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Lin CH, Liao HY, Lane HY, Chen CJ. Elucidating the Mechanisms of Sodium Benzoate in Alzheimer Disease: Insights from Quantitative Proteomics Analysis of Serum Samples. Int J Neuropsychopharmacol 2023; 26:856-866. [PMID: 37875373 PMCID: PMC10726399 DOI: 10.1093/ijnp/pyad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND N-methyl-D-aspartate receptors (NMDARs) are crucial components of brain function involved in memory and neurotransmission. Sodium benzoate is a promising NMDAR enhancer and has been proven to be a novel, safe, and efficient therapy for patients with Alzheimer disease (AD). However, in addition to the role of sodium benzoate as an NMDA enhancer, other mechanisms of sodium benzoate in treating AD are still unclear. To elucidate the potential mechanisms of sodium benzoate in Alzheimer disease, this study employed label-free quantitative proteomics to analyze serum samples from AD cohorts with and without sodium benzoate treatment. METHODS The serum proteins from each patient were separated into 24 fractions using an immobilized pH gradient, digested with trypsin, and then subjected to nanoLC‒MS/MS to analyze the proteome of all patients. The nanoLC‒MS/MS data were obtained with a label-free quantitative proteomic approach. Proteins with fold changes were analyzed with STRING and Cytoscape to find key protein networks/processes and hub proteins. RESULTS Our analysis identified 861 and 927 protein groups in the benzoate treatment cohort and the placebo cohort, respectively. The results demonstrated that sodium benzoate had the most significant effect on the complement and coagulation cascade pathways, amyloidosis disease, immune responses, and lipid metabolic processes. Moreover, Transthyretin, Fibrinogen alpha chain, Haptoglobin, Apolipoprotein B-100, Fibrinogen beta chain, Apolipoprotein E, and Alpha-1-acid glycoprotein 1 were identified as hub proteins in the protein‒protein interaction networks. CONCLUSIONS These findings suggest that sodium benzoate may exert its influence on important pathways associated with AD, thus contributing to the improvement in the pathogenesis of the disease.
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Affiliation(s)
- Chieh-Hsin Lin
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yi Liao
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Hsien-Yuan Lane
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Department of Psychiatry and Brain Disease Research Center, China Medical University Hospital, Taichung, Taiwan
- Department of Psychology, College of Medical and Health Sciences, Asia University, Taichung, Taiwan
| | - Chao-Jung Chen
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan
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2
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Cline EN, Alvarez C, Duan J, Patrie SM. Online μSEC 2-nRPLC-MS for Improved Sensitivity of Intact Protein Detection of IEF-Separated Nonhuman Primate Cerebrospinal Fluid Proteins. Anal Chem 2021; 93:16741-16750. [PMID: 34881887 PMCID: PMC10476446 DOI: 10.1021/acs.analchem.1c00396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteoform-resolved information, obtained by top-down (TD) "intact protein" proteomics, is expected to contribute substantially to the understanding of molecular pathogenic mechanisms and, in turn, identify novel therapeutic and diagnostic targets. However, the robustness of mass spectrometry (MS) analysis of intact proteins in complex biological samples is hindered by the high dynamic range in protein concentration and mass, protein instability, and buffer complexity. Here, we describe an evolutionary step for intact protein investigations through the online implementation of tandem microflow size-exclusion chromatography with nanoflow reversed-phase liquid chromatography and MS (μSEC2-nRPLC-MS). Online serial high-/low-pass SEC filtration overcomes the aforementioned hurdles to intact proteomic analysis through automated sample desalting/cleanup and enrichment of target mass ranges (5-155 kDa) prior to nRPLC-MS. The coupling of μSEC to nRPLC is achieved through a novel injection volume control (IVC) strategy of inserting protein trap columns, pre- and post-μSEC columns, to enable injection of dilute samples in high volumes without loss of sensitivity or resolution. Critical characteristics of the approach are tested via rigorous investigations on samples of varied complexity and chemical background. Application of the platform to cerebrospinal fluid (CSF) prefractionated by OFFGEL isoelectric focusing drastically increases the number of intact mass tags (IMTs) detected within the target mass range (5-30 kDa) in comparison to one-dimensional nRPLC-MS with approximately 100× less CSF than previous OFFGEL studies. Furthermore, the modular design of the μSEC2-nRPLC-MS platform is robust and promises significant flexibility for large-scale TDMS analysis of diverse samples either directly or in concert with other multidimensional fractionation steps.
