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Wang Y, Tong M. Protein Posttranslational Modification in Stemness Remodeling and Its Emerging Role as a Novel Therapeutic Target in Gastrointestinal Cancers. Int J Mol Sci 2023; 24:ijms24119173. [PMID: 37298124 DOI: 10.3390/ijms24119173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The posttranslational modifications (PTMs) of proteins, as critical mechanisms for protein regulation, are well known to enhance the functional diversity of the proteome and dramatically participate in complicated biological processes. Recent efforts in the field of cancer biology have illustrated the extensive landscape of PTMs and their crosstalk with a wide range of pro-tumorigenic signaling pathways that decisively contribute to neoplastic transformation, tumor recurrence, and resistance to oncotherapy. Cancer stemness is an emerging concept that maintains the ability of tumor cells to self-renew and differentiate and has been recognized as the root of cancer development and therapy resistance. In recent years, the PTM profile for modulating the stemness of various tumor types has been identified. This breakthrough has shed light on the underlying mechanisms by which protein PTMs maintain cancer stemness, initiate tumor relapse, and confer resistance to oncotherapies. This review focuses on the latest knowledge of protein PTMs in reprogramming the stemness of gastrointestinal (GI) cancer. A deeper understanding of abnormal PTMs in specific proteins or signaling pathways provides an opportunity to specifically target cancer stem cells and highlights the clinical relevance of PTMs as potential biomarkers and therapeutic targets for patients with GI malignancies.
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Affiliation(s)
- Yifei Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man Tong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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2
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Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. Mass Spectrom Rev 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
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Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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3
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Liang Y, Zhang L, Zhang Y. Chromatographic separation of peptides and proteins for characterization of proteomes. Chem Commun (Camb) 2023; 59:270-281. [PMID: 36504223 DOI: 10.1039/d2cc05568f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Characterization of proteomes aims to comprehensively characterize proteins in cells or tissues via two main strategies: (1) bottom-up strategy based on the separation and identification of enzymatic peptides; (2) top-down strategy based on the separation and identification of intact proteins. However, it is challenged by the high complexity of proteomes. Consequently, the improvements in peptide and protein separation technologies for simplifying the sample should be critical. In this feature article, separation columns for peptide and protein separation were introduced, and peptide separation technologies for bottom-up proteomic analysis as well as protein separation technologies for top-down proteomic analysis were summarized. The achievement, recent development, limitation and future trends are discussed. Besides, the outlook on challenges and future directions of chromatographic separation in the field of proteomics was also presented.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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4
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Wang C, Liang Y, Zhao B, Liang Z, Zhang L, Zhang Y. Ethane-Bridged Hybrid Monolithic Column with Large Mesopores for Boosting Top-Down Proteomic Analysis. Anal Chem 2022; 94:6172-6179. [PMID: 35412811 DOI: 10.1021/acs.analchem.1c05234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Top-down proteomics is challenged by the high complexity of biological samples. The coelution of intact proteins results in overlapped mass spectra, and hence, an increased peak capacity for protein separation is needed. Herein, ethane-bridged hybrid monoliths with well-defined large mesopores were successfully prepared based on the sol-gel condensation of 1,2-bis(trimethoxysilyl)ethane and tetramethoxysilane, followed by two-step base etching of the Si-O-Si domain while maintaining the Si-C-C-Si domain in the structure. Relatively homogeneous macropores of 1.1 μm and large mesopores of 24 nm were obtained, permitting fast mass transfer of large molecules and efficient diffusion without obstruction. The use of less hydrophobic C1 ligand further sharpened the peak shape and improved peak capacity. A 120 cm-long capillary column was used for top-down proteomic analysis of E. coli lysates under low backpressure with 16 MPa. High peak capacity of 646 was achieved within 240 min gradient. With MS/MS analysis, 959 proteoforms corresponding to 263 proteins could be unambiguously identified from E. coli lysates in a single run. Furthermore, to illustrate the separation performance for large proteoforms, such monoliths were applied to top-down analysis of the SEC fraction of E. coli lysates with Mw ranging from 30 to 70 kDa. With highly effective separation, 347 large proteoforms with Mw higher than 30 kDa were detected in the single 75 min run. These results showed great potential for top-down proteomic analysis in complex samples.
