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Samgina TY, Vasileva ID, Zubarev RA, Lebedev AT. EThcD as a Unique Tool for the Top-Down De Novo Sequencing of Intact Natural Ranid Amphibian Peptides. Anal Chem 2024. [PMID: 38979842 DOI: 10.1021/acs.analchem.4c02109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
De novo sequencing of any novel peptide/protein is a difficult task. Full sequence coverage, isomeric amino acid residues, inter- and intramolecular S-S bonds, and numerous other post-translational modifications make the investigators employ various chemical modifications, providing a variety of specific fragmentation MSn patterns. The chemical processes are time-consuming, and their yields never reach 100%, while the subsequent purification often leads to the loss of minor components of the initial peptide mixture. Here, we present the advantages of the EThcD method that enables establishing the full sequence of natural intact peptides of ranid frogs in de novo top-down mode without any chemical modifications. The method provides complete sequence coverage, including the cyclic disulfide section, and reliable identification of isomeric leucine/isoleucine residues. The proposed approach demonstrated its efficiency in the analysis of peptidomes of ranid frogs from several populations of Rana arvalis, Rana temporaria, and Pelophylax esculentus complexes.
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Affiliation(s)
- Tatiana Yu Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina D Vasileva
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177, Sweden
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia
| | - Albert T Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
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2
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Sadecki PW, Laws GD, Morgan JJ, Wommack AJ, Nawrot R, Hicks LM. The Greater Celandine: Identification and Characterization of an Antimicrobial Peptide from Chelidonium majus. JOURNAL OF NATURAL PRODUCTS 2024; 87:544-553. [PMID: 38366995 PMCID: PMC10959680 DOI: 10.1021/acs.jnatprod.3c00939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Chelidonium majus, known as Greater Celandine, is a latex-bearing plant that has been leveraged for its anticancer and antimicrobial properties. Herein, C. majus aerial tissue is mined for the presence of antimicrobial peptides. A highly abundant cysteine-rich peptide with a length of 25 amino acids, deemed CM-AMP1, is characterized through multiple mass spectrometric approaches. Electron-activated dissociation is leveraged to differentiate between isoleucine and leucine residues and complement conventional collision-induced dissociation to gain full sequence coverage of the full-length peptide. CM-AMP1 shares little sequence similarity with any proteins in publicly available databases, highlighting the novelty of its cysteine landscape and core motif. The presence of three disulfide bonds in the native peptide confers proteolytic stability, and antimicrobial activity is greatly decreased upon the alkylation of the cysteine residues. Synthetic variants of CM-AMP1 are used to confirm the activity of the full-length sequence and the core motif. To assess the biological impact, E. coli was grown in a sublethal concentration of CM-AMP1 and quantitative proteomics was used to identify proteins produced by the bacteria under stress, ultimately suggesting a membrane lytic antimicrobial mechanism of action. This study integrates multiple analytical methods for molecular and biological characterization of a unique antimicrobial peptide identified from C. majus.
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Affiliation(s)
- Patric W Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Garrett D Laws
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Johnathon J Morgan
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Andrew J Wommack
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Robert Nawrot
- Department of Molecular Virology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań 61-712, Poland
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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3
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Sergent I, Schutz T, Oswald L, Obeid G, Lutz JF, Charles L. Using Nitroxides To Model the Ion Mobility Behavior of Nitroxide-Ended Oligomers: A Bottom-up Approach To Predict Mobility Separation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:534-541. [PMID: 38345914 DOI: 10.1021/jasms.3c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Block-truncated poly(phosphodiester)s are digital macromolecules storing binary information that can be decoded by MS/MS sequencing of individual blocks released as primary fragments of the entire polymer. As such, they are ideal species for the serial sequencing methodology enabled by MS-(CID)-IMS-(CID)-MS coupling, where two activation stages are combined in-line with ion mobility spectrometry (IMS) separation. Yet, implementation of this coupling still requires efforts to achieve IMS resolution of inner blocks, that can be considered as small oligomers with α termination composed of one nitroxide decorated with a different tag. As shown by molecular dynamics simulation, these oligomers adopt a conformation where the tag points out of the coil formed by the chain. Accordingly, the sole nitroxide termination was investigated here as a model to reduce the cost of calculation aimed at predicting the shift of collision cross-section (CCS) induced by new tag candidates and extrapolate this effect to nitroxide-terminated oligomers. A library of 10 nitroxides and 7 oligomers was used to validate our calculation methods by comparison with experimental IMS data as well as our working assumption. Based on conformation predicted by theoretical calculation, three new tag candidates could be proposed to achieve the +40 Å2 CCS shift required to ensure IMS separation of oligomers regardless of their coded sequence.