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Affiliation(s)
- Erika N Cline
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Carina Alvarez
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Jiana Duan
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
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3
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OFFGEL and GELFrEE fractionation: Novel liquid-phase protein recovery strategies in proteomics studies. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Corbett JR, Robinson DE, Patrie SM. Robustness and Ruggedness of Isoelectric Focusing and Superficially Porous Liquid Chromatography with Fourier Transform Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:346-354. [PMID: 33274937 PMCID: PMC10476448 DOI: 10.1021/jasms.0c00355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An investigation of a multidimensional proteomics workflow composed of off-gel isoelectric focusing (IEF) and superficially porous liquid chromatography (SPLC) with Fourier transform mass spectrometry (FTMS) was completed in order to assess various figures of merit associated with intact protein measurements. Triplicate analysis performed at both high and low FTMS resolutions on the E. coli proteome resulted in ∼900 redundant proteoforms from 3 to 95 kDa. Normalization of the chromatographic axis to identified proteoforms enabled reproducible physicochemical property measurements between proteome replicates with inter-replicate variances of ±3 ppm mass error for proteoforms <30 kDa, ±1.1 Da for proteins >30 kDa, ±12 s retention time error, and ±0.21 pI units. The results for E. coli and standard proteins revealed a correlation between pI precision and proteoform abundance with species detected in multiple IEF fractions exhibiting pI precisions less than the theoretical resolution of the off-gel system (±0.05 vs ±0.17, respectively). Evaluation of differentially modified proteoforms of standard proteins revealed that high sample loads (100s μgrams) change the IEF pH gradient profile, leading to sample broadening that facilitates resolution of charged post-translational modifications (e.g., phosphorylation, sialylation). Despite the impact of sample load on IEF resolution, results on standard proteins measured directly or after being spiked into E. coli demonstrated that the reproducibility of the workflow permitted recombination of the MS signal across IEF fractions in a manner supporting the evaluation of three label-free quantitation metrics for intact protein studies (proteoforms, proteoform ratios, and protein) over 102-103 sample amount with low femtomole detection limits.
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Affiliation(s)
- John R Corbett
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
- Department of Bioengineering, UT Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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Abd El-Aziz TM, Soares AG, Stockand JD. Advances in venomics: Modern separation techniques and mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1160:122352. [PMID: 32971366 PMCID: PMC8174749 DOI: 10.1016/j.jchromb.2020.122352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/31/2022]
Abstract
Snake venoms are complex chemical mixtures of biologically active proteins and non-protein components. Toxins have a wide range of targets and effects to include ion channels and membrane receptors, and platelet aggregation and platelet plug formation. Toxins target these effectors and effects at high affinity and selectivity. From a pharmacological perspective, snake venom compounds are a valuable resource for drug discovery and development. However, a major challenge to drug discovery using snake venoms is isolating and analyzing the bioactive proteins and peptides in these complex mixtures. Getting molecular information from complex mixtures such as snake venoms requires proteomic analyses, generally combined with transcriptomic analyses of venom glands. The present review summarizes current knowledge and highlights important recent advances in venomics with special emphasis on contemporary separation techniques and bioinformatics that have begun to elaborate the complexity of snake venoms. Several analytical techniques such as two-dimensional gel electrophoresis, RP-HPLC, size exclusion chromatography, ion exchange chromatography, MALDI-TOF-MS, and LC-ESI-QTOF-MS have been employed in this regard. The improvement of separation approaches such as multidimensional-HPLC, 2D-electrophoresis coupled to soft-ionization (MALDI and ESI) mass spectrometry has been critical to obtain an accurate picture of the startling complexity of venoms. In the case of bioinformatics, a variety of software tools such as PEAKS also has been used successfully. Such information gleaned from venomics is important to both predicting and resolving the biological activity of the active components of venoms, which in turn is key for the development of new drugs based on these venom components.