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Affiliation(s)
- Chao Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Baofeng Zhao
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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5
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Liang Y, Wang C, Liang Z, Zhang L, Zhang Y. C18-Functionalized Amine-Bridged Hybrid Monoliths for Mass Spectrometry-Friendly Peptide Separation and Highly Sensitive Proteomic Analysis. Anal Chem 2022; 94:6084-6088. [PMID: 35404572 DOI: 10.1021/acs.analchem.1c04405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For proteomic analysis based on mass spectrometry (MS), high-performance peptide separation under MS-friendly conditions is of importance. To this end, a novel kind of amine-bridged hybrid monolith was developed by the sol-gel reaction of bis[3-(trimethoxysilyl)propyl]amine and allyltrimethoxysilane, followed by "thiol-ene" click functionalization of C18 groups. With the secondary amino groups bridged in the framework, the nonspecific adsorption from silanol groups could be decreased, so that peptide peak tailing under MS-friendly conditions was reduced, and half peak width was narrowed. Furthermore, such materials were facilely in situ prepared in the very narrow bore capillary with low backpressure for proteomic analysis of limited amounts of samples. Finally, 16,692 unique peptides corresponding to 3698 protein groups could be averagely identified from 10 ng Hela cell digests in a single 65 min run, and 5257 peptides corresponding to 1062 protein groups could be averagely identified from 200 pg digests in a single 60 min run. Such high sensitivity could be attributed to the decreased nonspecific adsorption, the narrowed peak width, and the miniaturization of the column. It is shown that such monoliths are promising for highly sensitive proteomic analysis, including single-cell proteomics.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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6
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Sheng Q, Wang L, Zhang L, Wang X, Qian S, Lan M, Qing G, Liang X. High-efficiency Two-dimensional Separation of Natural Products Based on β-Cyclodextrin Stationary Phase Working in Both Hydrophilic and Reversed Hydrophobic Modes. J Chromatogr A 2022; 1673:463069. [DOI: 10.1016/j.chroma.2022.463069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/09/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
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7
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Ye H, Zhou Y, Yang G, Yu T, Zhang Y, Zhao L, Xin Q, Han S. Protein fractionation of pH‐responsive brush‐modified ethylene vinyl alcohol copolymer membranes*. POLYM ENG SCI 2022. [DOI: 10.1002/pen.25904] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hui Ye
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
| | - Yining Zhou
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
| | - Guodong Yang
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
| | - Tengfei Yu
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
| | - Yuzhong Zhang
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
| | - Lizhi Zhao
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
| | - Qingping Xin
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
| | - Shurui Han
- State Key Laboratory of Separation Membranes and Membrane Processes School of Materials Science and Engineering, Tiangong University Tianjin PR China
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8
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Liu Y. A peptidoform based proteomic strategy for studying functions of post-translational modifications. Proteomics 2022; 22:e2100316. [PMID: 34878717 PMCID: PMC8959388 DOI: 10.1002/pmic.202100316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 02/03/2023]
Abstract
Protein post-translational modifications (PTMs) generate an enormous, but as yet undetermined, expansion of the produced proteoforms. In this Viewpoint, we firstly reviewed the concepts of proteoform and peptidoform. We show that many of the current PTM biological investigation and annotation studies largely follow a PTM site-specific rather than proteoform-specific approach. We further illustrate a potentially useful matching strategy in which a particular "modified peptidoform" is matched to the corresponding "unmodified peptidoform" as a reference for the quantitative analysis between samples and conditions. We suggest this strategy has the potential to provide more directly relevant information to learn the PTM site-specific biological functions. Accordingly, we advocate for the wider use of the nomenclature "peptidoform" in future bottom-up proteomic studies.