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Affiliation(s)
- Isaure Sergent
- Aix Marseille Université, CNRS, UMR 7273, Institut de Chimie Radicalaire (ICR), 13397 Marseille Cedex 20, France
| | - Thibault Schutz
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), 67000 Strasbourg, France
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 67034 Strasbourg Cedex 2, France
| | - Laurence Oswald
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 67034 Strasbourg Cedex 2, France
| | - Georgette Obeid
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), 67000 Strasbourg, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), 67000 Strasbourg, France
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 67034 Strasbourg Cedex 2, France
| | - Laurence Charles
- Aix Marseille Université, CNRS, UMR 7273, Institut de Chimie Radicalaire (ICR), 13397 Marseille Cedex 20, France
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4
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Samgina TY, Vasileva ID, Trebše P, Torkar G, Surin AK, Meng Z, Zubarev RA, Lebedev AT. Tandem Mass Spectrometry de novo Sequencing of the Skin Defense Peptides of the Central Slovenian Agile Frog Rana dalmatina. Molecules 2023; 28:7118. [PMID: 37894596 PMCID: PMC10608968 DOI: 10.3390/molecules28207118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Peptides released on frogs' skin in a stress situation represent their only weapon against micro-organisms and predators. Every species and even population of frog possesses its own peptidome being appropriate for their habitat. Skin peptides are considered potential pharmaceuticals, while the whole peptidome may be treated as a taxonomic characteristic of each particular population. Continuing the studies on frog peptides, here we report the peptidome composition of the Central Slovenian agile frog Rana dalmatina population. The detection and top-down de novo sequencing of the corresponding peptides was conducted exclusively by tandem mass spectrometry without using any chemical derivatization procedures. Collision-induced dissociation (CID), higher energy collision-induced dissociation (HCD), electron transfer dissociation (ETD) and combined MS3 method EThcD with stepwise increase of HCD energy were used for that purpose. MS/MS revealed the whole sequence of the detected peptides including differentiation between isomeric Leu/Ile, and the sequence portion hidden in the disulfide cycle. The array of the discovered peptide families (brevinins 1 and 2, melittin-related peptides (MRPs), temporins and bradykinin-related peptides (BRPs)) is quite similar to that of R. temporaria. Since the genome of this frog remains unknown, the obtained results were compared with the recently published transcriptome of R. dalmatina.
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Affiliation(s)
- Tatiana Yu. Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Irina D. Vasileva
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Polonca Trebše
- Faculty of Health Sciences, University of Ljubljana Zdravstvena Pot 5, 1000 Ljubljana, Slovenia;
| | - Gregor Torkar
- Department for Biology, Chemistry and Home Economics, University of Ljubljana Faculty of Education, Kardeljeva Ploščad 16, 1000 Ljubljana, Slovenia;
| | - Alexey K. Surin
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, 142290 Moscow, Russia;
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (Z.M.); (R.A.Z.)
| | - Roman A. Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (Z.M.); (R.A.Z.)
- The National Medical Research Center for Endocrinology, 115478 Moscow, Russia
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Albert T. Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
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Vasileva ID, Samgina TY, Meng Z, Zubarev RA, Lebedev AT. EThcD Benefits for the Sequencing Inside Intramolecular Disulfide Cycles of Amphibian Intact Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1979-1988. [PMID: 37525119 DOI: 10.1021/jasms.3c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Disulfide bonds formed by a pair of cysteine residues in the peptides' backbone represent a certain problem for their sequencing by means of mass spectrometry. As a rule, in proteomics, disulfide bonds should be cleaved before the analysis followed by some sort of chemical derivatization. That step is time-consuming and may lead to losses of minor peptides of the analyzed mixtures due to incomplete reaction, adsorption on the walls of the vials, etc. Certain problems in the de novo top-down sequencing of amphibian skin peptides are caused by the C-terminal disulfide loop, called the Rana box. Its reduction with or without subsequent derivatization was considered to be an unavoidable step before mass spectrometry. In the present study, EThcD demonstrated its efficiency in sequencing intact disulfide-containing peptides without any preliminary derivatization. Applied to the secretion of three frog species, EThcD provided the full sequence inside the intramolecular disulfide cycle for all S-S-containing peptides found in the samples, with the only exception being diarginine species. Proteolytic fragments, which are shorter than the original peptides, were helpful in some cases. HCD should be mentioned as a complementary tool to the EThcD tool, being useful as a confirmation method for some sequence details.
