycosphingolipidomics with an emphasis on sample preparation, mass spectrometry and tandem mass spectrometry-based structural characterization, label-free and labeling-based quantification. We also discuss the nomenclature of glycosphingolipids, and emerging technologies like ion mobility spectrometry in differentiation of glycosphingolipid isomers. The intrinsic advantages and shortcomings of each method are carefully critiqued in line with an individual's research goals. Finally, future perspectives on analytical sphingolipidomics are stated, including a need for novel and more sensive methods in isomer separation, low abundance species detection, and profiling the spatial distribution of glycosphingolipid molecular species in cells and tissues using imaging mass spectrometry.
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Affiliation(s)
- Rodell C Barrientos
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, 27412, United States; UNCG Center for Translational Biomedical Research, NC Research Campus, Kannapolis, NC, 28081, United States
| | - Qibin Zhang
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, 27412, United States; UNCG Center for Translational Biomedical Research, NC Research Campus, Kannapolis, NC, 28081, United States.
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19
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Bayat P, Lesage D, Cole RB. TUTORIAL: ION ACTIVATION IN TANDEM MASS SPECTROMETRY USING ULTRA-HIGH RESOLUTION INSTRUMENTATION. MASS SPECTROMETRY REVIEWS 2020; 39:680-702. [PMID: 32043643 DOI: 10.1002/mas.21623] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/23/2020] [Indexed: 05/16/2023]
Abstract
Tandem mass spectrometry involves isolation of specific precursor ions and their subsequent excitation through collision-, photon-, or electron-mediated activation techniques in order to induce unimolecular dissociation leading to formation of fragment ions. These powerful ion activation techniques, typically used in between mass selection and mass analysis steps for structural elucidation, have not only found a wide variety of analytical applications in chemistry and biology, but they have also been used to study the fundamental properties of ions in the gas phase. In this tutorial paper, a brief overview is presented of the theories that have been used to describe the activation of ions and their subsequent unimolecular dissociation. Acronyms of the presented techniques include CID, PQD, HCD, SORI, SID, BIRD, IRMPD, UVPD, EPD, ECD, EDD, ETD, and EID. The fundamental principles of these techniques are discussed in the context of their implementation on ultra-high resolution tandem mass spectrometers. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Parisa Bayat
- Faculté des Sciences et Ingénierie, Sorbonne Université, IPCM (UMR 8232), F-75252, Paris, France
| | - Denis Lesage
- Faculté des Sciences et Ingénierie, Sorbonne Université, IPCM (UMR 8232), F-75252, Paris, France
| | - Richard B Cole
- Faculté des Sciences et Ingénierie, Sorbonne Université, IPCM (UMR 8232), F-75252, Paris, France
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20
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Hanaichi S, Fujihara A. Identification and quantification of leucine and isoleucine residues in peptides using photoexcited tryptophan. Amino Acids 2020; 52:1107-1113. [PMID: 32710184 DOI: 10.1007/s00726-020-02875-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/19/2020] [Indexed: 10/23/2022]
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21
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Ochiai N, Murashima H, Fujihara A. Quantification of hydroxy groups in carbohydrates using gas-phase N2 adsorption. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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22
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Asakawa D, Takahashi H, Iwamoto S, Tanaka K. Characterization of Polyethers Using Tandem Mass Spectrometry with Hydrogen Abstraction Dissociation and Thermal Activation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:450-457. [PMID: 31951697 DOI: 10.1021/jasms.9b00148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The recently developed hydrogen radical-mediated fragmentation technique using an ion trap involving hydrogen attachment/abstraction dissociation-tandem mass spectrometry (HAD-MS/MS) was applied to the analysis of polyethylene glycol (PEG) and its derivatives. HAD was found to be initiated by hydrogen abstraction from carbon atoms in the polyether. Subsequently, the produced carbon-centered radical intermediates underwent radical-induced cleavage of their C-O bonds, with this process being facilitated by heating of the ion trap. The bond cleavage resulted in the formation of b fragments containing double bonds between carbon atoms. A counterpart c• alkoxy radical was discovered to be a fragile radical species. Consequently, c• underwent further radical-induced dissociation to produce small fragments during HAD-MS/MS with thermal activation. As a result, HAD-MS/MS with thermal activation through ion trap heating preferentially provided b fragments, facilitating identification of repeating units and individual end groups of the polyether analytes.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba Central 2, 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Hidenori Takahashi
- Koichi Tanaka Mass Spectrometry Research Laboratory , Shimadzu Corporation , 1 Nishinokyo-Kuwabaracho Nakagyo-ku , Kyoto 604-8511 , Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory , Shimadzu Corporation , 1 Nishinokyo-Kuwabaracho Nakagyo-ku , Kyoto 604-8511 , Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory , Shimadzu Corporation , 1 Nishinokyo-Kuwabaracho Nakagyo-ku , Kyoto 604-8511 , Japan
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23
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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24