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Affiliation(s)
- Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA,Department of Pharmacology, Yale University, School of Medicine, New Haven, CT 06520, USA,Corresponding author:
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9
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Yıldız S, Bilen Ç, Karakuş E. Purification of damson plum polyphenol oxidase by affinity chromatography and investigation of metal effects on enzyme activity. Prep Biochem Biotechnol 2022; 52:1019-1034. [PMID: 35015975 DOI: 10.1080/10826068.2021.2023825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Polyphenol oxidase (PPO) was firstly purified from damson plum as a high antioxidant source. PPO was treated by 0-80% ammonium sulfate precipitation and dialysis. Characterization results were determined for catechol, 4-methyl catechol, pyrogallol and caffeic acid as 0.05 M/pH: 7.2/25 °C; 0.2 M/pH: 4.5/10 °C; 0.01 M/pH: 6.8/5 °C, and 0.2 M/pH: 8.5/10 °C, respectively. Vmax and KM values were calculated for same substrates as 17,219.97 U/(mL*min) and 11.67 mM; 7309.72 U/(mL*min) and 5 mM; 12,580.12 U/(mL*min) and 3.74 mM; 12,100.41 U/(mL*min) and 6.25 mM, respectively. Catechol gave the highest Vmax value among substrates. Affinity purification was performed by using Sepharose 4B-L-Tyrosine-p-aminobenzoic acid and Sepharose 6B-L-Tyrosine-p-aminobenzoic acid. Single bands were approximately observed at 50 kDa for each affinity sample in SDS-PAGE and Native-PAGE. 93.88 and 10.46 purification-folds were obtained for PPO by reference Sepharose-4B and original Sepharose-6B gels. Metal effects upon PPO activity were also investigated due to the importance of enzymatic browning in foods. Cu+2 activation and Fe+2 inhibition were observed with a final metal concentration of 1 mM at 219.66 and 43.18%, respectively. PPO purification from damson plum by affinity chromatography, its characterization, stability evaluation by statistically, and effects of metal ions on damson plum PPO have not been investigated in the literature.
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Affiliation(s)
- Selinnur Yıldız
- Department of Chemistry, Yildiz Technical University, Istanbul, Turkey
| | - Çiğdem Bilen
- Department of Chemistry, Yildiz Technical University, Istanbul, Turkey
| | - Emine Karakuş
- Department of Chemistry, Yildiz Technical University, Istanbul, Turkey
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10
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Liang Y, Zhang L, Zhang Y. Monolithic Materials-Based RPLC-MS for Proteoform Separation and Identification. Methods Mol Biol 2022; 2500:43-53. [PMID: 35657586 DOI: 10.1007/978-1-0716-2325-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High-performance separation of proteoforms plays an important role in top-down proteomic ananlysis due to high complexity of the proteome. To this end, the functionalized ethylene-bridged hybrid monolithic materials have been developed for reversed-phase liquid chromatographic separation of proteoforms followed by online combination with high-resolution mass spectrometry (MS) for top-down proteomic analysis. Such monoliths have advantages of homogenously distributed functional groups in the framework, good chemical stability, and high permeability and, thus, show high resolution, good reproducibility, and low backpressure for proteoform separation. This chapter describes in detail the preparation of such monoliths and online combination with high-resolution MS for proteoform separation and identification.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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11
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Nosti AJ, Barrio LC, Calderón-Celis F, Soldado A, Encinar JR. Absolute quantification of proteins using element mass spectrometry and generic standards. J Proteomics 2022; 256:104499. [DOI: 10.1016/j.jprot.2022.104499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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12
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Halvorsen TG, McKitterick N, Kish M, Reubsaet L. Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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13
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Wang C, Tang R, Pan L, Wu W, Ma S, Wei Y, Ou J. Preparation of core-shell microporous organic polymer-coated silica microspheres for chromatographic separation and N-glycopeptides enrichment. J Sep Sci 2021; 45:1458-1468. [PMID: 34559936 DOI: 10.1002/jssc.202100466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 11/10/2022]
Abstract
Through a "one-pot" strategy, a layer of microporous organic polymer was coated onto the surface of monodisperse amino-functionalized silica microsphere via amino-aldehyde condensation reaction with core-shell structure. The change in chemical structure of material before and after modification was determined by Fourier-transform infrared spectroscopy and X-ray photoelectron spectroscopy. Due to existence of a large number of amino and aldehyde groups in microporous organic polymer shell, the water contact angle decreased from 56.8° (silica microspheres) to 34.7° (microporous organic polymer-coated silica microspheres). Based on these properties, microporous organic polymer-coated silica microspheres were employed as the stationary phase for capillary liquid chromatography and successfully offered baseline separation of polar small molecules. Additionally, the material could also be served as the sorbent of hydrophilic interaction chromatography to enrich glycopeptides from human serum digest. A total of 470 unique N-glycopeptides and 342 N-glycosylation sites mapped to 112 N-glycosylated proteins were unambiguously identified from 2 μL of human serum, exhibiting a promising application prospect of microporous organic polymer-coated silica microspheres in the pretreatment of proteomics samples.