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Affiliation(s)
- Irina D Vasileva
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
| | - Tatiana Yu Samgina
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Albert T Lebedev
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
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Tolpina MD, Vasileva ID, Samgina TY. Modern Approaches in de novo Sequencing of Nontryptic Peptides of Ranid and Hylid Frogs by Means of Mass Spectrometry: A Review. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822130081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Samgina TY, Vasileva ID, Trebse P, Torkar G, Surin AK, Meng Z, Zubarev RA, Lebedev AT. Mass Spectrometry Differentiation between Rana arvalis Populations Based on Their Skin Peptidome Composition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1480-1491. [PMID: 35820801 DOI: 10.1021/jasms.2c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Skin secretion of amphibians often represents the only weapon of these species against pathogens and predators. Peptides constitute the major portion of active molecules of that weapon and may be treated as potential pharmaceuticals for future generations. The first step of their efficient use involves establishing of their primary structure, i.e., sequencing. De novo sequencing by means of mass spectrometry was applied to Rana arvalis species, collected in the spring 2021 in Central Slovenia (vicinity of Ljubljana). HPLC-ESI-HRMS/MS with Orbitrap instruments was used to establish the skin peptidome of these species and compare it with the earlier identified skin peptidome of the Moscow population of Rana arvalis. Application of CID, HCD, ETD, and EThcD enabled detecting and sequencing 18 peptides; five of them were novel and may be treated as possible biomarkers of the Ljubljana population of Rana arvalis. Interestingly, representatives of two peptide families (temporins and brevinins 2) were not found in the Moscow population. MS3 modes, first of all EThcD, demonstrated their great potential in the de novo sequencing, including extraction of the sequence information from the intact peptides with disulfide cycle (rana box) in their structure and differentiation of isomeric Leu/Ile residues. Thus, all six isomeric residues were reliably distinguished in the novel melittin-related peptide AK-23-1. In addition, another post-translational modification dealing with carbonylation of the N-terminal Gly of novel temporin AVa was established using the MS3 mode. The obtained results demonstrate the efficiency of the use of MS3 tools in proteomics/peptidomics.
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Affiliation(s)
- Tatiana Yu Samgina
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
| | - Irina D Vasileva
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
| | - Polonca Trebse
- University of Ljubljana Faculty of Health Sciences, Zdravstvena pot 5, Ljubljana 1000 Slovenia
- MASSECO d.o.o. Erazmova 20, Postojna 6230, Slovenia
| | - Gregor Torkar
- University of Ljubljana Faculty of Education, Department for Biology, Chemistry and Home Economics, Kardeljeva ploščad 16, Ljubljana 1000 Slovenia
| | - Alexey K Surin
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow 142290, Russia
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177 Sweden
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177 Sweden
| | - Albert T Lebedev
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
- MASSECO d.o.o. Erazmova 20, Postojna 6230, Slovenia
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8
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Schulte D, Peng W, Snijder J. Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling. Anal Chem 2022; 94:10391-10399. [PMID: 35834437 PMCID: PMC9330293 DOI: 10.1021/acs.analchem.2c01300] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Antibodies can target a vast molecular diversity of antigens.
This
is achieved by generating a complementary diversity of antibody sequences
through somatic recombination and hypermutation. A full understanding
of the antibody repertoire in health and disease therefore requires
dedicated de novo sequencing methods. Next-generation
cDNA sequencing methods have laid the foundation of our current understanding
of the antibody repertoire, but these methods share one major limitation
in that they target the antibody-producing B-cells, rather than the
functional secreted product in bodily fluids. Mass spectrometry-based
methods offer an opportunity to bridge this gap between antibody repertoire
profiling and bulk serological assays, as they can access antibody
sequence information straight from the secreted polypeptide products.
In a step to meeting the challenge of mass spectrometry (MS)-based
antibody sequencing, we present a fast and simple software tool (Stitch)
to map proteomic short reads to user-defined templates with dedicated
features for both monoclonal antibody sequencing and profiling of
polyclonal antibody repertoires. We demonstrate the use of Stitch
by fully reconstructing two monoclonal antibody sequences with >98%
accuracy (including I/L assignment); sequencing a Fab from patient
serum isolated by reversed-phase liquid chromatography (LC) fractionation
against a high background of homologous antibody sequences; sequencing
antibody light chains from the urine of multiple-myeloma patients;
and profiling the IgG repertoire in sera from patients hospitalized
with COVID-19. We demonstrate that Stitch assembles a comprehensive
overview of the antibody sequences that are represented in the dataset
and provides an important first step toward analyzing polyclonal antibodies
and repertoire profiling.
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Affiliation(s)
- Douwe Schulte
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Weiwei Peng
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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9
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Zhang W, Yang C, Liu J, Liang Z, Shan Y, Zhang L, Zhang Y. Accurate discrimination of leucine and isoleucine residues by combining continuous digestion with multiple MS 3 spectra integration in protein sequence. Talanta 2022; 249:123666. [PMID: 35717752 DOI: 10.1016/j.talanta.2022.123666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/26/2022]
Abstract
Protein de novo sequencing based on tandem mass spectrometry is a crucial technology that enables the identification of peptides without searching databases and assembling unknown sequence proteins, especially for monoclonal antibodies (mAbs). However, the discrimination of leucine (Leu) and isoleucine (Ile) residues in the target protein sequence is still challenging. Herein, we developed an accurate method by continuous digestion with MS3-based fragmentation and multiple spectra integration (evaluated by combined verification score, CVS) to distinguish Leu and Ile residues. Continuous digestion promotes the diversity of peptides in order to expose more Leu and Ile at the N-terminal. CVS integrates multiple MS3 spectra to reduce the interference from noise and co-fragmented ions and improve accuracy. This method successfully resolved all 75 Leu/Ile in bovine serum albumin, especially 3 consecutive Leu/Ile. We further applied the method to analyze trastuzumab and 67 out of the 68 Leu/Ile from the light chain and heavy chain were accurately discriminated, demonstrating the great potential in mAbs sequencing.
