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Lu P, Shan M, Ji X, Deng F, Wang Y. EPURISp: Combining Enzymatic Digestion, Ultrafiltration, and Rapid In Situ Sample Purification for High-performance Proteomics. J Proteome Res 2023; 22:3392-3400. [PMID: 37747260 PMCID: PMC10563806 DOI: 10.1021/acs.jproteome.3c00505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Indexed: 09/26/2023]
Abstract
High-performance liquid tandem mass spectrometry (HPLC-MS) is widely employed for protein analysis in biological systems. However, conventional proteomic sample pretreatment methods suffer from multiple steps and poor reproducibility. In this study, we introduce EPURISp (Enzymatic Digestion with Ultrafiltration and Rapid In-situ Sample Purification), a novel proteomic pretreatment technique that combines enzymatic digestion, ultrafiltration, and one-step temperature-controlled vacuum drying for efficient desalting. The EPURISp method exhibits excellent protein recovery rates across a wide range of molecular weights and hydrophilicity, surpassing traditional C18 desalting approaches. Practical proteomic analysis (PXD044209) utilizing EPURISp demonstrates the highest protein identification yield with remarkable reproducibility, which is particularly advantageous in membrane protein identification. Notably, EPURISp exhibits superior performance in minimizing oxidation and deamidation modifications compared with conventional FASP methods. This innovative EPURISp method represents a significant advancement in proteomics analysis, providing reliable and efficient results for mass spectrometry.
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Affiliation(s)
- Ping Lu
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
| | - Mengyuan Shan
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
- School
of Medicine, Nankai University, Tianjin 300071, China
- Nankai
University Affiliated Eye Hospital, Nankai
University, Tianjin 300020, China
| | - Xuemeng Ji
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Fuqi Deng
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
- Nankai
University Affiliated Eye Hospital, Nankai
University, Tianjin 300020, China
- Clinical
College of Ophthalmology, Tianjin Medical
University, Tianjin 300070, China
| | - Yan Wang
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
- School
of Medicine, Nankai University, Tianjin 300071, China
- Nankai
University Affiliated Eye Hospital, Nankai
University, Tianjin 300020, China
- Clinical
College of Ophthalmology, Tianjin Medical
University, Tianjin 300070, China
- Nankai
University Eye Institute, Nankai University, Tianjin 300020, China
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Brandi J, Noberini R, Bonaldi T, Cecconi D. Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications. J Chromatogr A 2022; 1678:463352. [PMID: 35896048 DOI: 10.1016/j.chroma.2022.463352] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 10/17/2022]
Abstract
Post-translational modifications (PTMs) occur during or after protein biosynthesis and increase the functional diversity of proteome. They comprise phosphorylation, acetylation, methylation, glycosylation, ubiquitination, sumoylation (among many other modifications), and influence all aspects of cell biology. Mass-spectrometry (MS)-based proteomics is the most powerful approach for PTM analysis. Despite this, it is challenging due to low abundance and labile nature of many PTMs. Hence, enrichment of modified peptides is required for MS analysis. This review provides an overview of most common PTMs and a discussion of current enrichment methods for MS-based proteomics analysis. The traditional affinity strategies, including immunoenrichment, chromatography and protein pull-down, are outlined together with their strengths and shortcomings. Moreover, a special attention is paid to chemical enrichment strategies, such as capture by chemoselective probes, metabolic and chemoenzymatic labelling, which are discussed with an emphasis on their recent progress. Finally, the challenges and future trends in the field are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy.
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122 Milano, Italy.
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
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Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12040870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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Abstract
INTRODUCTION The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required. AREAS COVERED We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis. EXPERT OPINION N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
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Niedermaier S, Huesgen PF. Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140138. [DOI: 10.1016/j.bbapap.2018.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/31/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023]
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Li L, Yan G, Zhang X. A rapid and efficient method for N-termini analysis in short-lived proteins. Talanta 2019; 204:367-371. [DOI: 10.1016/j.talanta.2019.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/02/2019] [Accepted: 06/08/2019] [Indexed: 02/05/2023]
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Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
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Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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Recent advances in sample pre-treatment for emerging methods in proteomic analysis. Talanta 2017; 174:738-751. [DOI: 10.1016/j.talanta.2017.06.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 06/14/2017] [Accepted: 06/19/2017] [Indexed: 12/21/2022]
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12
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Chen L, Shan Y, Weng Y, Sui Z, Zhang X, Liang Z, Zhang L, Zhang Y. Hydrophobic Tagging-Assisted N-Termini Enrichment for In-Depth N-Terminome Analysis. Anal Chem 2016; 88:8390-5. [DOI: 10.1021/acs.analchem.6b02453] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Lingfan Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yichu Shan
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yejing Weng
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Xiaodan Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhen Liang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
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Li L, Yan G, Zhang X. Laser-assisted proteolysis for accelerating and enhancing protein N-termini analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1398-1402. [PMID: 27197032 DOI: 10.1002/rcm.7565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/18/2016] [Accepted: 03/13/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE Targeted analysis of protein N-termini contributes to elucidating the starting sites and post-translational modifications of mature protein N-termini. Tryptic digestion is important in protein N-termini analysis, as well as in conventional bottom-up proteomics strategies. It is essential to explore a new proteolysis method for the enhancement of protein N-termini analysis. METHODS Laser-assisted proteolysis was compared with conventional overnight proteolysis. Four standard proteins were studied as models and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. 100 pg of synthesized peptide was used as internal standard for comparison of N-terminus intensity. Laser-assisted proteolysis was demonstrated to accelerate and enhance N-termini analysis. A complex mouse liver proteome sample was used to validate the effect of laser-assisted proteolysis. RESULTS According to online database search, the number of matched peptides of four model proteins and the sequence coverage were comparable between the two proteolysis methods. Laser exposure time (40 s) could enhance the release of the N-terminus in model proteins. The number of identified N-termini in mouse liver was improved by 28.3% in the laser-assisted digest, compared to the conventional overnight digest. The time cost for digestion was shortened from overnight to 40 s. CONCLUSIONS Laser-assisted proteolysis was demonstrated to accelerate proteolysis and enhance N-termini analysis. If laser-assisted proteolysis was integrated into protein N-termini targeted methods, the performance of those methods should be improved. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lanting Li
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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