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Affiliation(s)
- Chenyang Wang
- Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China.,Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China
| | - Ruizhi Tang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China
| | - Lei Pan
- Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China.,Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China
| | - Wenrui Wu
- Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China.,Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China
| | - Shujuan Ma
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China
| | - Yinmao Wei
- Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China
| | - Junjie Ou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
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14
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Guzmán-Zapata D, Vargas-Morales BV, Loyola-Vargas VM. From genome scissors to molecular scalpel: evolution of CRISPR systems. Biotechnol Genet Eng Rev 2021; 37:82-104. [PMID: 34412573 DOI: 10.1080/02648725.2021.1962071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
From bizarre palindromic repeats to a bacterial defense mechanism, to genome editing tool, and more, Clustered Regularly Interspaced Short Palindromic Repeats or CRISPR has significantly impacted the way we study genome modification in less than a decade. In this review, we would like to highlight some key players over 30 years of research and explain this biotechnological tool's basic mechanisms. We also refer to the evolution of the CRISPR variants and some of the applications derived from them. The understanding and upgrading of this system will be a valuable tool in the years to come to solve some of the challenges in diverse fields from pharmaceuticals to therapeutics, from basic plant genetics to crop improvement, from metabolic engineering to waste management and industrial processing.
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Affiliation(s)
- Daniel Guzmán-Zapata
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, México
| | | | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, México
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15
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Skeene K, Khatri K, Soloviev Z, Lapthorn C. Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry. Biochim Biophys Acta Proteins Proteom 2021; 1869:140697. [PMID: 34246790 DOI: 10.1016/j.bbapap.2021.140697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022]
Abstract
Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.
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Affiliation(s)
- Kirsty Skeene
- Biopharm Process Research, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Kshitij Khatri
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Collegeville, PA 19406, USA.
| | - Zoja Soloviev
- Protein, Cellular and Structural Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Cris Lapthorn
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Stevenage SG1 2NY, UK.
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16
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Abstract
Improvements in single-cell protein analysis are required to study the cell-to-cell variation inherent to diseases, including cancer. Single-cell immunoblotting (scIB) offers proteoform detection specificity, but often relies on fluorescence-based readout and is therefore limited in multiplexing capability. Among rising multiplexed imaging methods is multiplexed ion beam imaging by time-of-flight (MIBI-TOF), a mass spectrometry imaging technology. MIBI-TOF employs metal-tagged antibodies that do not suffer from spectral overlap to the same degree as fluorophore-tagged antibodies. We report for the first-time MIBI-TOF of single-cell immunoblotting (scIB-MIBI-TOF). The scIB assay subjects single-cell lysate to protein immunoblotting on a microscale device consisting of a 50- to 75-μm thick hydrated polyacrylamide (PA) gel matrix for protein immobilization prior to in-gel immunoprobing. We confirm antibody-protein binding in the PA gel with indirect fluorescence readout of metal-tagged antibodies. Since MIBI-TOF is a layer-by-layer imaging technique, and our protein target is immobilized within a 3D PA gel layer, we characterize the protein distribution throughout the PA gel depth by fluorescence confocal microscopy and confirm that the highest signal-to-noise ratio is achieved by imaging the entirety of the PA gel depth. Accordingly, we report the required MIBI-TOF ion dose strength needed to image varying PA gel depths. Lastly, by imaging ∼42% of PA gel depth with MIBI-TOF, we detect two isoelectrically separated TurboGFP (tGFP) proteoforms from individual glioblastoma cells, demonstrating that highly multiplexed mass spectrometry-based readout is compatible with scIB.