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Foreman DJ, McLuckey SA. Recent Developments in Gas-Phase Ion/Ion Reactions for Analytical Mass Spectrometry. Anal Chem 2020; 92:252-266. [PMID: 31693342 PMCID: PMC6949396 DOI: 10.1021/acs.analchem.9b05014] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- David J Foreman
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907-2084 , United States
| | - Scott A McLuckey
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907-2084 , United States
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25
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Nguyen DT, Oki N, Fujihara A. Determination of enantiomeric excess of amino acids using photodissociation of cold gas-phase Na + -containing clusters. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:629-633. [PMID: 31094029 DOI: 10.1002/jms.4373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/15/2019] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Doan Thuc Nguyen
- Department of Chemistry, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Narumi Oki
- Department of Chemistry, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Akimasa Fujihara
- Department of Chemistry, Osaka Prefecture University, Osaka, 599-8531, Japan
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26
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Kuckova S, Cejnar P, Santrucek J, Hynek R. Characterization of proteins in cultural heritage using MALDI–TOF and LC–MS/MS mass spectrometric techniques. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
Identification of proteinaceous materials in artworks is of high interest to restorers-conservators, art historians and archaeologists, because it helps to shed light on the used painting techniques, to attribute unknown artworks, to make conclusions on prehistoric diets, etc. The chapter is devoted to the mass spectrometry instrumentation, evaluation of obtained data and it is showing several examples of the application of matrix-assisted laser desorption/ionization–time-of-flight and liquid chromatography–electrospray ionization–quadrupole–time-of-flight mass spectrometers on cultural heritage samples.
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27
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Iacobucci C, Schäfer M, Sinz A. Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis. MASS SPECTROMETRY REVIEWS 2019; 38:187-201. [PMID: 29660147 DOI: 10.1002/mas.21568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Free radical-initiated peptide sequencing (FRIPS) has recently been introduced as an analytical strategy to create peptide radical ions in a predictable and effective way by collisional activation of specifically modified peptides ions. FRIPS is based on the unimolecular dissociation of open-shell ions and yields fragments that resemble those obtained by electron capture dissociation (ECD) or electron transfer dissociation (ETD). In this review article, we describe the fundamentals of FRIPS and highlight its fruitful combination with chemical cross-linking/mass spectrometry (MS) as a highly promising option to derive complementary structural information of peptides and proteins. FRIPS does not only yield exhaustive sequence information of cross-linked peptides, but also defines the exact cross-linking sites of the connected peptides. The development of more advanced FRIPS cross-linkers that extend the FRIPS-based cross-linking/MS approach to the study of large protein assemblies and protein interaction networks can be eagerly anticipated.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), D-06120, Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Cologne, D-50939, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), D-06120, Germany
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28
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Potel CM, Lemeer S, Heck AJR. Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update. Anal Chem 2018; 91:126-141. [PMID: 30457327 PMCID: PMC6322148 DOI: 10.1021/acs.analchem.8b04746] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clement M Potel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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29
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Chen X, Wang Z, Wong YLE, Wu R, Zhang F, Chan TWD. Electron-ion reaction-based dissociation: A powerful ion activation method for the elucidation of natural product structures. MASS SPECTROMETRY REVIEWS 2018; 37:793-810. [PMID: 29603345 DOI: 10.1002/mas.21563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/12/2018] [Indexed: 05/16/2023]
Abstract
The structural elucidation of natural products (NPs) remains a challenge due to their structurally diversities and unpredictable functionalities, motifs, and scaffolds. Tandem mass spectrometry (MS/MS) is an effective method that assists the full elucidation of complicated NP structures. Ion activation methods play a key role in determining the fragmentation pathways and the structural information obtained from MS/MS. Electron-ion reaction-based dissociation (ExD) methods, including electron capture dissociation (ECD), electron transfer dissociation (ETD), electron-induced dissociation (EID), and electron detachment dissociation (EDD), can induce the breakage of specific chemical bonds and the generation of distinct fragment ions. This review article provides an overview of the mechanisms, instrumentation, and typical applications related to ExD MS/MS in the structural elucidation of NPs, primarly including lipids, oligosaccharides, glycoconjugates, metabolites, and pharmaceutical drugs. This work aims to reveal the capacity and potential of ExD mass spectrometry in analyzing NPs and consequently helping the NP communities to utilize the modern capabilities of MS/MS in the discovery and evaluation of novel NPs.
