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Bashyal A, Brodbelt JS. Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation. MASS SPECTROMETRY REVIEWS 2024; 43:289-326. [PMID: 36165040 PMCID: PMC10040477 DOI: 10.1002/mas.21811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
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Borbély A, Pethő L, Szabó I, Al-Majidi M, Steckel A, Nagy T, Kéki S, Kalló G, Csősz É, Mező G, Schlosser G. Structural Characterization of Daunomycin-Peptide Conjugates by Various Tandem Mass Spectrometric Techniques. Int J Mol Sci 2021; 22:ijms22041648. [PMID: 33562082 PMCID: PMC7914584 DOI: 10.3390/ijms22041648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 11/16/2022] Open
Abstract
The use of peptide-drug conjugates has generated wide interest as targeted antitumor therapeutics. The anthracycline antibiotic, daunomycin, is a widely used anticancer agent and it is often conjugated to different tumor homing peptides. However, comprehensive analytical characterization of these conjugates via tandem mass spectrometry (MS/MS) is challenging due to the lability of the O-glycosidic bond and the appearance of MS/MS fragment ions with little structural information. Therefore, we aimed to investigate the optimal fragmentation conditions that suppress the prevalent dissociation of the anthracycline drug and provide good sequence coverage. In this study, we comprehensively compared the performance of common fragmentation techniques, such as higher energy collisional dissociation (HCD), electron transfer dissociation (ETD), electron-transfer higher energy collisional dissociation (EThcD) and matrix-assisted laser desorption/ionization–tandem time-of-flight (MALDI-TOF/TOF) activation methods for the structural identification of synthetic daunomycin-peptide conjugates by high-resolution tandem mass spectrometry. Our results showed that peptide backbone fragmentation was inhibited by applying electron-based dissociation methods to conjugates, most possibly due to the “electron predator” effect of the daunomycin. We found that efficient HCD fragmentation was largely influenced by several factors, such as amino acid sequences, charge states and HCD energy. High energy HCD and MALDI-TOF/TOF combined with collision induced dissociation (CID) mode are the methods of choice to unambiguously assign the sequence, localize different conjugation sites and differentiate conjugate isomers.
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Affiliation(s)
- Adina Borbély
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
| | - Lilla Pethő
- Eötvös Loránd Research Network, Supported Research Groups, Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (L.P.); (I.S.); (G.M.)
| | - Ildikó Szabó
- Eötvös Loránd Research Network, Supported Research Groups, Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (L.P.); (I.S.); (G.M.)
| | - Mohammed Al-Majidi
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Arnold Steckel
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Tibor Nagy
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (S.K.)
| | - Sándor Kéki
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (T.N.); (S.K.)
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Gábor Mező
- Eötvös Loránd Research Network, Supported Research Groups, Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (L.P.); (I.S.); (G.M.)
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group and Department of Analytical Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (A.B.); (M.A.-M.); (A.S.)
- Correspondence: ; Tel.: +36-1-372-2500
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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Selective chemoprecipitation to enrich nitropeptides from complex proteomes for mass-spectrometric analysis. Nat Protoc 2014; 9:882-95. [PMID: 24651500 DOI: 10.1038/nprot.2014.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-translational protein nitration has attracted interest owing to its involvement in cellular signaling, effects on protein function and potential as biomarker of nitroxidative stress. We describe a procedure for enriching nitropeptides for mass spectrometry (MS)-based proteomics that is a simple and reliable alternative to immunoaffinity-based methods. The starting material for this procedure is a proteolytic digest. The peptides are reacted with formaldehyde and sodium cyanoborohydride to dimethylate all the N-terminal and side chain amino groups. Sodium dithionite is added subsequently to reduce the nitro groups to amines; in theory, the only amino groups present will have originally been nitro groups. The peptide sample is then applied to a solid-phase active ester reagent (SPAER), and those peptides with amino groups will be selectively and covalently captured. Release of the peptides on hydrolysis with trifluoroacetic acid (TFA) results in peptides that have a 4-formyl-benzamido group where the nitro group used to be. In qualitative setups, the procedure can be used to identify proteins modified by reactive nitrogen species and to determine the specific sites of their nitration. Quantitative measurements can be performed by stable-isotope labeling of the peptides in the reductive dimethylation step. Preparation of the SPAER takes about 1 d. Enrichment of nitropeptides requires about 2 d, and sample preparations need 1-30 h, depending on the experimental design. LC-MS/MS assays take from 4 h to several days and data processing can be done in 1-7 d.
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