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Affiliation(s)
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, California 94025, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, California 94025, United States
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, California 94025, United States
| | - Amy E Herr
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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17
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Montero-Calle A, Barderas R. Analysis of Protein-Protein Interactions by Protein Microarrays. Methods Mol Biol 2021; 2344:81-97. [PMID: 34115353 DOI: 10.1007/978-1-0716-1562-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The analysis of the proteome and the interactome would be useful for a better understanding of the pathophysiology of several disorders, allowing the identification of potential specific markers for early diagnosis and prognosis, as well as potential targets of intervention. Among different proteomic approaches, high-density protein microarrays have become an interesting tool for the screening of protein-protein interactions and the interactome definition of disease-associated dysregulated proteins. This information might contribute to the identification of altered signaling pathways and protein functions involved in the pathogenesis of a disease. Remarkably, protein microarrays have been already satisfactorily employed for the study of protein-protein interactions in cancer, allergy, or neurodegenerative diseases. Here, we describe the utilization of recombinant protein microarrays for the identification of protein-protein interactions to help in the definition of disease-specific dysregulated interactomes.
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Affiliation(s)
- Ana Montero-Calle
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Madrid, Spain.
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18
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Sheng Q, Wang C, Li X, Qin H, Ye M, Xiong Y, Wang X, Li X, Lan M, Li J, Ke Y, Qing G, Liang X. Highly Efficient Separation of Methylated Peptides Utilizing Selective Complexation between Lysine and 18-Crown-6. Anal Chem 2020; 92:15663-15670. [PMID: 33169968 DOI: 10.1021/acs.analchem.0c04158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein methylation is one of the most common and important post-translational modifications, and it plays vital roles in epigenetic regulation, signal transduction, and chromatin metabolism. However, due to the diversity of methylation forms, slight difference between methylated sites and nonmodified ones, and ultralow abundance, it is extraordinarily challenging to capture and separate methylated peptides from biological samples. Here, we introduce a simple and highly efficient method to separate methylated and nonmethylated peptides using 18-crown-6 as a mobile phase additive in high-performance liquid chromatography. Selective complexation between lysine and 18-crown-6 remarkably increases the retention of the peptides on a C18 stationary phase, leading to an excellent baseline separation between the lysine methylated and nonmethylated peptides. A possible binding mechanism is verified by nuclear magnetic resonance titration, biolayer interferometry technology, and quantum chemistry calculation. Through establishment of a simple enrichment methodology, a good selectivity is achieved and four methylated peptides with greatly improved signal-to-noise (S/N) ratios are successfully separated from a complex peptide sample containing 10-fold bovine serum albumin tryptic digests. By selecting rLys N as an enzyme to digest histone, methylation information in the histone could be well identified based on our enrichment method. This study will open an avenue and provide a novel insight for selective enrichment of lysine methylated peptides in post-translational modification proteomics.
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Affiliation(s)
- Qianying Sheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Cunli Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xiaopei Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Hongqiang Qin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yuting Xiong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xue Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junyan Li
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yanxiong Ke
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
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19
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Brown KA, Melby JA, Roberts DS, Ge Y. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev Proteomics 2020; 17:719-733. [PMID: 33232185 PMCID: PMC7864889 DOI: 10.1080/14789450.2020.1855982] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
Abstract
Introduction- A better understanding of the underlying molecular mechanism of diseases is critical for developing more effective diagnostic tools and therapeutics toward precision medicine. However, many challenges remain to unravel the complex nature of diseases. Areas covered- Changes in protein isoform expression and post-translation modifications (PTMs) have gained recognition for their role in underlying disease mechanisms. Top-down mass spectrometry (MS)-based proteomics is increasingly recognized as an important method for the comprehensive characterization of proteoforms that arise from alternative splicing events and/or PTMs for basic and clinical research. Here, we review the challenges, technological innovations, and recent studies that utilize top-down proteomics to elucidate changes in the proteome with an emphasis on its use to study heart diseases. Expert opinion- Proteoform-resolved information can substantially contribute to the understanding of the molecular mechanisms underlying various diseases and for the identification of novel proteoform targets for better therapeutic development . Despite the challenges of sequencing intact proteins, top-down proteomics has enabled a wealth of information regarding protein isoform switching and changes in PTMs. Continuous developments in sample preparation, intact protein separation, and instrumentation for top-down MS have broadened its capabilities to characterize proteoforms from a range of samples on an increasingly global scale.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin, United States
