1
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Renzone G, Arena S, Scaloni A. Cross-linking reactions in food proteins and proteomic approaches for their detection. MASS SPECTROMETRY REVIEWS 2022; 41:861-898. [PMID: 34250627 DOI: 10.1002/mas.21717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Various protein cross-linking reactions leading to molecular polymerization and covalent aggregates have been described in processed foods. They are an undesired side effect of processes designed to reduce bacterial load, extend shelf life, and modify technological properties, as well as being an expected result of treatments designed to modify raw material texture and function. Although the formation of these products is known to affect the sensory and technological properties of foods, the corresponding cross-linking reactions and resulting protein polymers have not yet undergone detailed molecular characterization. This is essential for describing how their generation can be related to food processing conditions and quality parameters. Due to the complex structure of cross-linked species, bottom-up proteomic procedures developed to characterize various amino acid modifications associated with food processing conditions currently offer a limited molecular description of bridged peptide structures. Recent progress in cross-linking mass spectrometry for the topological characterization of protein complexes has facilitated the development of various proteomic methods and bioinformatic tools for unveiling bridged species, which can now also be used for the detailed molecular characterization of polymeric cross-linked products in processed foods. We here examine their benefits and limitations in terms of evaluating cross-linked food proteins and propose future scenarios for application in foodomics. They offer potential for understanding the protein cross-linking formation mechanisms in processed foods, and how the inherent beneficial properties of treated foodstuffs can be preserved or enhanced.
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Affiliation(s)
- Giovanni Renzone
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Simona Arena
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
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2
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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3
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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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4
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Jang HS, Gu X, Cooley RB, Porter JJ, Henson RL, Willi T, DiDonato JA, Hazen SL, Mehl RA. Efficient Site-Specific Prokaryotic and Eukaryotic Incorporation of Halotyrosine Amino Acids into Proteins. ACS Chem Biol 2020; 15:562-574. [PMID: 31994864 DOI: 10.1021/acschembio.9b01026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-translational modifications (PTMs) of protein tyrosine (Tyr) residues can serve as a molecular fingerprint of exposure to distinct oxidative pathways and are observed in abnormally high abundance in the majority of human inflammatory pathologies. Reactive oxidants generated during inflammation include hypohalous acids and nitric oxide-derived oxidants, which oxidatively modify protein Tyr residues via halogenation and nitration, respectively, forming 3-chloroTyr, 3-bromoTyr, and 3-nitroTyr. Traditional methods for generating oxidized or halogenated proteins involve nonspecific chemical reactions that result in complex protein mixtures, making it difficult to ascribe observed functional changes to a site-specific PTM or to generate antibodies sensitive to site-specific oxidative PTMs. To overcome these challenges, we generated a system to efficiently and site-specifically incorporate chloroTyr, bromoTyr, and iodoTyr, and to a lesser extent nitroTyr, into proteins in both bacterial and eukaryotic expression systems, relying on a novel amber stop codon-suppressing mutant synthetase (haloTyrRS)/tRNA pair derived from the Methanosarcina barkeri pyrrolysine synthetase system. We used this system to study the effects of oxidation on HDL-associated protein paraoxonase 1 (PON1), an enzyme with important antiatherosclerosis and antioxidant functions. PON1 forms a ternary complex with HDL and myeloperoxidase (MPO) in vivo. MPO oxidizes PON1 at tyrosine 71 (Tyr71), resulting in a loss of PON1 enzymatic function, but the extent to which chlorination or nitration of Tyr71 contributes to this loss of activity is unclear. To better understand this biological process and to demonstrate the utility of our GCE system, we generated PON1 site-specifically modified at Tyr71 with chloroTyr and nitroTyr in Escherichia coli and mammalian cells. We demonstrate that either chlorination or nitration of Tyr71 significantly reduces PON1 enzymatic activity. This tool for site-specific incorporation of halotyrosine will be critical to understanding how exposure of proteins to hypohalous acids at sites of inflammation alters protein function and cellular physiology. In addition, it will serve as a powerful tool for generating antibodies that can recognize site-specific oxidative PTMs.