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Affiliation(s)
- Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chao Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science 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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10
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Gadush MV, Sautto GA, Chandrasekaran H, Bensussan A, Ross TM, Ippolito GC, Person MD. Template-Assisted De Novo Sequencing of SARS-CoV-2 and Influenza Monoclonal Antibodies by Mass Spectrometry. J Proteome Res 2022; 21:1616-1627. [PMID: 35653804 DOI: 10.1021/acs.jproteome.1c00913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we used multiple enzyme digestions, coupled with higher-energy collisional dissociation (HCD) and electron-transfer/higher-energy collision dissociation (EThcD) fragmentation to develop a mass-spectrometric (MS) method for determining the complete protein sequence of monoclonal antibodies (mAbs). The method was refined on an mAb of a known sequence, a SARS-CoV-1 antireceptor binding domain (RBD) spike monoclonal antibody. The data were searched using Supernovo to generate a complete template-assisted de novo sequence for this and two SARS-CoV-2 mAbs of known sequences resulting in correct sequences for the variable regions and correct distinction of Ile and Leu residues. We then used the method on a set of 25 antihemagglutinin (HA) influenza antibodies of unknown sequences and determined high confidence sequences for >99% of the complementarity determining regions (CDRs). The heavy-chain and light-chain genes were cloned and transfected into cells for recombinant expression followed by affinity purification. The recombinant mAbs displayed binding curves matching the original mAbs with specificity to the HA influenza antigen. Our findings indicate that this methodology results in almost complete antibody sequence coverage with high confidence results for CDR regions on diverse mAb sequences.
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Affiliation(s)
- Michelle V Gadush
- Center for Biomedical Research Support, Biological Mass Spectrometry Facility, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Giuseppe A Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia 30602, United States
| | - Hamssika Chandrasekaran
- Center for Biomedical Research Support, Biological Mass Spectrometry Facility, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Alena Bensussan
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia 30602, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Maria D Person
- Center for Biomedical Research Support, Biological Mass Spectrometry Facility, The University of Texas at Austin, Austin, Texas 78712, United States
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11
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Edwards HM, Wu HT, Julian RR, Jackson GP. Differentiation of leucine and isoleucine residues in peptides using charge transfer dissociation mass spectrometry (CTD-MS). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9246. [PMID: 34927767 DOI: 10.1002/rcm.9246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
RATIONALE The function of a protein or the binding affinity of an antibody can be substantially altered by the replacement of leucine (Leu) with isoleucine (Ile), and vice versa, so the ability to identify the correct isomer using mass spectrometry can help resolve important biological questions. Tandem mass spectrometry approaches for Leu/Ile (Xle) discrimination have been developed, but they all have certain limitations. METHODS Four model peptides and two wild-type peptide sequences containing either Leu or Ile residues were subjected to charge transfer dissociation (CTD) mass spectrometry on a modified three-dimensional ion trap. The peptides were analyzed in both the 1+ and 2+ charge states, and the results were compared to conventional collision-induced dissociation spectra of the same peptides obtained using the same instrument. RESULTS CTD resulted in 100% sequence coverage for each of the studied peptides and provided a variety of side-chain cleavages, including d, w and v ions. Using CTD, reliable d and w ions of Xle residues were observed more than 80% of the time. When present, d ions are typically greater than 10% of the abundance of the corresponding a ions from which they derive, and w ions are typically more abundant than the z ions from which they derive. CONCLUSIONS CTD has the benefit of being applicable to both 1+ and 2+ precursor ions, and the overall performance is comparable to that of other high-energy activation techniques like hot electron capture dissociation and UV photodissociation. CTD does not require chemical modifications of the precursor peptides, nor does it require additional levels of isolation and fragmentation.
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Affiliation(s)
- Halle M Edwards
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, USA
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12
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Lebedev AT, Vasileva ID, Samgina TY. FT-MS in the de novo top-down sequencing of natural nontryptic peptides. MASS SPECTROMETRY REVIEWS 2022; 41:284-313. [PMID: 33347655 DOI: 10.1002/mas.21678] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.
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Affiliation(s)
- Albert T Lebedev
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Irina D Vasileva
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Y Samgina
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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13
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DeLuca KF, Mick JE, Ide AH, Lima WC, Sherman L, Schaller KL, Anderson SM, Zhao N, Stasevich TJ, Varma D, Nilsson J, DeLuca JG. Generation and diversification of recombinant monoclonal antibodies. eLife 2021; 10:72093. [PMID: 34970967 PMCID: PMC8763395 DOI: 10.7554/elife.72093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies are indispensable tools used for a large number of applications in both foundational and translational bioscience research; however, there are drawbacks to using traditional antibodies generated in animals. These include a lack of standardization leading to problems with reproducibility, high costs of antibodies purchased from commercial sources, and ethical concerns regarding the large number of animals used to generate antibodies. To address these issues, we have developed practical methodologies and tools for generating low-cost, high-yield preparations of recombinant monoclonal antibodies and antibody fragments directed to protein epitopes from primary sequences. We describe these methods here, as well as approaches to diversify monoclonal antibodies, including customization of antibody species specificity, generation of genetically encoded small antibody fragments, and conversion of single chain antibody fragments (e.g. scFv) into full-length, bivalent antibodies. This study focuses on antibodies directed to epitopes important for mitosis and kinetochore function; however, the methods and reagents described here are applicable to antibodies and antibody fragments for use in any field.
