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Štěpánová S, Kašička V. Determination of physicochemical parameters of (bio)molecules and (bio)particles by capillary electromigration methods. J Sep Sci 2024; 47:e2400174. [PMID: 38867483 DOI: 10.1002/jssc.202400174] [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: 03/06/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024]
Abstract
The review provides an overview of recent developments and applications of capillary electromigration (CE) methods for the determination of important physicochemical parameters of various (bio)molecules and (bio)particles. These parameters include actual and limiting (absolute) ionic mobilities, effective electrophoretic mobilities, effective charges, isoelectric points, electrokinetic potentials, hydrodynamic radii, diffusion coefficients, relative molecular masses, acidity (ionization) constants, binding constants and stoichiometry of (bio)molecular complexes, changes of Gibbs free energy, enthalpy and entropy and rate constants of chemical reactions and interactions, retention factors and partition and distribution coefficients. For the determination of these parameters, the following CE methods are employed: zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography. In the individual sections, the procedures for the determination of the above parameters by the particular CE methods are described.
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Affiliation(s)
- Sille Štěpánová
- Electromigration methods, Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Kašička
- Electromigration methods, Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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2
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Qadir R, Anwar F, Naseem K, Tahir MH, Alhumade H. Enzyme-Assisted Extraction of Phenolics from Capparis spinosa Fruit: Modeling and Optimization of the Process by RSM and ANN. ACS OMEGA 2022; 7:33031-33038. [PMID: 36157770 PMCID: PMC9494429 DOI: 10.1021/acsomega.2c02850] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 07/15/2022] [Indexed: 06/16/2023]
Abstract
The current study intends to appraise the effect of enzyme complexes on the recovery of phenolics from Capparis spinosa fruit extract using the response surface methodology (RSM) and artificial neural networking (ANN). Enzymatic treatment of C. spinosa fruit extract was optimized under a set of conditions (enzyme concentration, pH, temperature, and time) against each enzyme formulation such as Kemzyme Plus Dry, Natuzyme, and Zympex-014. The extract yield observed for Kemzyme Plus Dry (42.00%) was noted to be higher than those for Zympex-014 (39.80%) and Natuzyme (38.50%). Based on the higher results, the values of Kemzyme Plus Dry-based extract were further employed in different parameters of RSM. The F-value (16.03) and p-values (<0.05) implied that the selected model is significant. Similarly, the higher values for the coefficient of determination (R 2) at 0.9740 and adjusted R 2 (adj. R 2) at 0.9132 indicated that the model is significant in relation to given experimental parameters. ANN-predicted values were very close to the experimental values, which demonstrated the applicability of the ANN model. Antioxidant activities also exhibited profound results in terms of total phenolic content values (24.76 mg GAE/g), total flavonoid content values (24.56 mg CE/g), and the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay (IC50) (5.12 mg/mL). Scanning electron microscopy revealed that after enzymatic hydrolysis, the cell walls were broken as compared with nonhydrolyzed materials. Five phenolics, namely, quercetin, m-coumaric acid, sinapic acid, kaempferol, and p-coumaric acid, were identified from C. spinosa extract by gas chromatography-mass spectrometry (GC/MS). The results of this study reveal that the proposed optimization techniques, using Kemzyme Plus Dry among others, had a positive effect on the recovery of phenolic bioactive compounds and thus increased the antioxidant potential of C. spinosa fruit extract.