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Affiliation(s)
- Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Science), Shandong, P.R. China
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Ze Wang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Y-L Elaine Wong
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Ri Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Feng Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, P. R. China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
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30
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Morgan TE, Ellacott SH, Wootton CA, Barrow MP, Bristow AWT, Perrier S, O’Connor PB. Coupling Electron Capture Dissociation and the Modified Kendrick Mass Defect for Sequencing of a Poly(2-ethyl-2-oxazoline) Polymer. Anal Chem 2018; 90:11710-11715. [DOI: 10.1021/acs.analchem.8b03591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tomos E. Morgan
- Department of Chemistry, University of Warwick, Coventry, Midlands CV4 7AL, U.K
| | - Sean H. Ellacott
- Department of Chemistry, University of Warwick, Coventry, Midlands CV4 7AL, U.K
| | | | - Mark P. Barrow
- Department of Chemistry, University of Warwick, Coventry, Midlands CV4 7AL, U.K
| | | | - Sebastien Perrier
- Department of Chemistry, University of Warwick, Coventry, Midlands CV4 7AL, U.K
| | - Peter B. O’Connor
- Department of Chemistry, University of Warwick, Coventry, Midlands CV4 7AL, U.K
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31
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De Vijlder T, Valkenborg D, Lemière F, Romijn EP, Laukens K, Cuyckens F. A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation. MASS SPECTROMETRY REVIEWS 2018; 37:607-629. [PMID: 29120505 PMCID: PMC6099382 DOI: 10.1002/mas.21551] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 05/10/2023]
Abstract
The identification of unknown molecules has been one of the cornerstone applications of mass spectrometry for decades. This tutorial reviews the basics of the interpretation of electrospray ionization-based MS and MS/MS spectra in order to identify small-molecule analytes (typically below 2000 Da). Most of what is discussed in this tutorial also applies to other atmospheric pressure ionization methods like atmospheric pressure chemical/photoionization. We focus primarily on the fundamental steps of MS-based structural elucidation of individual unknown compounds, rather than describing strategies for large-scale identification in complex samples. We critically discuss topics like the detection of protonated and deprotonated ions ([M + H]+ and [M - H]- ) as well as other adduct ions, the determination of the molecular formula, and provide some basic rules on the interpretation of product ion spectra. Our tutorial focuses primarily on the fundamental steps of MS-based structural elucidation of individual unknown compounds (eg, contaminants in chemical production, pharmacological alteration of drugs), rather than describing strategies for large-scale identification in complex samples. This tutorial also discusses strategies to obtain useful orthogonal information (UV/Vis, H/D exchange, chemical derivatization, etc) and offers an overview of the different informatics tools and approaches that can be used for structural elucidation of small molecules. It is primarily intended for beginning mass spectrometrists and researchers from other mass spectrometry sub-disciplines that want to get acquainted with structural elucidation are interested in some practical tips and tricks.
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Affiliation(s)
- Thomas De Vijlder
- Pharmaceutical Development & Manufacturing Sciences (PDMS)Janssen Research & DevelopmentBeerseBelgium
| | - Dirk Valkenborg
- Interuniversity Institute for Biostatistics and Statistical BioinformaticsHasselt UniversityDiepenbeekBelgium
- Center for Proteomics (CFP)University of AntwerpAntwerpBelgium
- Flemish Institute for Technological Research (VITO)MolBelgium
| | - Filip Lemière
- Center for Proteomics (CFP)University of AntwerpAntwerpBelgium
- Department of Chemistry, Biomolecular and Analytical Mass SpectrometryUniversity of AntwerpAntwerpBelgium
| | - Edwin P. Romijn
- Pharmaceutical Development & Manufacturing Sciences (PDMS)Janssen Research & DevelopmentBeerseBelgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, Advanced Database Research and Modelling (ADReM)University of AntwerpAntwerpBelgium
- Biomedical Informatics Network Antwerp (Biomina)University of AntwerpAntwerpBelgium
| | - Filip Cuyckens
- Pharmacokinetics, Dynamics & MetabolismJanssen Research & DevelopmentBeerseBelgium
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Fujihara A, Okawa Y. Chiral and molecular recognition of monosaccharides by photoexcited tryptophan in cold gas-phase noncovalent complexes as a model for chemical evolution in interstellar molecular clouds. Anal Bioanal Chem 2018; 410:6279-6287. [DOI: 10.1007/s00216-018-1238-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/18/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022]
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Liang Z, McGuinness KN, Crespo A, Zhong W. Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:903-912. [PMID: 29372552 DOI: 10.1007/s13361-017-1855-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/23/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. Graphical Abstract ᅟ.
