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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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2
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Boschetti E, Righetti PG. Low-Abundance Protein Enrichment for Medical Applications: The Involvement of Combinatorial Peptide Library Technique. Int J Mol Sci 2023; 24:10329. [PMID: 37373476 DOI: 10.3390/ijms241210329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The discovery of low- and very low-abundance proteins in medical applications is considered a key success factor in various important domains. To reach this category of proteins, it is essential to adopt procedures consisting of the selective enrichment of species that are present at extremely low concentrations. In the past few years pathways towards this objective have been proposed. In this review, a general landscape of the enrichment technology situation is made first with the presentation and the use of combinatorial peptide libraries. Then, a description of this peculiar technology for the identification of early-stage biomarkers for well-known pathologies with concrete examples is given. In another field of medical applications, the determination of host cell protein traces potentially present in recombinant therapeutic proteins, such as antibodies, is discussed along with their potentially deleterious effects on the health of patients on the one hand, and on the stability of these biodrugs on the other hand. Various additional applications of medical interest are disclosed for biological fluids investigations where the target proteins are present at very low concentrations (e.g., protein allergens).
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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4
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Development of an Efficient Solid-Phase Microextraction Monolithic Column for the Analysis of Estrogens in Human Urine and Serum Samples. Chromatographia 2022. [DOI: 10.1007/s10337-022-04178-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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He W, Wang Q, Tian X, Pan G. Recapitulating dynamic ECM ligand presentation at biomaterial interfaces: Molecular strategies and biomedical prospects. EXPLORATION 2022; 2:20210093. [PMCID: PMC10191035 DOI: 10.1002/exp.20210093] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Wenbo He
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang P. R. China
| | - Qinghe Wang
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang P. R. China
| | - Xiaohua Tian
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang P. R. China
- School of Chemistry and Chemical Engineering Jiangsu University Zhenjiang P. R. China
| | - Guoqing Pan
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang P. R. China
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Zhang T, Li Y, Zhao X, Li W, Sun X, Li J, Lu R. A novel recyclable absorption material with boronate affinity. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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Li H, He H, Liu Z. Recent progress and application of boronate affinity materials in bioanalysis. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116271] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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He M, Wang R, He Y, Shen J, Liu C, Wang C, Wei Y. Multidentate boronate magnetic adsorbent assembled with polyhedral oligomeric silsesquioxanes and intramolecular diboronic acid for improving the binding strength toward glycoproteins. J Chromatogr A 2019; 1607:460401. [PMID: 31376983 DOI: 10.1016/j.chroma.2019.460401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/20/2022]
Abstract
Boronate affinity is an important method for the enrichment and separation of cis-diol containing compounds, but most of the conventional boronate materials suffer from weak binding strength as well as low binding capacity towards glycoproteins due to the use of single boronic acids as ligands. In this work, a novel multidentate boronate magnetic adsorbent was assembled by using amined polyhedral oligomeric silsesquioxane as spacer and a diboronic acid as ligand. The specially designed adsorbent exhibited high adsorption capacity for cis-diols due to the high density of phenylbronic acid moieties. More interestingly, the dissociation constants toward glycoproteins on the material were lowered to be ∼10-6 M, being at least 3 orders lower than the single boronic acid bonded adsorbents. By comparing the binding properties of small molecules containing one and two pairs of cis-diols, the enhanced binding strength of glycoproteins on the multidentate boronate magnetic adsorbent was attributed to the synergistic binding of glycoproteins on the special interface. The new materials successfully captured glycoproteins from 1000-fold diluted egg white, suggesting that the material could be an optional alternative adsorbent for enriching trace glycoproteins from complex bio-samples.
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Affiliation(s)
- Maofang He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Material Science, Northwest University, Xi'an 710127, PR China; College of Pharmacy, Institute of Medicine, Xi'an Medical University, Xi'an, 710021, PR China
| | - Rong Wang
- College of Pharmacy, Institute of Medicine, Xi'an Medical University, Xi'an, 710021, PR China
| | - Yijia He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Material Science, Northwest University, Xi'an 710127, PR China
| | - Jiwei Shen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Material Science, Northwest University, Xi'an 710127, PR China
| | - Chunye Liu
- College of Pharmacy, Institute of Medicine, Xi'an Medical University, Xi'an, 710021, PR China
| | - Chaozhan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Material Science, Northwest University, Xi'an 710127, PR China
| | - Yinmao Wei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Material Science, Northwest University, Xi'an 710127, PR China.