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Affiliation(s)
- Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Xiaodong Gu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Joseph J. Porter
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Rachel L. Henson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Taylor Willi
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Joseph A. DiDonato
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
- Center for Microbiome & Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Stanley L. Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
- Center for Microbiome & Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
- Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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5
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Nybo T, Davies MJ, Rogowska-Wrzesinska A. Analysis of protein chlorination by mass spectrometry. Redox Biol 2019; 26:101236. [PMID: 31181457 PMCID: PMC6557747 DOI: 10.1016/j.redox.2019.101236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 01/04/2023] Open
Abstract
Chlorination of tyrosine is a commonly known effect/consequence of myeloperoxidase activity at sites of inflammation, and detection of 3-chlorotyrosine has been used as biomarker for inflammatory diseases. However, few studies have addressed site specific chlorination in proteins, and no methods for large scale chloroproteomics studies have yet been published. In this study, we present an optimized mass spectrometry based protocol to identify and quantify chlorinated peptides from single proteins modified by HOCl (100 and 500 μM, within estimated pathophysiological levels), at a high level of sensitivity and accuracy. Particular emphasis was placed on 1) sensitive and precise detection of modification sites, 2) the avoidance of loss or artefactual creation of modifications, 3) accurate quantification of peptide abundance and reduction of missing values problem, 4) monitoring the dynamics of modification in samples exposed to different oxidant concentrations and 5) development of guidelines for verification of chlorination sites assignment. A combination of an optimised sample preparation protocol, and improved data analysis approaches have allowed identification of 33 and 15 chlorination sites in laminin and fibronectin, respectively, reported in previous manuscripts [1,2]. The method was subsequently tested on murine basement membrane extract, which contains high levels of laminin in a complex mixture. Here, 10 of the major chlorination sites in laminin were recapitulated, highlighting the utility of the method in detecting damage in complex samples. An optimized mass spectrometry method is presented to detect protein chlorination. Reduction and alkylation leads to loss of chlorinated residues. Identification of modification sites in fibronectin and laminin induced by HOCl. Quantification of relative site occupancy (RSO) of chlorinated residues. Largest chloroproteomics dataset to date.
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Affiliation(s)
- Tina Nybo
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark; Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
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6
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Sánchez-Illana Á, Parra-Llorca A, Escuder-Vieco D, Pallás-Alonso CR, Cernada M, Gormaz M, Vento M, Kuligowski J. Biomarkers of oxidative stress derived damage to proteins and DNA in human breast milk. Anal Chim Acta 2018. [DOI: 10.1016/j.aca.2018.01.054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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7
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Sharma A, Kumar V, Chatrath A, Dev A, Prasad R, Sharma AK, Tomar S, Kumar P. In vitro metal catalyzed oxidative stress in DAH7PS: Methionine modification leads to structure destabilization and induce amorphous aggregation. Int J Biol Macromol 2018; 106:1089-1106. [DOI: 10.1016/j.ijbiomac.2017.08.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 11/28/2022]
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8
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Pilo AL, Zhao F, McLuckey SA. Gas-Phase Oxidation via Ion/Ion Reactions: Pathways and Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:991-1004. [PMID: 28050870 PMCID: PMC5438755 DOI: 10.1007/s13361-016-1554-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/31/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
Here, we provide an overview of pathways available upon the gas-phase oxidation of peptides and DNA via ion/ion reactions and explore potential applications of these chemistries. The oxidation of thioethers (i.e., methionine residues and S-alkyl cysteine residues), disulfide bonds, S-nitrosylated cysteine residues, and DNA to the [M+H+O]+ derivative via ion/ion reactions with periodate and peroxymono-sulfate anions is demonstrated. The oxidation of neutral basic sites to various oxidized structures, including the [M+H+O]+, [M-H]+, and [M-H-NH3]+ species, via ion/ion reactions is illustrated and the oxidation characteristics of two different oxidizing reagents, periodate and persulfate anions, are compared. Lastly, the highly efficient generation of molecular radical cations via ion/ion reactions with sulfate radical anion is summarized. Activation of the newly generated molecular radical peptide cations results in losses of various neutral side chains, several of which generate dehydroalanine residues that can be used to localize the amino acid from which the dehydroalanine was generated. The chemistries presented herein result in a diverse range of structures that can be used for a variety of applications, including the identification and localization of S-alkyl cysteine residues, the oxidative cleavage of disulfide bonds, and the generation of molecular radical cations from even-electron doubly protonated peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Feifei Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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9