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Affiliation(s)
- Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Antonio G Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
| | - James D Stockand
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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Huang C, Hou C, Ijaz M, Yan T, Li X, Li Y, Zhang D. Proteomics discovery of protein biomarkers linked to meat quality traits in post-mortem muscles: Current trends and future prospects: A review. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.09.030] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Gel electrophoresis-based plant proteomics: Past, present, and future. Happy 10th anniversary Journal of Proteomics! J Proteomics 2019; 198:1-10. [DOI: 10.1016/j.jprot.2018.08.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/21/2018] [Accepted: 08/26/2018] [Indexed: 02/03/2023]
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8
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Dor M, Eperon S, Lalive PH, Guex-Crosier Y, Hamedani M, Salvisberg C, Turck N. Investigation of the global protein content from healthy human tears. Exp Eye Res 2019; 179:64-74. [DOI: 10.1016/j.exer.2018.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/01/2018] [Accepted: 10/11/2018] [Indexed: 01/03/2023]
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9
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Maurye P, Basu A, Naskar M, Bandyopadhyay TK, Biswas JK. A tetrad apparatus for protein gel casting, electrophoresis, staining, and scanning techniques with dual sensors for automatic detection of gel polymerization and protein migration. Electrophoresis 2018; 39:2943-2953. [PMID: 30221383 DOI: 10.1002/elps.201800252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 11/07/2022]
Abstract
Recent advancements in biochemical sciences have facilitated researchers to explore the structure and function of macro molecules in a cell. PAGE is one of the most favored and adapted laboratory techniques. Due to its simple and economical procedures, several variants or new modifications are routinely observed in the basic electrophoresis technique that comprises gel casting, electrophoresis, staining, and imaging process which consequently necessitates additional apparatuses/components in the laboratory. Operation of these additional apparatuses/components lengthens the pre- and postelectrophoresis procedures involving many intermittent tedious and time-consuming steps. A universal apparatus that can facilitate all such associated techniques is lacking and is of utmost importance for fast and effective results. An apparatus that can perform synchronized action of slab gel casting (16 × 16 cm), electrophoresis (SDS-PAGE), dye staining (Coomassie), and imaging (scanning) techniques with real-time monitoring through sensor technology is described in this article. The estimated cost (∼$150) of fabrication of the apparatus is very economical and simple assembly procedure of the main apparatus can be completed within ∼30 min after fabrication.
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Affiliation(s)
- Praveen Maurye
- ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Arpita Basu
- ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Malay Naskar
- ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Tapas Kumar Bandyopadhyay
- Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, West Bengal, India
| | - Jayanta Kumar Biswas
- Department of Ecological Studies and the International International Centre for Ecological Engineering, University of Kalyani, Kalyani, West Bengal, India
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Smith J, Davey G, Polom K, Roviello F, Bones J. Mining the acidic serum proteome utilizing off-gel isoelectric focusing and label free quantitative liquid chromatography mass spectrometry. J Chromatogr A 2018; 1566:32-43. [DOI: 10.1016/j.chroma.2018.06.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 12/25/2022]
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11
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Zhuang Q, Cao W, Ni Y, Wang Y. Synthesis-identification integration: One-pot hydrothermal preparation of fluorescent nitrogen-doped carbon nanodots for differentiating nucleobases with the aid of multivariate chemometrics analysis. Talanta 2018; 185:491-498. [DOI: 10.1016/j.talanta.2018.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/10/2018] [Accepted: 04/07/2018] [Indexed: 12/31/2022]
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12
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Use of liquid isoelectric focusing (OFFGEL) on the discovery of meat tenderness biomarkers. J Proteomics 2018; 183:25-33. [PMID: 29751105 DOI: 10.1016/j.jprot.2018.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/25/2018] [Accepted: 05/07/2018] [Indexed: 11/22/2022]
Abstract
Protein biomarkers of meat tenderness are known to be of primary importance for the prediction of meat quality, and hence, industry profitability. Proteome analysis was performed on meat from 8 Main Anjou beef cattle, previously classified as tender or tough meats by Warner Bratzler shear force measurements. Myofibrillar fraction of Longissimus thoracis muscle was separated by a novel fractionation approach based on liquid isoelectric focusing (OFFGEL) and further analyzed by SDS-PAGE and liquid chromatography coupled to tandem mass spectrometry. Obtained OFFGEL fraction profiles were reproducible allowing the comparison of both meat qualities and revealing 7 protein bands capable to discriminate between tender and tough samples. The proteins present in these bands were troponin T, Heat Shock protein beta-1, creatine kinase, actin, troponin C, myosins 1 and 2 and myozenin-1. The latter protein has not been previously reported as a marker of meat tenderness. SIGNIFICANCE This study introduces an innovative proteomic approach for the study of muscle proteome. The fact of obtaining fractions in liquid state after OFFGEL fractionation allows for a faster analysis of proteins by mass spectrometry, being an interesting alternative to more classical proteomic approaches based on two dimensional gel electrophoresis (2-DE).