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Affiliation(s)
- Zhidan Liang
- Analytical Research and Development, MRL, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | - Kenneth N McGuinness
- Chemistry Modeling and Informatics, MRL, Merck and Co., Inc., Kenilworth, NJ, 07033, USA
| | - Alejandro Crespo
- Chemistry Modeling and Informatics, MRL, Merck and Co., Inc., Kenilworth, NJ, 07033, USA
| | - Wendy Zhong
- Analytical Research and Development, MRL, Merck and Co., Inc., Rahway, NJ, 07065, USA.
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34
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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35
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Fort KL, Cramer CN, Voinov VG, Vasil'ev YV, Lopez NI, Beckman JS, Heck AJR. Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer. J Proteome Res 2017; 17:926-933. [PMID: 29249155 PMCID: PMC5799867 DOI: 10.1021/acs.jproteome.7b00622] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As the application of mass spectrometry intensifies in scope and diversity, the need for advanced instrumentation addressing a wide variety of analytical needs also increases. To this end, many modern, top-end mass spectrometers are designed or modified to include a wider range of fragmentation technologies, for example, ECD, ETD, EThcD, and UVPD. Still, the majority of instrument platforms are limited to more conventional methods, such as CID and HCD. While these latter methods have performed well, the less conventional fragmentation methods have been shown to lead to increased information in many applications including middle-down proteomics, top-down proteomics, glycoproteomics, and disulfide bond mapping. We describe the modification of the popular Q Exactive Orbitrap mass spectrometer to extend its fragmentation capabilities to include ECD. We show that this modification allows ≥85% matched ion intensity to originate from ECD fragment ion types as well as provides high sequence coverage (≥60%) of intact proteins and high fragment identification rates with ∼70% of ion signals matched. Finally, the ECD implementation promotes selective disulfide bond dissociation, facilitating the identification of disulfide-linked peptide conjugates. Collectively, this modification extends the capabilities of the Q Exactive Orbitrap mass spectrometer to a range of new applications.
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Affiliation(s)
- Kyle L Fort
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center , Utrecht 3584 CH, The Netherlands
| | - Christian N Cramer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Utrecht 3584 CH, The Netherlands.,Protein Engineering, Global Research Novo Nordisk A/S , Novo Nordisk Park, 2760 Måløv, Denmark.,Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Valery G Voinov
- e-MSion, Inc. , 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Yury V Vasil'ev
- e-MSion, Inc. , 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Nathan I Lopez
- e-MSion, Inc. , 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
| | - Joseph S Beckman
- e-MSion, Inc. , 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center , Utrecht 3584 CH, The Netherlands
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36
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Qi Y, Müller MJ, Volmer DA. Activation of Reactive MALDI Adduct Ions Enables Differentiation of Dihydroxylated Vitamin D Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2532-2537. [PMID: 28842822 DOI: 10.1007/s13361-017-1775-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Vitamin D compounds are secosteroids, which are best known for their role in bone health. More recent studies have shown that vitamin D metabolites and catabolites such as dihydroxylated species (e.g., 1,25- and 24,25-dihydroxyvitamin D3) play key roles in the pathologies of various diseases. Identification of these isomers by mass spectrometry is challenging and currently relies on liquid chromatography, as the isomers exhibit virtually identical product ion spectra under collision induced dissociation conditions. Here, we developed a simple MALDI-CID method that utilizes ion activation of reactive analyte/matrix adducts to distinguish isomeric dihydroxyvitamin D3 species, without the need for chromatography separation or chemical derivatization techniques. Specifically, reactive 1,5-diaminonaphthalene adducts of dihydroxyvitamin D3 compounds formed during MADI were activated and specific cleavages in the secosteroid's backbone structure were achieved that produced isomer-diagnostic fragment ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Yulin Qi
- Institute of Bioanalytical Chemistry, Saarland University, D-66123, Saarbrücken, Germany
| | - Miriam J Müller
- Institute of Bioanalytical Chemistry, Saarland University, D-66123, Saarbrücken, Germany
| | - Dietrich A Volmer
- Institute of Bioanalytical Chemistry, Saarland University, D-66123, Saarbrücken, Germany.