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Cháfer-Pericás C, Stefanovic V, Sánchez-Illana Á, Escobar J, Cernada M, Cubells E, Núñez-Ramiro A, Andersson S, Vento M, Kuligowski J. Novel biomarkers in amniotic fluid for early assessment of intraamniotic infection. Free Radic Biol Med 2015; 89:734-40. [PMID: 26456057 DOI: 10.1016/j.freeradbiomed.2015.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 10/22/2022]
Abstract
Intra-amniotic infection/inflammation (IAI) is associated with preterm birth, short and long-term adverse clinical outcomes and oxidative stress. The diagnosis of IAI is based on histological and clinical findings; however, often these results are unspecific. Therefore, efforts have been directed towards validating reliable methods for patients lacking overt clinical symptoms. In this study, amniotic fluid (AF) samples were prospectively collected from 23 women grouped into two categories (with or without IAI) following clinical, microbiological and histological criteria. AFs were analyzed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) for the determination of the following biomarkers: oxidized and nitrated tyrosines (Tyr), 8-hydroxy-2'-deoxyguanosine (8OHdG), oxidized glutathione (GSSG) and glutathione sulfonamide (GSA). 3-NO2-Tyrosine (3NO2-Tyr) and GSSG concentrations in AF were not identified as significantly relevant biomarkers in the presence of IAI. However, inflammatory biomarkers such as GSA (p=0.002) and 3-Chloro-Tyrosine [3Cl-Tyr (p=0.049)], and oxidative stress biomarker 8OHdG (p=0.021) were significantly increased in AF with IAI as compared to normal controls. Biomarkers of inflammation and oxidative stress determined in AF samples could represent a new approach towards an early diagnosis of IAI and subsequent chorioamnionitis in the clinical setting.
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Affiliation(s)
- Consuelo Cháfer-Pericás
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain
| | - Vedran Stefanovic
- Department of Obstetrics and Gynecology, Fetomaternal Medical Center, Helsinki University Central Hospital and University of Helsinki, Haartmaninkatu 2, 00029, Helsinki, Finland
| | - Ángel Sánchez-Illana
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain
| | - Javier Escobar
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain
| | - María Cernada
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain
| | - Elena Cubells
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain
| | - Antonio Núñez-Ramiro
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain
| | - Sture Andersson
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 11, PO Box 281, 00029, Helsinki, Finland
| | - Máximo Vento
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain; Division of Neonatology, University & Polytechnic Hospital La Fe, Avenida Fernando Abril Martorell 106; 46026 Valencia, Spain.
| | - Julia Kuligowski
- Neonatal Research Unit, Health Research Institute La Fe, Valencia, Avenida Fernando Abril Martorell 106; 46026 Valencia; Spain.
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10
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Kostyukevich Y, Zhdanova E, Kononikhin A, Popov I, Kukaev E, Nikolaev E. Observation of the multiple halogenation of peptides in the electrospray ionization source. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:899-905. [PMID: 26349644 DOI: 10.1002/jms.3599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/11/2015] [Accepted: 03/27/2015] [Indexed: 06/05/2023]
Abstract
The chlorination of peptides and proteins is an important posttranslational modification, which is a physiological signature of an enzyme myeloperoxidase and can serve as a potential biomarker of some diseases (Parkinson's disease, Alzheimer's disease, etc.). The quantification of the chlorinated peptides has been very challenging in part due to their low levels and artifacts associated with sample preparation. One of the most convenient and promising methods to detect and investigate the chlorinated peptides in the biological samples is the electrospray ionization (ESI) mass spectrometry coupled to the fragmentation techniques (collision-induced dissociation and electron capture dissociation/electron transfer dissociation). We have shown that if the chlorine anions are present in the solution, then the peptide can undergo the chlorination during the ESI ionization. The effect was found to depend on the values of electric potentials of metal parts of the ESI interface. It was found that the grounding of ESI syringe results in the formation of an additional electric loop leading to the electrolytic production of Cl2 and as a consequence the hypochlorous acid inside the ESI needle. Hypochlorous acid reacts with amino groups of peptides and proteins producing chloramine or causing the protein cleavage. In the paper, it is shown on the example of the solution of the several peptides in the presence of HCl that by manipulating the ESI syringe potential, it is possible to create complexes with up to five Cl atoms for sample peptides when the ESI is operated in the positive mode.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Ekaterina Zhdanova
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
| | - Eugene Kukaev
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
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11
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Tveen-Jensen K, Gesellchen F, Wilson R, Spickett CM, Cooper JM, Pitt AR. Interfacing low-energy SAW nebulization with Liquid Chromatography-Mass Spectrometry for the analysis of biological samples. Sci Rep 2015; 5:9736. [PMID: 25978651 PMCID: PMC4432867 DOI: 10.1038/srep09736] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/10/2015] [Indexed: 01/29/2023] Open
Abstract
Soft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid, and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.