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13
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Shimazaki Y, Ochi Y, Fujimura K. Microscale isolation of native forms of lysozyme from chicken egg white by gel isoelectric focusing. Electrophoresis 2018; 39:1054-1061. [DOI: 10.1002/elps.201700445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Youji Shimazaki
- Department of Chemistry and biology; Graduate School of Science and Engineering; Ehime University; Matsuyama Japan
- Faculty of Science; Ehime University; Matsuyama Japan
| | - Yoshiko Ochi
- Faculty of Science; Ehime University; Matsuyama Japan
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Paik YK, Omenn GS, Hancock WS, Lane L, Overall CM. Advances in the Chromosome-Centric Human Proteome Project: looking to the future. Expert Rev Proteomics 2017; 14:1059-1071. [PMID: 29039980 DOI: 10.1080/14789450.2017.1394189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on 'missing proteins (MPs)', which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs. Areas covered: We will cover the scope, historic background, progress, challenges and future prospects of C-HPP. This review also addresses the question of how we can best improve the methodological approaches, select the optimal biological samples, and recommend stringent protocols for the identification and characterization of MPs. A new strategy for functional analysis of some of those annotated proteins having unknown function will also be discussed. Expert commentary: If the project moves well by reshaping the original goals, the current working modules and team work in the proposed extended planning period, it is anticipated that a progressively more detailed draft of an accurate chromosome-based proteome map will become available with functional information.
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Affiliation(s)
- Young-Ki Paik
- a Yonsei Proteome Research Center and Department of Biochemistry , Yonsei University , Seoul , Korea
| | - Gilbert S Omenn
- b Department of Computational Medicine & Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - William S Hancock
- c Department of Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , USA
| | - Lydie Lane
- d Department of Human Protein Sciences, Faculty of Medicine , University of Geneva , Geneva , Switzerland.,e Swiss Institute of Bioinformatics , Geneva , Switzerland
| | - Christopher M Overall
- f Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , University of British Columbia , Vancouver , Canada
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Kraiem H, Zouari F, Abderrazek RB, Manon Y, Ayeb ME, Fillaudeau L, Bedoui J, Bouhaouala-Zahar B. Two-Dimensional Isoelectric Focusing OFFGEL, Micro-Fluidic Lab-on-Chip Electrophoresis and FTIR for Assessment of Long-Term Stability of rhG-CSF Formulation. IEEE Trans Nanobioscience 2017; 16:694-702. [PMID: 29053450 DOI: 10.1109/tnb.2017.2763779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recombinant human granulocyte colony-stimulating factor (rhG-CSF) has been increasingly recognized from among one of the most abundant families of biosimilars. Upon long-term storage, the rhG-CSF is subject to subtle chemical modifications that rapidly occur and, in particular, produce deaminated variants with divergent charge. Indeed, changes in charge from glutamine deamination may alter the way rhG-SCF will refold and the structure of resulting molecule. To assess this charge heterogeneity, 2-D gel electrophoresis has limited application. Recent micro-fluidic- based technical advances offer a great alternative method to better control liquid volumes on a minute scale. Here, we used IEF OFFGEL-lab-on-chip electrophoresis for 2-D separation of the rhG-CSF peptides according to their isoelectric point (pI) and molecular weight (kDa). We used an rhG-CSF commercial therapeutic formulation, kept refrigerated 24 months after expiry. The samples were analyzed for particulate matter and charge variants. Subsequently, the secondary structure was assessed by FTIR spectroscopy and residual biological activity was recorded. Interestingly, we showed an additional band in the acidic gel area above and below the most intense protein band (fractions 10, 11, and 12 at 22.84s). This observation reveals the presence of the rhG-CSF variant charges without any additional high molecular weight impurity or biological activity decrease. We conclude that after two years of storage, the rhG-CSF solution maintained its native secondary structure with little -sheet deviation, as reflected in the 1622 cm-1 and 1695 cm-1. These data demonstrated that a combined strategy is a more suitable and accurate analytical assessment of the rhG-CSF and recombinant protein-based biosimilars.
