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Greer SM, Sidoli S, Coradin M, Schack Jespersen M, Schwämmle V, Jensen ON, Garcia BA, Brodbelt JS. Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy. Anal Chem 2018; 90:10425-10433. [PMID: 30063333 PMCID: PMC6383154 DOI: 10.1021/acs.analchem.8b02320] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ability to map combinatorial patterns of post-translational modifications (PTMs) of proteins remains challenging for traditional bottom-up mass spectrometry workflows. There are also hurdles associated with top-down approaches related to limited data analysis options for heavily modified proteoforms. These shortcomings have accelerated interest in middle-down MS methods that focus on analysis of large peptides generated by specific proteases in conjunction with validated bioinformatics strategies to allow quantification of isomeric histoforms. Mapping multiple PTMs simultaneously requires the ability to obtain high sequence coverage to allow confident localization of the modifications, and 193 nm ultraviolet photodissociation (UVPD) has been shown to cause extensive fragmentation for large peptides and proteins. Histones are an ideal system to test the ability of UVPD to characterize multiple modifications, as the combinations of PTMs are the underpinning of the biological significance of histones and at the same time create an imposing challenge for characterization. The present study focuses on applying 193 nm UVPD to the identification and localization of PTMs on histones by UVPD and comparison to a popular alternative, electron-transfer dissociation (ETD), via a high-throughput middle-down LC/MS/MS strategy. Histone Coder and IsoScale, bioinformatics tools for verification of PTM assignments and quantification of histone peptides, were adapted for UVPD data and applied in the present study. In total, over 300 modified forms were identified, and the distributions of PTMs were quantified between UVPD and ETD. Significant differences in patterns of PTMs were found for histones from HeLa cells prior to and after treatment with a deacetylase inhibitor. Additional fragment ion types generated by UVPD proved essential for extensive characterization of the most heavily modified forms (>5 PTMs).
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Affiliation(s)
- Sylvester M Greer
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Mariel Coradin
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Malena Schack Jespersen
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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Tavano OL, Berenguer-Murcia A, Secundo F, Fernandez-Lafuente R. Biotechnological Applications of Proteases in Food Technology. Compr Rev Food Sci Food Saf 2018; 17:412-436. [DOI: 10.1111/1541-4337.12326] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Olga Luisa Tavano
- Faculty of Nutrition; Alfenas Federal Univ.; 700 Gabriel Monteiro da Silva St Alfenas MG 37130-000 Brazil
| | - Angel Berenguer-Murcia
- Inorganic Chemistry Dept. and Materials Science Inst.; Alicante Univ.; Ap. 99 E-03080 Alicante Spain
| | - Francesco Secundo
- Istit. di Chimica del Riconoscimento Molecolare; CNR; v. Mario Bianco 9 20131 Milan Italy
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