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Affiliation(s)
- Karina Tveen-Jensen
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Frank Gesellchen
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Rab Wilson
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Jonathan M Cooper
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
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12
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Trnková L, Dršata J, Boušová I. Oxidation as an important factor of protein damage: Implications for Maillard reaction. J Biosci 2015; 40:419-39. [DOI: 10.1007/s12038-015-9523-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Verrastro I, Pasha S, Jensen KT, Pitt AR, Spickett CM. Mass spectrometry-based methods for identifying oxidized proteins in disease: advances and challenges. Biomolecules 2015; 5:378-411. [PMID: 25874603 PMCID: PMC4496678 DOI: 10.3390/biom5020378] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/20/2015] [Accepted: 03/23/2015] [Indexed: 01/02/2023] Open
Abstract
Many inflammatory diseases have an oxidative aetiology, which leads to oxidative damage to biomolecules, including proteins. It is now increasingly recognized that oxidative post-translational modifications (oxPTMs) of proteins affect cell signalling and behaviour, and can contribute to pathology. Moreover, oxidized proteins have potential as biomarkers for inflammatory diseases. Although many assays for generic protein oxidation and breakdown products of protein oxidation are available, only advanced tandem mass spectrometry approaches have the power to localize specific oxPTMs in identified proteins. While much work has been carried out using untargeted or discovery mass spectrometry approaches, identification of oxPTMs in disease has benefitted from the development of sophisticated targeted or semi-targeted scanning routines, combined with chemical labeling and enrichment approaches. Nevertheless, many potential pitfalls exist which can result in incorrect identifications. This review explains the limitations, advantages and challenges of all of these approaches to detecting oxidatively modified proteins, and provides an update on recent literature in which they have been used to detect and quantify protein oxidation in disease.
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Affiliation(s)
- Ivan Verrastro
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Sabah Pasha
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Karina Tveen Jensen
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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14
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Houée-Lévin C, Bobrowski K, Horakova L, Karademir B, Schöneich C, Davies MJ, Spickett CM. Exploring oxidative modifications of tyrosine: An update on mechanisms of formation, advances in analysis and biological consequences. Free Radic Res 2015; 49:347-73. [DOI: 10.3109/10715762.2015.1007968] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Anjum NA, Sofo A, Scopa A, Roychoudhury A, Gill SS, Iqbal M, Lukatkin AS, Pereira E, Duarte AC, Ahmad I. Lipids and proteins--major targets of oxidative modifications in abiotic stressed plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:4099-121. [PMID: 25471723 DOI: 10.1007/s11356-014-3917-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/24/2014] [Indexed: 05/18/2023]
Abstract
Stress factors provoke enhanced production of reactive oxygen species (ROS) in plants. ROS that escape antioxidant-mediated scavenging/detoxification react with biomolecules such as cellular lipids and proteins and cause irreversible damage to the structure of these molecules, initiate their oxidation, and subsequently inactivate key cellular functions. The lipid- and protein-oxidation products are considered as the significant oxidative stress biomarkers in stressed plants. Also, there exists an abundance of information on the abiotic stress-mediated elevations in the generation of ROS, and the modulation of lipid and protein oxidation in abiotic stressed plants. However, the available literature reflects a wide information gap on the mechanisms underlying lipid- and protein-oxidation processes, major techniques for the determination of lipid- and protein-oxidation products, and on critical cross-talks among these aspects. Based on recent reports, this article (a) introduces ROS and highlights their relationship with abiotic stress-caused consequences in crop plants, (b) examines critically the various physiological/biochemical aspects of oxidative damage to lipids (membrane lipids) and proteins in stressed crop plants, (c) summarizes the principles of current technologies used to evaluate the extent of lipid and protein oxidation, (d) synthesizes major outcomes of studies on lipid and protein oxidation in plants under abiotic stress, and finally, (e) considers a brief cross-talk on the ROS-accrued lipid and protein oxidation, pointing to the aspects unexplored so far.