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Michelland S, Bourgoin-Voillard S, Cunin V, Tollance A, Bertolino P, Slais K, Seve M. Low-molecular-weight color pI markers to monitor on-line the peptide focusing process in OFFGEL fractionation. Electrophoresis 2017; 38:2034-2041. [DOI: 10.1002/elps.201700075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sylvie Michelland
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | - Sandrine Bourgoin-Voillard
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | - Valérie Cunin
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | - Axel Tollance
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | | | - Karel Slais
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic v.v.i.; Brno Czech Republic
| | - Michel Seve
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
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17
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Qin L, Liu X, Liu S, Liu Y, Yang Y, Yang H, Chen Y, Chen L. Differentially expressed proteins underlying childhood cortical dysplasia with epilepsy identified by iTRAQ proteomic profiling. PLoS One 2017; 12:e0172214. [PMID: 28222113 PMCID: PMC5319751 DOI: 10.1371/journal.pone.0172214] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/01/2017] [Indexed: 02/06/2023] Open
Abstract
Cortical dysplasia accounts for at least 14% of epilepsy cases, and is mostly seen in children. However, the understanding of molecular mechanisms and pathogenesis underlying cortical dysplasia is limited. The aim of this cross-sectional study is to identify potential key molecules in the mechanisms of cortical dysplasia by screening the proteins expressed in brain tissues of childhood cortical dysplasia patients with epilepsy using isobaric tags for relative and absolute quantitation-based tandem mass spectrometry compared to controls, and several differentially expressed proteins that are not reported to be associated with cortical dysplasia previously were selected for validation using real-time polymerase chain reaction, immunoblotting and immunohistochemistry. 153 out of 3340 proteins were identified differentially expressed between childhood cortical dysplasia patients and controls. And FSCN1, CRMP1, NDRG1, DPYSL5, MAP4, and FABP3 were selected for validation and identified to be increased in childhood cortical dysplasia patients, while PRDX6 and PSAP were identified decreased. This is the first report on differentially expressed proteins in childhood cortical dysplasia. We identified differential expression of FSCN1, CRMP1, NDRG1, DPYSL5, MAP4, FABP3, PRDX6 and PSAP in childhood cortical dysplasia patients, these proteins are involved in various processes and have various function. These results may provide new directions or targets for the research of childhood cortical dysplasia, and may be helpful in revealing molecular mechanisms and pathogenesis and/or pathophysiology of childhood cortical dysplasia if further investigated.
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Affiliation(s)
- Lu Qin
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Xi Liu
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Shiyong Liu
- Department of Neurosurgery, The Xinqiao Hospital of Third Military Medical University, Chongqing, People’s Republic of China
| | - Yi Liu
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yixuan Yang
- Department of Infectious Disease, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Hui Yang
- Department of Neurosurgery, The Xinqiao Hospital of Third Military Medical University, Chongqing, People’s Republic of China
| | - Yangmei Chen
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Lifen Chen
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- * E-mail:
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18
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Pergande MR, Cologna SM. Isoelectric Point Separations of Peptides and Proteins. Proteomes 2017; 5:proteomes5010004. [PMID: 28248255 PMCID: PMC5372225 DOI: 10.3390/proteomes5010004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/03/2017] [Accepted: 01/08/2017] [Indexed: 12/20/2022] Open
Abstract
The separation of ampholytic components according to isoelectric point has played an important role in isolating, reducing complexity and improving peptide and protein detection. This brief review outlines the basics of isoelectric focusing, including a summary of the historical achievements and considerations in experimental design. Derivative methodologies of isoelectric focusing are also discussed including common detection methods used. Applications in a variety of fields using isoelectric point based separations are provided as well as an outlook on the field for future studies.