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20
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Uzdensky AB. Multifunctional Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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21
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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22
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Zhang X, Wang Y, Zhong T, Feng X. Optimal spacer arm microenvironment for the immobilization of recombinant Protein A on heterofunctional amino-epoxy agarose supports. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Sajjadi SH, Goharshadi EK, Ahmadzadeh H. Heat dissipation in slab gel electrophoresis: The effect of embedded TiO 2 nanoparticles on the thermal profiles. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1118-1119:63-69. [PMID: 31029035 DOI: 10.1016/j.jchromb.2019.04.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/13/2019] [Accepted: 04/14/2019] [Indexed: 12/28/2022]
Abstract
Despite the fast development of novel and high-resolution electrophoresis techniques such as capillary-based methods and microfluidic devices, the slab gel electrophoresis is still a popular method for the separation of biomolecules in medicine and biology. It is a low cost and simple method and offers high throughput. However, this technique is limited to low voltages leading to slow separations. Producing the heat during the electrophoresis known as Joule heating inevitably leads to a rise in the gel temperature. For the first time, this work offers a whole gel temperature measurement by using a thermal camera which presents accurate temperature profiles in the gel with a resolution of more than 10 pixel/mm2 and a precision of 0.1 °C. Titania, TiO2, nanoparticles (NPs) were embedded into the polyacrylamide (PA) gel to improve the electrophoretic separation of proteins. By embedding 0.025% w/v TiO2 NPs, heat dissipation increases by 16.5% at applied voltage of 200 V compared with that of PA gel with no embedded TiO2 NPs. The thermal images showed that the composite gel was 2.5 °C in average cooler than PA gel after 15 min of electrophoresis run at 200 V. The maximum separation voltage increased by 30 V in the composite PA/TiO2 gel compared with the pure PA gel. Moreover, the average number of theoretical plates over the 10 protein peaks, as a criterion of separation performance, increased by about 63% at 180 V when TiO2 NPs were included into the gel.
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Affiliation(s)
- Sayyed Hashem Sajjadi
- Chemistry Department, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Elaheh K Goharshadi
- Chemistry Department, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran; Nano Research Center, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran.
| | - Hossein Ahmadzadeh
- Chemistry Department, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
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24
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Roberts DS, Chen B, Tiambeng TN, Wu Z, Ge Y, Jin S. Reproducible Large-Scale Synthesis of Surface Silanized Nanoparticles as an Enabling Nanoproteomics Platform: Enrichment of the Human Heart Phosphoproteome. Nano Res 2019; 12:1473-1481. [PMID: 31341559 PMCID: PMC6656398 DOI: 10.1007/s12274-019-2418-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A reproducible synthetic strategy was developed for facile large-scale (200 mg) synthesis of surface silanized magnetite (Fe3O4) nanoparticles (NPs) for biological applications. After further coupling a phosphate-specific affinity ligand, these functionalized magnetic NPs were used for the highly specific enrichment of phosphoproteins from a complex biological mixture. Moreover, correlating the surface silane density of the silanized magnetite NPs to their resultant enrichment performance established a simple and reliable quality assurance control to ensure reproducible synthesis of these NPs routinely in large scale and optimal phosphoprotein enrichment performance from batch-to-batch. Furthermore, by successful exploitation of a top-down phosphoproteomics strategy that integrates this high throughput nanoproteomics platform with online liquid chromatography (LC) and tandem mass spectrometry (MS/MS), we were able to specifically enrich, identify, and characterize endogenous phosphoproteins from highly complex human cardiac tissue homogenate. This nanoproteomics platform possesses a unique combination of scalability, specificity, reproducibility, and efficiency for the capture and enrichment of low abundance proteins in general, thereby enabling downstream proteomics applications.
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Affiliation(s)
- David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Timothy N. Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706, USA
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25
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Bults P, Spanov B, Olaleye O, van de Merbel NC, Bischoff R. Intact protein bioanalysis by liquid chromatography – High-resolution mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1110-1111:155-167. [DOI: 10.1016/j.jchromb.2019.01.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/20/2019] [Accepted: 01/31/2019] [Indexed: 02/07/2023]
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26
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Burger B, Hernández Sánchez LF, Lereim RR, Barsnes H, Vaudel M. Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets. J Proteome Res 2018; 17:3801-3809. [PMID: 30251541 DOI: 10.1021/acs.jproteome.8b00464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics data sets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected from the literature. Due to their central role, the content of the functional knowledgebases directly influences the outcome of pathway analyses. In this study, we investigate the structure of the current pathway knowledge, as exemplified by Reactome, discuss the consequences for biological interpretation, and outline possible improvements in the use of pathway knowledgebases. By providing a view of the underlying protein interaction network, we aim to help pathway analysis users manage their expectations and better identify possible artifacts in the results.