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Affiliation(s)
- Naser A Anjum
- CESAM-Centre for Environmental & Marine Studies and Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal,
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Li W, Kerwin JL, Schiel J, Formolo T, Davis D, Mahan A, Benchaar SA. Structural Elucidation of Post-Translational Modifications in Monoclonal Antibodies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Wenzhou Li
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - James L. Kerwin
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - John Schiel
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Trina Formolo
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Darryl Davis
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Andrew Mahan
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Sabrina A. Benchaar
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
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Sadowska-Bartosz I, Ott C, Grune T, Bartosz G. Posttranslational protein modifications by reactive nitrogen and chlorine species and strategies for their prevention and elimination. Free Radic Res 2014; 48:1267-84. [PMID: 25119970 DOI: 10.3109/10715762.2014.953494] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins are subject to various posttranslational modifications, some of them being undesired from the point of view of metabolic efficiency. Prevention of such modifications is expected to provide new means of therapy of diseases and decelerate the process of aging. In this review, modifications of proteins by reactive nitrogen species and reactive halogen species, is briefly presented and means of prevention of these modifications and their sequelae are discussed, including the denitrase activity and inhibitors of myeloperoxidase.
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Affiliation(s)
- I Sadowska-Bartosz
- Department of Biochemistry and Cell Biology, University of Rzeszów , Rzeszów , Poland
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18
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Arena S, Salzano AM, Renzone G, D'Ambrosio C, Scaloni A. Non-enzymatic glycation and glycoxidation protein products in foods and diseases: an interconnected, complex scenario fully open to innovative proteomic studies. MASS SPECTROMETRY REVIEWS 2014; 33:49-77. [PMID: 24114996 DOI: 10.1002/mas.21378] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/09/2013] [Accepted: 03/09/2013] [Indexed: 06/02/2023]
Abstract
The Maillard reaction includes a complex network of processes affecting food and biopharmaceutical products; it also occurs in living organisms and has been strictly related to cell aging, to the pathogenesis of several (chronic) diseases, such as diabetes, uremia, cataract, liver cirrhosis and various neurodegenerative pathologies, as well as to peritoneal dialysis treatment. Dozens of compounds are involved in this process, among which a number of protein-adducted derivatives that have been simplistically defined as early, intermediate and advanced glycation end-products. In the last decade, various bottom-up proteomic approaches have been successfully used for the identification of glycation/glycoxidation protein targets as well as for the characterization of the corresponding adducts, including assignment of the modified amino acids. This article provides an updated overview of the mass spectrometry-based procedures developed to this purpose, emphasizing their partial limits with respect to current proteomic approaches for the analysis of other post-translational modifications. These limitations are mainly related to the concomitant sheer diversity, chemical complexity, and variable abundance of the various derivatives to be characterized. Some challenges to scientists are finally proposed for future proteomic investigations to solve main drawbacks in this research field.
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Affiliation(s)
- Simona Arena
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy
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19
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Silva AMN, Vitorino R, Domingues MRM, Spickett CM, Domingues P. Post-translational modifications and mass spectrometry detection. Free Radic Biol Med 2013; 65:925-941. [PMID: 24002012 DOI: 10.1016/j.freeradbiomed.2013.08.184] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/22/2013] [Accepted: 08/24/2013] [Indexed: 12/14/2022]
Abstract
In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.
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Affiliation(s)
- André M N Silva
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M Rosário M Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7 ET, United Kingdom
| | - Pedro Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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20
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Spickett CM, Reis A, Pitt AR. Use of narrow mass-window, high-resolution extracted product ion chromatograms for the sensitive and selective identification of protein modifications. Anal Chem 2013; 85:4621-7. [PMID: 23534669 DOI: 10.1021/ac400131f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein modifications, including oxidative modifications, glycosylations, and oxidized lipid-protein adducts, are becoming increasingly important as biomarkers and in understanding disease etiology. There has been a great deal of interest in mapping these on Apo B100 from low density lipoprotein (LDL). We have used extracted ion chromatograms of product ions generated using a very narrow mass window from high-resolution tandem mass spectrometric data collected on a rapid scanning quadrupole time-of-flight (QTOF) instrument, to selectively and sensitively detect modified peptides and identify the site and nature of a number of protein modifications in parallel. We have demonstrated the utility of this method by characterizing for the first time oxidized phospholipid adducts to LDL and human serum albumin and for the detection of glycosylation and kynurenin formation from the oxidation of tryptophan residues in LDL.