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Affiliation(s)
- Rahman Qadir
- Institute
of Chemistry, University of Sargodha, Sargodha 41000, Pakistan
| | - Farooq Anwar
- Institute
of Chemistry, University of Sargodha, Sargodha 41000, Pakistan
| | - Khalida Naseem
- Department
of Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54000, Pakistan
| | - Mudassir Hussain Tahir
- Department
of Chemistry, Division of Science and Technology, University of Education, Lahore 54000, Pakistan
| | - Hesham Alhumade
- K.A.CARE
Energy Research and Innovation Center, King
Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department
of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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3
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Chen W, McCool EN, Sun L, Zang Y, Ning X, Liu X. Evaluation of Machine Learning Models for Proteoform Retention and Migration Time Prediction in Top-Down Mass Spectrometry. J Proteome Res 2022; 21:1736-1747. [PMID: 35616364 PMCID: PMC9250612 DOI: 10.1021/acs.jproteome.2c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Reversed-phase liquid
chromatography (RPLC) and capillary zone
electrophoresis (CZE) are two primary proteoform separation methods
in mass spectrometry (MS)-based top-down proteomics. Proteoform retention
time (RT) prediction in RPLC and migration time (MT) prediction in
CZE provide additional information for accurate proteoform identification
and quantification. While existing methods are mainly focused on peptide
RT and MT prediction in bottom-up MS, there is still a lack of methods
for proteoform RT and MT prediction in top-down MS. We systematically
evaluated eight machine learning models and a transfer learning method
for proteoform RT prediction and five models and the transfer learning
method for proteoform MT prediction. Experimental results showed that
a gated recurrent unit (GRU)-based model with transfer learning achieved
a high accuracy (R = 0.978) for proteoform RT prediction
and that the GRU-based model and a fully connected neural network
model obtained a high accuracy of R = 0.982 and 0.981
for proteoform MT prediction, respectively.
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Affiliation(s)
- Wenrong Chen
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United Staes
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United Staes
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United Staes
| | - Yong Zang
- Department of Biostatics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, Indiana 46202, United Staes
| | - Xia Ning
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United Staes.,Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio 43210, United Staes.,Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United Staes
| | - Xiaowen Liu
- Tulane Center for Biomedical Informatics and Genomics, Tulane University, New Orleans, Louisiana 70112, United Staes.,Deming Department of Medicine, Tulane University, New Orleans, Louisiana 70112, United Staes
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Chen D, Yang Z, Shen X, Sun L. Capillary Zone Electrophoresis-Tandem Mass Spectrometry As an Alternative to Liquid Chromatography-Tandem Mass Spectrometry for Top-down Proteomics of Histones. Anal Chem 2021; 93:4417-4424. [PMID: 33650845 PMCID: PMC8564867 DOI: 10.1021/acs.analchem.0c04237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Top-down proteomics (TDP) is an ideal approach for deciphering the histone code and it routinely employs reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS). Because of the extreme complexity of histones regarding the number of proteoforms, new analytical tools with high-capacity separation and highly sensitive detection of proteoforms are required for TDP of histones. Here we present capillary zone electrophoresis (CZE)-MS/MS via the electro-kinetically pumped sheath-flow CE-MS interface for large-scale top-down delineation of histone proteoforms. CZE-MS/MS identified a comparable number of proteoforms to RPLC-MS/MS from a calf histone sample with more than 30-fold less sample consumption (75-ng vs. Three μg), indicating its substantially higher sensitivity. We identified about 400 histone proteoforms from the calf histone sample using two-dimensional size-exclusion chromatography (SEC)-CZE-MS/MS with less than 300-ng proteins consumed. We identified histone proteoforms carrying various tentative post-translational modifications (PTMs), for example, acetylation, methylation (mono-, di-, and tri-), phosphorylation, and succinylation. The electrophoretic mobility (μef) of unmodified histone proteoforms can be predicted accurately (R2 = 0.98) with an optimized semiempirical model based on our recent work. The results render CZE-MS/MS as a useful tool for deciphering the histone code in a proteoform-specific manner and on a global scale.