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Affiliation(s)
- Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
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19
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Khalilpour A, Kilic T, Khalilpour S, Álvarez MM, Yazdi IK. Proteomic-based biomarker discovery for development of next generation diagnostics. Appl Microbiol Biotechnol 2016; 101:475-491. [PMID: 28013407 DOI: 10.1007/s00253-016-8029-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/09/2023]
Abstract
In the post-genome age, proteomics is receiving significant attention because they provide an invaluable source of biological structures and functions at the protein level. The search for disease-specific biomarkers for diagnostic and/or therapeutic applications is one of the areas that proteomics is having a significant impact. Thus, the identification of a "good" biomarker enables a more accurate early diagnosis and prognosis of disease. Rapid advancements in mass spectrometry (MS) instrumentation, liquid chromatography MS (LCMS), protein microarray technology, and other protein profiling methodologies have a substantial expansion of our toolbox to identify disease-specific protein and peptide biomarkers. This review covers a selection of widely used proteomic technologies for biomarker discovery. In addition, we describe the most commonly used approaches for diagnosis based on proteomic biomarkers and further discuss trends and critical challenges during development of cost-effective rapid diagnostic tests and microfluidic diagnostic systems based on proteomic biomarkers.
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Affiliation(s)
- Akbar Khalilpour
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA. .,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Tugba Kilic
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620, Izmir, Turkey.,Department of Biotechnology, Institute of Science, Ege University, 35100, Izmir, Turkey
| | - Saba Khalilpour
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Mario Moisés Álvarez
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Iman K Yazdi
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02139, USA
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20
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Chen H, Zhu Z, Yu H, Lu JJ, Liu S. Simple Means for Fractionating Protein Based on Isoelectric Point without Ampholyte. Anal Chem 2016; 88:9293-9. [PMID: 27571344 DOI: 10.1021/acs.analchem.6b02856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this paper, we develop a simple electrokinetic means for fractionating protein samples according to their pI values without using ampholytes. The method uses inexpensive equipment, and its consumables are primarily ammonium acetate buffers. A key component of its apparatus is a dialysis membrane interface that eliminates electrolysis-caused protein oxidation/reduction and constrains proteins in the desired places. We demonstrate its feasibility for fractionating standard proteins and real-world samples. With the elimination of ampholytes, we can analyze the fractionated proteins directly by a matrix assisted laser desorption/ionization time-of-flight mass spectrometer. Important experimental parameters are also discussed in order to obtain good fractionation results.
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Affiliation(s)
- Huang Chen
- Department of Chemistry and Biochemistry, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zaifang Zhu
- Department of Chemistry and Biochemistry, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Haiqing Yu
- Department of Chemistry and Biochemistry, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Joann Juan Lu
- Department of Chemistry and Biochemistry, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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21
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Abd El Aziz TM, Bourgoin-Voillard S, Combemale S, Beroud R, Fadl M, Seve M, De Waard M. Fractionation and proteomic analysis of the Walterinnesia aegyptia snake venom using OFFGEL and MALDI-TOF-MS techniques. Electrophoresis 2016; 36:2594-605. [PMID: 26178575 DOI: 10.1002/elps.201500207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/18/2015] [Accepted: 06/25/2015] [Indexed: 11/05/2022]
Abstract
Animal venoms are complex mixtures of more than 100 different compounds, including peptides, proteins, and nonprotein compounds such as lipids, carbohydrates, and metal ions. In addition, the existing compounds show a wide range of molecular weights and concentrations within these venoms, making separation and purification procedures quite tedious. Here, we analyzed for the first time by MS the advantages of using the OFFGEL technique in the separation of the venom components of the Egyptian Elapidae Walterinnesia aegyptia snake compared to two classical methods of separation, SEC and RP-HPLC. We demonstrate that OFFGEL separates venom components over a larger scale of fractions, preserve respectable resolution with regard to the presence of a given compound in adjacent fractions and allows the identification of a greater number of ions by MS (102 over 134 total ions). We also conclude that applying several separating techniques (SEC and RP-HPLC in addition to OFFGEL) provides complementary results in terms of ion detection (21 more for SEC and 22 more with RP-HPLC). As a result, we provide a complete list of 134 ions present in the venom of W. aegyptia by using all these techniques combined.