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Affiliation(s)
- Corinne M Spickett
- Life and Health Sciences, Aston University, Aston Triangle, Birmingham, United Kingdom
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21
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Tveen-Jensen K, Reis A, Mouls L, Pitt AR, Spickett CM. Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples. J Proteomics 2013; 92:71-9. [PMID: 23603107 DOI: 10.1016/j.jprot.2013.03.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/29/2013] [Accepted: 03/31/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS(3) ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run.This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. BIOLOGICAL SIGNIFICANCE The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions.
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Abstract
Background Fungal allergens are ubiquitous; however, little progress has been made understanding fungal allergenic material removal from indoor environments. Purpose We investigated removal of environmental allergenic material derived from Alternaria and Cladosporium using sodium hypochlorite in vivo and in vitro. Methods Freeze dried allergen extract from Alternaria alternata and Cladosporium herbarum was treated with hypochlorite concentrations of 322, 88, 38, 16, 3, 0.3, and 0 mM, respectively. Remaining native allergenic material was quantified using enzyme immunoassay and remaining viable fungal material was evaluated. Results The results of treating Alternaria or Cladosporium extract with sodium hypochlorite are immediate and obvious. Concentrations greater than 100 mM remove color and concentrations between 100 and 38 mM partially uncolored the extract. Immunoassay for total antigenic and allergenic material remaining after treatment with sodium hypochlorite including 2 concentrations recommended for killing fungus confirmed a general destruction of antigenic and allergenic material at concentrations of 38 mM or greater. Conclusions This work confirms the ability of solutions of sodium hypochlorite to denature fungal allergenic material from common outdoor and indoor fungi A. alternata and C. herbarum. Destruction of recognized antigenic and allergenic epitopes occurs at hypochlorite concentrations commonly used for household cleaning.
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Bachi A, Dalle-Donne I, Scaloni A. Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises. Chem Rev 2012. [DOI: 10.1021/cr300073p] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Angela Bachi
- Biological Mass Spectrometry Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
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Zhang Z, Shen J, Jin N, Chen L, Yang Z. Possible dimers of hypochlorous acid (HOCl) arising from hydrogen- and halogen-bond interactions. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Facile identification of photocleavable reactive metabolites and oxidative stress biomarkers in proteins via mass spectrometry. Anal Bioanal Chem 2012; 403:2269-77. [DOI: 10.1007/s00216-012-5867-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/01/2012] [Accepted: 02/10/2012] [Indexed: 10/28/2022]
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26
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Todorovski T, Fedorova M, Hoffmann R. Identification of isomeric 5-hydroxytryptophan- and oxindolylalanine-containing peptides by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:453-459. [PMID: 22689620 DOI: 10.1002/jms.2058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cells continuously produce reactive oxidative species that can modify all cellular components. In proteins, for example, cysteine, methionine, tryptophan (Trp), and tyrosine residues are particularly prone to oxidation. Here, we report two new approaches to distinguish two isomeric oxidation products of Trp residues, i.e. 5-hydroxytryptophan (5-HTP) and oxindolylalanine (Oia) residues, in peptides. First, 2-nitrobenzenesulfenyl chloride, known to derivatize Trp residues in position 2 of the indole ring, was used to label 5-HTP residues. The mass shift of 152.98 m/z units allowed identifying 5-HTP- besides Trp-containing peptides by mass spectrometry, whereas Oia residues were not labeled. Second, fragmentation of the Oia- and 5-HTP-derived immonium ions at m/z 175.08 produced ions characteristic for each residue that allowed their identification even in the presence of y(1) ions at m/z 175.12 derived from peptides with C-terminal arginine residues. The pseudo MS(3) spectra acquired on a quadrupole time-of-flight hybrid mass spectrometer displayed two signals at m/z 130.05 and m/z 132.05 characteristic for Oia-containing peptides and a group of six signals (m/z 103.04, 120.04, 130.04, 133.03, 146.04, and 148.04) for 5-HTP-cointaining peptides. In both cases, the relative signal intensities appeared to be independent of the sequence providing a specific fingerprint of each oxidative modification.