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Affiliation(s)
- Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
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5
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Chen D, Lubeckyj RA, Yang Z, McCool EN, Shen X, Wang Q, Xu T, Sun L. Predicting Electrophoretic Mobility of Proteoforms for Large-Scale Top-Down Proteomics. Anal Chem 2020; 92:3503-3507. [PMID: 32043875 PMCID: PMC7543059 DOI: 10.1021/acs.analchem.9b05578] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Large-scale top-down proteomics characterizes proteoforms in cells globally with high confidence and high throughput using reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) or capillary zone electrophoresis (CZE)-MS/MS. The false discovery rate (FDR) from the target-decoy database search is typically deployed to filter identified proteoforms to ensure high-confidence identifications (IDs). It has been demonstrated that the FDRs in top-down proteomics can be drastically underestimated. An alternative approach to the FDR can be useful for further evaluating the confidence of proteoform IDs after the database search. We argue that predicting retention/migration time of proteoforms from the RPLC/CZE separation accurately and comparing their predicted and experimental separation time could be a useful and practical approach. Based on our knowledge, there is still no report in the literature about predicting separation time of proteoforms using large top-down proteomics data sets. In this pilot study, for the first time, we evaluated various semiempirical models for predicting proteoforms' electrophoretic mobility (μef) using large-scale top-down proteomics data sets from CZE-MS/MS. We achieved a linear correlation between experimental and predicted μef of E. coli proteoforms (R2 = 0.98) with a simple semiempirical model, which utilizes the number of charges and molecular mass of each proteoform as the parameters. Our modeling data suggest that the complete unfolding of proteoforms during CZE separation benefits the prediction of their μef. Our results also indicate that N-terminal acetylation and phosphorylation both decrease the proteoforms' charge by roughly one charge unit.
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Affiliation(s)
- Daoyang Chen
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
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Enzyme-assisted extraction of Momordica balsamina L. fruit phenolics: process optimized by response surface methodology. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2018. [DOI: 10.1007/s11694-018-9982-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Batool F, Iqbal S, Akbar J. Impact of metal ionic characteristics on adsorption potential of Ficus carica leaves using QSPR modeling. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2018; 53:276-281. [PMID: 29281503 DOI: 10.1080/03601234.2017.1410046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The present study describes Quantitative Structure Property Relationship (QSPR) modeling to relate metal ions characteristics with adsorption potential of Ficus carica leaves for 13 selected metal ions (Ca+2, Cr+3, Co+2, Cu+2, Cd+2, K+1, Mg+2, Mn+2, Na+1, Ni+2, Pb+2, Zn+2, and Fe+2) to generate QSPR model. A set of 21 characteristic descriptors were selected and relationship of these metal characteristics with adsorptive behavior of metal ions was investigated. Stepwise Multiple Linear Regression (SMLR) analysis and Artificial Neural Network (ANN) were applied for descriptors selection and model generation. Langmuir and Freundlich isotherms were also applied on adsorption data to generate proper correlation for experimental findings. Model generated indicated covalent index as the most significant descriptor, which is responsible for more than 90% predictive adsorption (α = 0.05). Internal validation of model was performed by measuring [Formula: see text] (0.98). The results indicate that present model is a useful tool for prediction of adsorptive behavior of different metal ions based on their ionic characteristics.
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Affiliation(s)
- Fozia Batool
- a Department of Chemistry , University of Sargodha , Sargodha , Punjab Province , Pakistan
| | - Shahid Iqbal
- a Department of Chemistry , University of Sargodha , Sargodha , Punjab Province , Pakistan
| | - Jamshed Akbar
- a Department of Chemistry , University of Sargodha , Sargodha , Punjab Province , Pakistan
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8
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Krokhin OV, Anderson G, Spicer V, Sun L, Dovichi NJ. Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis. Anal Chem 2017; 89:2000-2008. [PMID: 28208305 DOI: 10.1021/acs.analchem.6b04544] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A multiparametric sequence-specific model for predicting peptide electrophoretic mobility has been developed using large-scale bottom-up proteomic CE-MS data (5% (∼0.8M) acetic acid as background electrolyte). Peptide charge (Z) and size (molecular mass, M) are the two major factors determining electrophoretic mobility, in complete agreement with previous studies. The extended size of the data set (>4000 peptides) permits access to many sequence-specific factors that impact peptide mobility. The presence of acidic residues Asp and Glu near the peptide N-terminus is by far the most prominent among them. The induction effect of the side chain of N-terminal Asp reduces the basicity of the N-terminal amino group and, as hence, its charge, by ∼0.27 units, lowering mobility. The correlation of the model (R2 ∼ 0.995) indicates that the peptide separation process in CZE is relatively simple and can be predicted to a much higher precision than current RP-HPLC models. Similar to RP-HPLC prediction studies, we anticipate future developments that introduce peptide migration standards, collect larger data sets for modeling through the alignment of multiple CZE-MS acquisitions, and study of the behavior of peptides carrying post-translational modifications. The increased size of data sets will also permit investigation of the fine-scale effects of peptide secondary structure on peptide mobility. We observed that peptides with higher helical propensity tend to have higher than predicted electrophoretic mobility; the incorporation of these features into CZE migration models will require significantly larger data sets.