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Affiliation(s)
- Tarek Mohamed Abd El Aziz
- INSERM U836, Grenoble Neuroscience Institute, LabEx Ion Channels, Science and Therapeutics, France.,University Grenoble Alpes, Grenoble, France.,Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Sandrine Bourgoin-Voillard
- University Grenoble Alpes, Grenoble, France.,INSERM, IAB, PROMETHEE Proteomic Platform, Grenoble, France.,CHU de Grenoble, IAB, Institut de Biologie et de Pathologie, PROMETHEE Proteomic Platform, Grenoble, France
| | | | - Rémy Beroud
- Smartox Biotechnology, Saint-Martin d'Hères, France
| | - Mahmoud Fadl
- Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Michel Seve
- University Grenoble Alpes, Grenoble, France.,INSERM, IAB, PROMETHEE Proteomic Platform, Grenoble, France.,CHU de Grenoble, IAB, Institut de Biologie et de Pathologie, PROMETHEE Proteomic Platform, Grenoble, France
| | - Michel De Waard
- INSERM U836, Grenoble Neuroscience Institute, LabEx Ion Channels, Science and Therapeutics, France.,University Grenoble Alpes, Grenoble, France.,Smartox Biotechnology, Saint-Martin d'Hères, France
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22
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Dissolved proteins characterization and speciation studies of metal-protein complexes in marine sediment pore water. Microchem J 2016. [DOI: 10.1016/j.microc.2015.10.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Magdeldin S, Elguoshy A, Yoshida Y, Hirao Y, Xu B, Zhang Y, Yamamoto K, Takimoto H, Fujinaka H, Kinoshita N, Yamamoto T. Complementary Protein and Peptide OFFGEL Fractionation for High-Throughput Proteomic Analysis. Anal Chem 2015; 87:8481-8. [DOI: 10.1021/acs.analchem.5b01911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sameh Magdeldin
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
- Department
of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Amr Elguoshy
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
- Biotechnology
Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Yutaka Yoshida
- Department
of Structural Pathology, Institute of Nephrology, Graduate
School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yoshitoshi Hirao
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Bo Xu
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Ying Zhang
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Hiroki Takimoto
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Hidehiko Fujinaka
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Naohiko Kinoshita
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
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24
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Wei Y, Zhou W, Liu J, Chai Y, Xiang Y, Yuan R. Label-free and homogeneous aptamer proximity binding assay for fluorescent detection of protein biomarkers in human serum. Talanta 2015; 141:230-4. [PMID: 25966407 DOI: 10.1016/j.talanta.2015.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/25/2015] [Accepted: 04/02/2015] [Indexed: 12/17/2022]
Abstract
By using the aptamer proximity binding assay strategy, the development of a label-free and homogeneous approach for fluorescent detection of human platelet-derived growth factor BB (PDGF-BB) is described. Two G-quadruplex forming sequence-linked aptamers bind to the PDGF-BB proteins, which leads to the increase in local concentration of the aptamers and promotes the formation of the G-quadruplex structures. Subsequently, the fluorescent dye, N-methylmesoporphyrin IX, binds to these G-quadruplex structures and generates enhanced fluorescence emission signal for sensitive detection of PDGF-BB. The association of the aptamers to the PDGF-BB proteins is characterized by using native polyacrylamide gel electrophoresis. The experimental conditions are optimized to reach an estimated detection limit of 3.2nM for PDGF-BB. The developed method is also selective and can be applied for monitoring PDGF-BB in human serum samples. With the advantages of label-free and homogeneous detection, the demonstrated approach can be potentially employed to detect other biomarkers in a relatively simple way.
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Affiliation(s)
- Yulian Wei
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jun Liu
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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25
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Moritz B, Schnaible V, Kiessig S, Heyne A, Wild M, Finkler C, Christians S, Mueller K, Zhang L, Furuya K, Hassel M, Hamm M, Rustandi R, He Y, Solano OS, Whitmore C, Park SA, Hansen D, Santos M, Lies M. Evaluation of capillary zone electrophoresis for charge heterogeneity testing of monoclonal antibodies. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 983-984:101-10. [DOI: 10.1016/j.jchromb.2014.12.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 01/30/2023]
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