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9
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Chen Y, Huang A, Zhang Y, Bie Z. Recent advances of boronate affinity materials in sample preparation. Anal Chim Acta 2019; 1076:1-17. [DOI: 10.1016/j.aca.2019.04.050] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 11/28/2022]
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10
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Kuvayskaya A, Vasiliev A. Functionalization of silica gel by ultrasound-assisted surface Suzuki coupling. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Abstract
Glycosylation is one of the most ubiquitous and complex post-translational modifications (PTMs). It plays pivotal roles in various biological processes. Studies at the glycopeptide level are typically considered as a downstream work resulting from enzymatic digested glycoproteins. Less attention has been focused on glycosylated endogenous signaling peptides due to their low abundance, structural heterogeneity and the lack of enabling analytical tools. Here, protocols are presented to isolate and characterize glycosylated neuropeptides utilizing nanoflow liquid chromatography coupled with mass spectrometry (LC-MS). We first demonstrate how to extract neuropeptides from raw tissues and perform further separation/cleanup before MS analysis. Then we describe hybrid MS methods for glycosylated neuropeptide profiling and site-specific analysis. We also include recommendations for data analysis to identify glycosylated neuropeptides in crustaceans where a complete neuropeptide database is still lacking. Other strategies and future directions are discussed to provide readers with alternative approaches and further unravel biological complexity rendered by glycosylation.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States; School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States.
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Development of a new in-line coupling of a miniaturized boronate affinity monolithic column with reversed-phase silica monolithic capillary column for analysis of cis-diol-containing nucleoside compounds. J Chromatogr A 2019; 1597:209-213. [DOI: 10.1016/j.chroma.2019.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 12/27/2022]
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14
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A practical approach to enrich intact tryptic N-glycopeptides through size exclusion chromatography and hydrophilicity (SELIC) using an acrylamide-agarose composite gel system. Anal Chim Acta 2019; 1058:107-116. [PMID: 30851844 DOI: 10.1016/j.aca.2019.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/14/2019] [Accepted: 01/22/2019] [Indexed: 12/18/2022]
Abstract
Increasing researches proved that abnormal glycosylation is strongly correlated with many diseases. Specially, site-specific glycosylation and its associated heterogeneity are closely related to the function and activity of the glycoprotein. However, intact N-glycopeptide analysis still faces great challenges because the presence of highly abundant non-glycosylated peptides would suppress the ionization of lowly abundant glycopeptides. In the present study, we developed a practical intact tryptic N-glycopeptide enrichment method using acrylamide-agarose composite gel that combined the size exclusion chromatography and hydrophilic (named SELIC) effects, aimed to remove the detergent rapidly and effectively, as well as enrich intact N-glycopeptides while extracting peptides. This is a useful tool to facilitate the intact N-glycopeptides analysis of complex protein mixtures, particularly for samples that extracted from formalin-fixed and paraffin-embedded (FFPE) tissues by SDS. Using this method, we successfully identified 700 site-specific intact tryptic N-glycopeptides corresponding to 261 glycosylation sites on 191 glycoproteins from FFPE thymoma tissues.
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Ikegami T. Hydrophilic interaction chromatography for the analysis of biopharmaceutical drugs and therapeutic peptides: A review based on the separation characteristics of the hydrophilic interaction chromatography phases. J Sep Sci 2019; 42:130-213. [DOI: 10.1002/jssc.201801074] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tohru Ikegami
- Faculty of Molecular Chemistry and Engineering; Kyoto Institute of Technology; Kyoto Japan
- Institute of Pharmaceutical Sciences; Pharmaceutical (Bio-) Analysis; Eberhard-Karls Universität Tübingen; Tübingen Germany
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Ying LL, Wang DY, Yang HP, Deng XY, Peng C, Zheng C, Xu B, Dong LY, Wang X, Xu L, Zhang YW, Wang XH. Synthesis of boronate-decorated polyethyleneimine-grafted porous layer open tubular capillaries for enrichment of polyphenols in fruit juices. J Chromatogr A 2018; 1544:23-32. [DOI: 10.1016/j.chroma.2018.02.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/11/2018] [Accepted: 02/21/2018] [Indexed: 10/18/2022]
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