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Affiliation(s)
- Keith F DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Jeanne E Mick
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Amy Hodges Ide
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Wanessa C Lima
- Geneva Antibody Facility, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lori Sherman
- CU Cancer Center Cell Technologies Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Kristin L Schaller
- Department of Pediatric Hematology, Oncology and Bone Marrow Transplant, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Steven M Anderson
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Dileep Varma
- Department of Cell and Developmental Biology, Northwestern University, Chicago, United States
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Germany
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
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14
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Timms M, Steel R. Defining the specificity of recombinant human erythropoietin confirmation in equine samples by liquid chromatography-tandem mass spectrometry. Drug Test Anal 2021; 14:676-689. [PMID: 34898016 DOI: 10.1002/dta.3210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022]
Abstract
The proteotypic human EPO peptides YLLEAK (T4), SLTTLLR (T11), TITADTFR (T14), and VYSNFLR (T17) are often used to confirm the presence of recombinant human EPO (rhEPO) in equine samples. Each of these peptides contains one or more isomeric leucine or isoleucine amino acids, raising the possibility that a simple leucine/isoleucine substitution could lead to a false identification when compared with a rhEPO reference standard. To examine this possibility variants of these four peptides were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These studies indicate that confirmation of rhEPO in equine samples by immuno-affinity capture and LC-MS/MS analysis is true and accurate. It was also found that chromatography played a greater role in determining LC-MS/MS specificity than tandem mass spectrometry and that, in the case of more hydrophilic peptides, the accuracy of peptide identification could be enhanced by the inclusion of 13 C and 15 N labelled peptide internal standards.
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Affiliation(s)
- Mark Timms
- Biological Research Unit, Racing Analytical Services Ltd, Flemington, Victoria, Australia
| | - Rohan Steel
- Biological Research Unit, Racing Analytical Services Ltd, Flemington, Victoria, Australia
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15
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Watts E, Potts GK, Ready DB, George Thompson AM, Lee J, Escobar EE, Patterson MJ, Brodbelt JS. Characterization of HLA-A*02:01 MHC Immunopeptide Antigens Enhanced by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2021; 93:13134-13142. [PMID: 34553926 DOI: 10.1021/acs.analchem.1c01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying major histocompatibility complex (MHC) class I immunopeptide antigens represents a key step in the development of immune-based targeted therapeutics and vaccines. However, the complete characterization of these antigens by tandem mass spectrometry remains challenging due to their short sequence length, high degree of hydrophobicity, and/or lack of sufficiently basic amino acids. This study seeks to address the potential for 193 nm ultraviolet photodissociation (UVPD) to improve the analysis of MHC class I immunopeptides by offering enhanced characterization of these sequences in lower charge states and differentiation of prominent isomeric leucine and isoleucine residues in the HLA-A*02:01 motif. Although electron transfer dissociation-higher energy collisional dissociation (EThcD) offered some success in the differentiation of leucine and isoleucine, 193 nm UVPD was able to confirm the identity of nearly 60% of leucine and isoleucine residues in a synthetic peptide mixture. Furthermore, 193 nm UVPD led to significantly more peptide identifications and higher scoring metrics than EThcD for peptides obtained from immunoprecipitation of MHC class I immunopeptides from in vitro cell culture. Additionally, 193 nm UVPD represents a promising complementary technique to higher-energy collisional dissociation (HCD), in which 424 of the 2593 peptides identified by 193 nm UVPD were not identified by HCD in HLA-A*02:01-specific immunoprecipitation and 804 of the 3300 peptides identified by 193 nm UVPD were not identified by HCD for pan HLA-A, -B, and -C immunoprecipitation. These results highlight that 193 nm UVPD offers an option for the characterization of immunopeptides, including differentiation of leucine and isoleucine residues.