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Affiliation(s)
- Toni Todorovski
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
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27
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Todorovski T, Fedorova M, Hoffmann R. Mass spectrometric characterization of peptides containing different oxidized tryptophan residues. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1030-1038. [PMID: 22012669 DOI: 10.1002/jms.1984] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The term reactive oxygen species refers to small molecules that can oxidize, for example, nearby proteins, especially cysteine, methionine, tryptophan, and tyrosine residues. Tryptophan oxidation is always irreversible in the cell and can yield several oxidation products, such as 5-hydroxy-tryptophan (5-HTP), oxindolylalanine (Oia), kynurenine (Kyn), and N-formyl-kynurenine (NFK). Because of the severe effects that oxidized tryptophan residues can have on proteins, there is a great need to develop generally applicable and highly sensitive techniques to identify the oxidized residue and the oxidation product. Here, the fragmentation behavior of synthetic peptides corresponding to sequences recently identified in three skeletal muscle proteins as containing oxidized tryptophan residues were studied using postsource decay and collision-induced dissociation (CID) in matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF)/TOF mass spectrometry (MS) and CID in an electrospray ionization (ESI) double quadrupole TOF-MS. For each sequence, a panel of five different peptides containing Trp, 5-HTP, Kyn, NFK, or Oia residue was studied. It was always possible to identify the modified positions by the y-series and also to distinguish the different oxidation products by characteristic fragment ions in the lower mass range by tandem MS. NFK- and Kyn-containing peptides displayed an intense signal at m/z 174.1, which could be useful in identifying accordingly modified peptides by a sensitive precursor ion scan. Most importantly, it was always possible to distinguish isomeric 5-HTP and Oia residues. In ESI- and MALDI-MS/MS, this was achieved by the signal intensity ratios of two signals obtained at m/z 130.1 and 146.1. In addition, high collision energy CID in the MALDI-TOF/TOF-MS also permitted the identification of these two isomeric residues by their v- and w-ions, respectively.
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Affiliation(s)
- Toni Todorovski
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
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Roeser J, Bischoff R, Bruins AP, Permentier HP. Oxidative protein labeling in mass-spectrometry-based proteomics. Anal Bioanal Chem 2010; 397:3441-55. [PMID: 20155254 PMCID: PMC2911539 DOI: 10.1007/s00216-010-3471-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 01/07/2023]
Abstract
Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)-mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade.
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Affiliation(s)
- Julien Roeser
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Andries P. Bruins
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar P. Permentier
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Allmer J. Existing bioinformatics tools for the quantitation of post-translational modifications. Amino Acids 2010; 42:129-38. [DOI: 10.1007/s00726-010-0614-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 04/27/2010] [Indexed: 12/25/2022]
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Protein oxidation: role in signalling and detection by mass spectrometry. Amino Acids 2010; 42:5-21. [PMID: 20401673 DOI: 10.1007/s00726-010-0585-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 03/26/2010] [Indexed: 01/10/2023]
Abstract
Proteins can undergo a wide variety of oxidative post-translational modifications (oxPTM); while reversible modifications are thought to be relevant in physiological processes, non-reversible oxPTM may contribute to pathological situations and disease. The oxidant is also important in determining the type of oxPTM, such as oxidation, chlorination or nitration. The best characterized oxPTMs involved in signalling modulation are partial oxidations of cysteine to disulfide, glutathionylated or sulfenic acid forms that can be reversed by thiol reductants. Proline hydroxylation in HIF signalling is also quite well characterized, and there is increasing evidence that specific oxidations of methionine and tyrosine may have some biological roles. For some proteins regulated by cysteine oxidation, the residues and molecular mechanism involved have been extensively studied and are well understood, such as the protein tyrosine phosphatase PTP1B and MAP3 kinase ASK1, as well as transcription factor complex Keap1-Nrf2. The advances in understanding of the role oxPTMs in signalling have been facilitated by advances in analytical technology, in particular tandem mass spectrometry techniques. Combinations of peptide sequencing by collisionally induced dissociation and precursor ion scanning or neutral loss to select for specific oxPTMs have proved very useful for identifying oxidatively modified proteins and mapping the sites of oxidation. The development of specific labelling and enrichment procedures for S-nitrosylation or disulfide formation has proved invaluable, and there is ongoing work to establish analogous methods for detection of nitrotyrosine and other modifications.
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KINUMI T, OSAKA I, HAYASHI A, KAWAI T, MATSUMOTO H, TSUJIMOTO K. Protein Carbonylation Detected with Light and Heavy Isotope-Labeled 2,4-Dinitrophenylhydrazine by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. ACTA ACUST UNITED AC 2009. [DOI: 10.5702/massspec.57.371] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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