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37
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Alexander WM, Ficarro SB, Adelmant G, Marto JA. multiplierz
v2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700091] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/25/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
Affiliation(s)
- William M. Alexander
- Department of Cancer Biology and Blais Proteomics Center; Dana-Farber Cancer Institute; Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; Boston MA USA
| | - Scott B. Ficarro
- Department of Cancer Biology and Blais Proteomics Center; Dana-Farber Cancer Institute; Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; Boston MA USA
| | - Guillaume Adelmant
- Department of Cancer Biology and Blais Proteomics Center; Dana-Farber Cancer Institute; Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; Boston MA USA
| | - Jarrod A. Marto
- Department of Cancer Biology and Blais Proteomics Center; Dana-Farber Cancer Institute; Boston MA USA
- Department of Oncologic Pathology; Dana-Farber Cancer Institute; Boston MA USA
- Department of Pathology; Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
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38
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Quick MM, Mehaffey MR, Johns RW, Parker WR, Brodbelt JS. SITS Derivatization of Peptides to Enhance 266 nm Ultraviolet Photodissociation (UVPD). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1462-1472. [PMID: 28315237 DOI: 10.1007/s13361-017-1650-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 06/06/2023]
Abstract
N-terminal derivatization of peptides with the chromogenic reagent 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid (SITS) is demonstrated to enhance the efficiency of 266 nm ultraviolet photodissociation (UVPD). Attachment of the chromophore results in a mass shift of 454 Da and provides significant gains in the number and abundances of diagnostic fragment ions upon UVPD. Activation of SITS-tagged peptides with 266 nm UVPD leads to many fragment ions akin to the a/b/y ions commonly produced by CID, along with other sequence ions (c, x, and z) typically accessed through higher energy pathways. Extreme bias towards C-terminal fragment ions is observed upon activation of SITS-tagged peptides using multiple 266 nm laser pulses. Due to the high reaction efficiency of the isothiocyanate coupling to the N-terminus of peptides, we demonstrate the ability to adapt this strategy to a high-throughput LC-MS/MS workflow with 266 nm UVPD. Graphical Abstract ᅟ.
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Affiliation(s)
- M Montana Quick
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Robert W Johns
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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Baba T, Campbell JL, Le Blanc JCY, Baker PRS, Hager JW, Thomson BA. Development of a Branched Radio-Frequency Ion Trap for Electron Based Dissociation and Related Applications. Mass Spectrom (Tokyo) 2017; 6:A0058. [PMID: 28630811 PMCID: PMC5469727 DOI: 10.5702/massspectrometry.a0058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/02/2017] [Indexed: 11/23/2022] Open
Abstract
Collision-induced dissociation (CID) is the most common tool for molecular analysis in mass spectrometry to date. However, there are difficulties associated with many applications because CID does not provide sufficient information to permit details of the molecular structures to be elucidated, including post-translational-modifications in proteomics, as well as isomer differentiation in metabolomics and lipidomics. To face these challenges, we are developing fast electron-based dissociation devices using a novel radio-frequency ion trap (i.e., a branched ion trap). These devices have the ability to perform electron capture dissociation (ECD) on multiply protonated peptide/proteins; in addition, the electron impact excitation of ions from organics (EIEIO) can be also performed on singly charged molecules using such a device. In this article, we review the development of this technology, in particular on how reaction speed for EIEIO analyses on singly charged ions can be improved. We also overview some unique, recently reported applications in both lipidomics and glycoproteomics.
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40
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Qi Y, Volmer DA. Structural analysis of small to medium-sized molecules by mass spectrometry after electron-ion fragmentation (ExD) reactions. Analyst 2016; 141:794-806. [PMID: 26725919 DOI: 10.1039/c5an02171e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron capture dissociation (ECD) is a tandem mass spectrometry (MS/MS) method that utilizes the interaction of ions and electrons. Its unique ability to preserve labile bonds distinguishes it from conventional threshold-based MS/MS methods, the most important of which is collision-induced dissociation (CID). During the last decade, ECD has opened up several new venues in protein analyses, for example top-down sequencing, identification of post-translational modifications, and characterization of protein-protein interactions. In recent years, a number of related dissociation techniques, so-called ExD techniques, particularly electron transfer dissociation (ETD), electron detachment dissociation (EDD), electron induced dissociation (EID), and negative electron transfer dissociation (NETD), have emerged and have extended the application range of ion-electron dissociations further. Importantly, ExD techniques have been applied beyond protein analyses, which is the focus of the current paper. This short introduction describes the application of ExD to small and medium-sized molecules and reviews important applications to natural products, biomedical compounds, synthetic molecules, crude oils, and environmental toxins.
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Affiliation(s)
- Yulin Qi
- Institute of Bioanalytical Chemistry, Saarland University, 66123 Saarbrücken, Germany.
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