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Affiliation(s)
- Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | - Gregory K Potts
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Damien B Ready
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | | | - Janice Lee
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | | | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
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16
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Samgina TY, Vasileva ID, Kovalev SV, Trebse P, Torkar G, Surin AK, Zubarev RA, Lebedev AT. Differentiation of Central Slovenian and Moscow populations of Rana temporaria frogs using peptide biomarkers of temporins family. Anal Bioanal Chem 2021; 413:5333-5347. [PMID: 34235566 DOI: 10.1007/s00216-021-03506-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022]
Abstract
Skin secretion represents the only means of defense for the majority of frog species. That phenomenon is based on the fact that the main components of the secretion are peptides demonstrating greatly varying types of bioactivity. They fulfill regulatory functions, fight microorganisms and may be even helpful against predators. These peptides are considered to be rather promising pharmaceuticals of future generation as according to the present knowledge microorganisms are unlikely to develop resistance to them. Mass spectrometry sequencing of these peptides is the most efficient first step of their study providing reliably their primary structures, i.e., amino acids sequence and S-S bond motif. Besides discovering new bioactive peptides, mass spectrometry appears to be an efficient tool of taxonomy studies, allowing for distinguishing not only between closely related species, but also between populations of the same species. Application of several tandem mass spectrometry tools (CID, HCD, ETD, EThcD) available with Orbitrap mass analyzer allowed us to obtain full sequence of about 60 peptides in the secretion of Slovenian population of brown ranid frog Rana temporaria. The problem of sequence inside C-terminal cycle formed by two Cys and differentiation of isomeric Leu and Ile residues was done in top-down mode without any derivatization steps. Besides general biomarkers of Rana temporaria species, Central Slovenian population of Rana temporaria demonstrates six novel temporins and one brevinin 1, which may be treated as biomarkers of that population.
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Affiliation(s)
- T Yu Samgina
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia.
| | - I D Vasileva
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - S V Kovalev
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - P Trebse
- University of Ljubljana Faculty of Health Sciences, Zdravstvena pot 5, 1000, Ljubljana, Slovenia
| | - G Torkar
- Department for Biology, Chemistry and Home Economics, University of Ljubljana Faculty of Education, Kardeljeva ploščad 16, 1000, Ljubljana, Slovenia
| | - A K Surin
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow, 142290, Russia
| | - R A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177, Stockholm, Sweden.,Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
| | - A T Lebedev
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia.
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17
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Samgina TY, Tolpina MD, Surin AK, Kovalev SV, Bosch RA, Alonso IP, Garcia FA, Gonzalez Lopez LJ, Lebedev AT. Manual mass spectrometry de novo sequencing of the anionic host defense peptides of the Cuban Treefrog Osteopilus septentrionalis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9061. [PMID: 33527491 DOI: 10.1002/rcm.9061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Host defense peptides accumulated in the skin glands of the animals constitute the basis of the adaptive and immune system of amphibians. The peptidome of the Cuban frog Osteopilus septentrionalis was established using tandem mass spectrometry as the best analytical tool to elucidate the sequence of these peptides. METHODS Manual interpretation of complementary collision-induced dissociation (CID), higher energy collision-induced dissociation (HCD), and electron transfer dissociation (ETD) tandem mass spectra recorded with an Orbitrap Elite mass spectrometer in liquid chromatography/mass spectrometry (LC/MS) mode was used to sequence the peptide components of the frog skin secretion, obtained by mild electrostimulation. RESULTS Although the vast majority of amphibian peptides discovered so far are cationic, surprisingly only anionic peptides were identified in the skin secretion of the Cuban frog Osteopilus septentrionalis. Mass spectrometry allowed the sequences to be established of 16 representatives of new peptide families: septenins 1 and septenins 2. The highest sequence coverage when dealing with these anionic peptides was obtained with CID normalized collision energy 35 and HCD normalized collision energy 28. CONCLUSIONS Mirror-symmetrical peptides are sequenced using N-terminal acetylation. Acetylated Ser is reliably distinguished from isomeric Glu by the loss of ketene from b-ions containing the corresponding residue. Calculations of the physicochemical and structural properties of the discovered anionic septenins 1 and 2 allowed the mechanism of their interaction with microbe cells to be postulated.
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Affiliation(s)
- Tatiana Y Samgina
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Maria D Tolpina
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Alexey K Surin
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow, 142290, Russia
| | - Sergey V Kovalev
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Roberto Alonso Bosch
- Museum of Natural History "Felipe Poey", Faculty of Biology, University of Havana, Havana, Cuba
| | - Isel Pascual Alonso
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | | | - Luis Javier Gonzalez Lopez
- Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana, Cuba
| | - Albert T Lebedev
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
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18
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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19
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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20
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Götze S, Stallforth P. Structure elucidation of bacterial nonribosomal lipopeptides. Org Biomol Chem 2020; 18:1710-1727. [DOI: 10.1039/c9ob02539a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.