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Affiliation(s)
- Bram Burger
- Computational Biology Unit (CBU), Department of Informatics , University of Bergen , 5020 Bergen , Norway.,Proteomics Unit (PROBE), Department of Biomedicine , University of Bergen , 5020 Bergen , Norway
| | - Luis Francisco Hernández Sánchez
- KG Jebsen Center for Diabetes Research, Department of Clinical Science , University of Bergen , 5020 Bergen , Norway.,Center for Medical Genetics and Molecular Medicine , Haukeland University Hospital , 5020 Bergen , Norway
| | - Ragnhild Reehorst Lereim
- Computational Biology Unit (CBU), Department of Informatics , University of Bergen , 5020 Bergen , Norway.,Proteomics Unit (PROBE), Department of Biomedicine , University of Bergen , 5020 Bergen , Norway
| | - Harald Barsnes
- Computational Biology Unit (CBU), Department of Informatics , University of Bergen , 5020 Bergen , Norway.,Proteomics Unit (PROBE), Department of Biomedicine , University of Bergen , 5020 Bergen , Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science , University of Bergen , 5020 Bergen , Norway.,Center for Medical Genetics and Molecular Medicine , Haukeland University Hospital , 5020 Bergen , Norway
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27
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Chen CH, Feng H, Guo R, Li P, Laserna AKC, Ji Y, Ng BH, Li SFY, Khan SH, Paulus A, Chen SM, Karger AE, Wenz M, Ferrer DL, Huhmer AF, Krupke A. Intact NIST monoclonal antibody characterization—Proteoforms, glycoforms—Using CE-MS and CE-LIF. ACTA ACUST UNITED AC 2018. [DOI: 10.1080/23312009.2018.1480455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Chien-Hsun Chen
- Thermo Fisher Scientific, Chromatography and Mass Spectrometry, 355 River Oaks Parkway, San Jose, CA 95134, USA
- Thermo Fisher Scientific, Life Science Solutions, 180 Oyster Point Parkway, South San Francisco, CA 94080, USA
| | - Huatao Feng
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore S117543, Singapore
| | - Rui Guo
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore S117543, Singapore
| | - Pingjing Li
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore S117543, Singapore
| | - Anna Karen C. Laserna
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore S117543, Singapore
| | - Ya Ji
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore S117543, Singapore
| | - Bao Hui Ng
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore S117543, Singapore
| | - Sam Fong Yau Li
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore S117543, Singapore
| | - Shaheer H. Khan
- Thermo Fisher Scientific, Life Science Solutions, 180 Oyster Point Parkway, South San Francisco, CA 94080, USA
| | - Aran Paulus
- Thermo Fisher Scientific, Chromatography and Mass Spectrometry, 355 River Oaks Parkway, San Jose, CA 95134, USA
| | - Shiaw-Min Chen
- Thermo Fisher Scientific, Life Science Solutions, 180 Oyster Point Parkway, South San Francisco, CA 94080, USA
| | - Achim E. Karger
- Thermo Fisher Scientific, Life Science Solutions, 180 Oyster Point Parkway, South San Francisco, CA 94080, USA
| | - Michael Wenz
- Thermo Fisher Scientific, Life Science Solutions, 180 Oyster Point Parkway, South San Francisco, CA 94080, USA
| | - Daniel Lopez Ferrer
- Thermo Fisher Scientific, Chromatography and Mass Spectrometry, 355 River Oaks Parkway, San Jose, CA 95134, USA
| | - Andreas F. Huhmer
- Thermo Fisher Scientific, Chromatography and Mass Spectrometry, 355 River Oaks Parkway, San Jose, CA 95134, USA
| | - Andreas Krupke
- Thermo Fisher Scientific, Life Science Solutions, 180 Oyster Point Parkway, South San Francisco, CA 94080, USA
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