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Affiliation(s)
- Sebastian Götze
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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21
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Liang Z, Yu X, Zhong W. Peptide Sequence Influence on the Differentiation of Valine and Norvaline by Hot Electron Capture Dissociation. Anal Chem 2019; 91:4381-4387. [PMID: 30786210 DOI: 10.1021/acs.analchem.8b04808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Isomeric amino acid residues such as valine (Val) and norvaline (Nva) are common in recombinant proteins. The mis-incorporation of Nva for leucine (Leu) causes heterogeneity and in some cases even toxicity. Previous studies have shown that hot electron capture dissociation (HECD) is able to differentiate Val from Nva by producing diagnostic w ions on custom designed synthetic model peptides. To broaden the utilization of HECD in proteomic studies and to define the critical structural features, a thorough investigation was performed on representative peptides including specifically designed synthetic peptides as well as biological peptides bearing tryptic digest-like features and peptides with post-translational modifications. Experimental evidence confirmed that the formation of a w ion is directly dependent upon the presence of the corresponding z ion. The results suggested that a charge carrier residue at the C-terminus is promoting the formation of diagnostic w ions for Nva. Thus, peptides resulting from trypsin digestion, with arginine (Arg) or lysine (Lys) at the C-terminus, can be analyzed using the HECD method. Post-translational modification (PTM) such as phosphorylation did not prevent the generation of the requisite side chain fragmentation w ions. These results suggest the general applicability of HECD for unambiguous identification of Val and Nva especially in structure characterization of therapeutic proteins.
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Affiliation(s)
- Zhidan Liang
- Analytical Research & Development, Merck Research Laboratories , Merck & Co., Inc. , Rahway , New Jersey 07065 , United States
| | - Xiang Yu
- Department of Pharmacokinetics, Pharmacodynamics, & Drug Metabolism (PPDM), Merck Research Laboratories , Merck & Co., Inc. , West Point , Pennsylvania 19486 , United States
| | - Wendy Zhong
- Analytical Research & Development, Merck Research Laboratories , Merck & Co., Inc. , Rahway , New Jersey 07065 , United States
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22
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Darula Z, Pap Á, Medzihradszky KF. Extended Sialylated O-Glycan Repertoire of Human Urinary Glycoproteins Discovered and Characterized Using Electron-Transfer/Higher-Energy Collision Dissociation. J Proteome Res 2018; 18:280-291. [PMID: 30407017 DOI: 10.1021/acs.jproteome.8b00587] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A relatively novel activation technique, electron-transfer/higher-energy collision dissociation (EThcD) was used in the LC-MS/MS analysis of tryptic glycopeptides enriched with wheat germ agglutinin from human urine samples. We focused on the characterization of mucin-type O-glycopeptides. EThcD in a single spectrum provided information on both the peptide modified and the glycan carried. Unexpectedly, glycan oxonium ions indicated the presence of O-acetyl, and even O-diacetyl-sialic acids. B and Y fragment ions revealed that (i) in core 1 structures the Gal residue featured the O-acetyl-sialic acid, when there was only one in the glycan; (ii) several glycopeptides featured core 1 glycans with disialic acids, in certain instances O-acetylated; (iii) the disialic acid was linked to the GalNAc residue whatever the degree of O-acetylation; (iv) core 2 isomers with a single O-acetyl-sialic acid were chromatographically resolved. Glycan fragmentation also helped to decipher additional core 2 oligosaccharides: a LacdiNAc-like structure, glycans carrying sialyl LewisX/A at different stages of O-acetylation, and blood antigens. A sialo core 3 structure was also identified. We believe this is the first study when such structures were characterized from a very complex mixture and were linked not only to a specific protein, but also the sites of modifications have been determined.
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Affiliation(s)
- Zsuzsanna Darula
- Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62. , H-6726 Szeged , Hungary
| | - Ádám Pap
- Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62. , H-6726 Szeged , Hungary.,Doctoral School in Biology, Faculty of Science and Informatics , University of Szeged , Kozep fasor 52. , H-6726 Szeged , Hungary
| | - Katalin F Medzihradszky
- Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62. , H-6726 Szeged , Hungary
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23
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Maibom-Thomsen S, Heissel S, Mørtz E, Højrup P, Bunkenborg J. Discrimination of Isoleucine and Leucine by Dimethylation-Assisted MS3. Anal Chem 2018; 90:9055-9059. [DOI: 10.1021/acs.analchem.8b01375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sheila Maibom-Thomsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
- Alphalyse A/S, Unsbjergvej 4D, Odense SØ 5220, Denmark
| | - Søren Heissel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Ejvind Mørtz
- Alphalyse A/S, Unsbjergvej 4D, Odense SØ 5220, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
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24
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Pap A, Klement E, Hunyadi-Gulyas E, Darula Z, Medzihradszky KF. Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1210-1220. [PMID: 29730764 DOI: 10.1007/s13361-018-1945-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined. Thus, we investigated the reasons why was it so, to help to improve the identification success rate. Focusing on O-linked glycopeptides, we noticed that in EThcD, larger glycan oxonium ions better survive the activation than those in HCD. These fragments, combined with reducing terminal Y ions, provide important information about the glycan(s) present, so we investigated whether filtering the peaklists for glycan oxonium ions indicating the presence of a tetra- or hexasaccharide structure would help to reveal all molecules containing such glycans. Our study showed that intact glycans frequently do not survive even mild supplemental activation, meaning one cannot rely on these oxonium ions exclusively. We found that ETD efficiency is still a limiting factor, and for highly glycosylated peptides, the only information revealed in EThcD was related to the glycan structures. The limited overlap of results delivered by the two search engines draws attention to the fact that automated data interpretation of O-linked glycopeptides is not even close to being solved. Graphical abstract ᅟ.
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Affiliation(s)
- Adam Pap
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Eva Klement
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Eva Hunyadi-Gulyas
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsuzsanna Darula
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
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25
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Samgina TY, Kovalev SV, Tolpina MD, Trebse P, Torkar G, Lebedev AT. EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:842-852. [PMID: 29299834 DOI: 10.1007/s13361-017-1857-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/19/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops. Graphical Abstract ᅟ.
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Affiliation(s)
- Tatiana Yu Samgina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V Kovalev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Miriam D Tolpina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Polonca Trebse
- Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Torkar
- Faculty of Education, University of Ljubljana, Ljubljana, Slovenia
| | - Albert T Lebedev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia.
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26
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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27
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Darula Z, Medzihradszky KF. Analysis of Mammalian O-Glycopeptides-We Have Made a Good Start, but There is a Long Way to Go. Mol Cell Proteomics 2018; 17:2-17. [PMID: 29162637 PMCID: PMC5750848 DOI: 10.1074/mcp.mr117.000126] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Indexed: 12/18/2022] Open
Abstract
Glycosylation is perhaps the most common post-translational modification. Recently there has been growing interest in cataloging the glycan structures, glycoproteins, and specific sites modified and deciphering the biological functions of glycosylation. Although the results are piling up for N-glycosylation, O-glycosylation is seriously trailing behind. In our review we reiterate the difficulties researchers have to overcome in order to characterize O-glycosylation. We describe how an ingenious cell engineering method delivered exciting results, and what could we gain from "wild-type" samples. Although we refer to the biological role(s) of O-glycosylation, we do not provide a complete inventory on this topic.
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Affiliation(s)
- Zsuzsanna Darula
- From the ‡Laboratory of Proteomics Research, Biological Research Centre, Hungarian Academy of Sciences, H-6726, 62 Temesvari krt, Szeged, Hungary
| | - Katalin F Medzihradszky
- From the ‡Laboratory of Proteomics Research, Biological Research Centre, Hungarian Academy of Sciences, H-6726, 62 Temesvari krt, Szeged, Hungary;
- §Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, Genentech Hall, N472A, MC 2240, 600 16th Street, San Francisco, California 94158-2517
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28
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Kovalyov SV, Zhokhov SS, Onoprienko LV, Vaskovsky BV, Lebedev AT. Exploration of doubtful cases of leucine and isoleucine discrimination in mass spectrometric peptide sequencing by electron-transfer and higher-energy collision dissociation-based method. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:376-384. [PMID: 29183199 DOI: 10.1177/1469066717730705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Electron-transfer dissociation (ETD) and electron-transfer and higher-energy collision dissociation (EThcD) spectra of short tryptic peptides with leucine/isoleucine residues in neighboring positions demonstrate intensive w-ions. On the contrary, u-ions possess very low intensities (if present at all). Therefore radical site migration is negligible in the applied conditions while ETD (EThcD) spectra allow for the reliable discrimination of the isomeric residues in the sequencing process. The presence of a fragment ion 43.055 mass units lower than z2-ion of peptides with IK sequence at their C-termini was shown to be a result of alternative fragmentation starting from the loss of propylammonium ion from the doubly protonated peptide molecule and formation of an oxazole fragment ion.
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Affiliation(s)
- Sergey V Kovalyov
- 1 Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey S Zhokhov
- 1 Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Ludmila V Onoprienko
- 2 Shemyakin-Ovchinnikov Insitiute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Boris V Vaskovsky
- 2 Shemyakin-Ovchinnikov Insitiute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Albert T Lebedev
- 1 Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
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29
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Zhou XX, Zeng WF, Chi H, Luo C, Liu C, Zhan J, He SM, Zhang Z. pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning. Anal Chem 2017; 89:12690-12697. [DOI: 10.1021/acs.analchem.7b02566] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xie-Xuan Zhou
- State
Key Laboratory of Computer Architecture, Institute of Computing Technology
(ICT), Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Feng Zeng
- University of Chinese Academy of Sciences, Beijing, China
- Key
Laboratory of Intelligent Information Processing of CAS, ICT, Chinese Academy of Sciences, Beijing 100190, China
| | - Hao Chi
- University of Chinese Academy of Sciences, Beijing, China
- Key
Laboratory of Intelligent Information Processing of CAS, ICT, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunjie Luo
- State
Key Laboratory of Computer Architecture, Institute of Computing Technology
(ICT), Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- University of Chinese Academy of Sciences, Beijing, China
- Key
Laboratory of Intelligent Information Processing of CAS, ICT, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianfeng Zhan
- State
Key Laboratory of Computer Architecture, Institute of Computing Technology
(ICT), Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Si-Min He
- University of Chinese Academy of Sciences, Beijing, China
- Key
Laboratory of Intelligent Information Processing of CAS, ICT, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhifei Zhang
- Capital Medical University, Beijing 100069, China
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