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Affiliation(s)
| | | | | | - Liangliang Sun
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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9
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Abstract
Peptides are an important class of analytes in chemistry, biochemistry, food chemistry, as well as medical and pharmaceutical sciences including biomarker analysis in peptidomics and proteomics. As a high-resolution technique, capillary electrophoresis (CE) is well suited for the analysis of polar compounds such as peptides. In addition, CE is orthogonal to high-performance liquid chromatography (HPLC) as both techniques are based on different physicochemical separation principles. For the successful development of peptide separations by CE, operational parameters including puffer pH, buffer concentration and buffer type, applied voltage, capillary dimensions, as well as background electrolyte additives such as detergents, ion-pairing reagents, cyclodextrins, (poly)amines, and soluble polymers have to be considered and optimized.
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Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical Chemistry, University of Jena, Philosophenweg 14, Jena, 07743, Germany.
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10
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Zhong S, Zou D, Zhao B, Zhang D, Li X, Wang H. Electrophoretic behavior of DNA-methyl-CpG-binding domain protein complexes revealed by capillary electrophoreses laser-induced fluorescence. Electrophoresis 2015; 36:3088-93. [DOI: 10.1002/elps.201500336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Shangwei Zhong
- College of Chemistry and Chemical Engineering; University of Chinese Academy of Sciences; Beijing P. R. China
| | - Dandan Zou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
| | - Bailin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
| | - Xiangjun Li
- College of Chemistry and Chemical Engineering; University of Chinese Academy of Sciences; Beijing P. R. China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
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11
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Barroso A, Giménez E, Benavente F, Barbosa J, Sanz-Nebot V. Modelling the electrophoretic migration behaviour of peptides and glycopeptides from glycoprotein digests in capillary electrophoresis-mass spectrometry. Anal Chim Acta 2014; 854:169-77. [PMID: 25479881 DOI: 10.1016/j.aca.2014.10.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/08/2014] [Accepted: 10/26/2014] [Indexed: 10/24/2022]
Abstract
In this study, the classical semiempirical relationships between the electrophoretic mobility and the charge-to-mass ratio (me vs. q/M(α)) were used to model the migration behaviour of peptides and glycopeptides originated from the digestion of recombinant human erythropoietin (rhEPO), a biologically and therapeutically relevant glycoprotein. The Stoke's law (α=1/3), the classical polymer model (α=1/2) and the Offord's surface law (α=2/3) were evaluated to predict migration of peptides and glycopeptides, with and without sialic acids (SiA), in rhEPO digested with trypsin and trypsin-neuraminidase. The Stoke's law resulted in better correlations for the set of peptides used to evaluate the models, while glycopeptides fitted better with the classical polymer model. Once predicted migration times with both models, it was easy to simulate their separation electropherogram. Results were later validated predicting migration and simulating separation of a different set of rhEPO glycopeptides and also human transferrin (Tf) peptides and glycopeptides. The excellent agreement between the experimental and the simulated electropherograms with rhEPO and Tf digests confirmed the potential applicability of this simple strategy to predict, in general, the peptide-glycopeptide electrophoretic map of any digested glycoprotein.
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Affiliation(s)
- Albert Barroso
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - José Barbosa
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
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Català-Clariana S, Benavente F, Giménez E, Barbosa J, Sanz-Nebot V. Identification of bioactive peptides in hypoallergenic infant milk formulas by CE-TOF-MS assisted by semiempirical model of electromigration behavior. Electrophoresis 2014; 34:1886-94. [PMID: 23564639 DOI: 10.1002/elps.201200547] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 02/05/2023]
Abstract
Biologically active peptides derived from complex bovine milk protein hydrolysates are of particular interest in food science and nutrition because they have been shown to play different physiological roles, providing benefits in human health. In this study, we used CE-TOF-MS for separation and identification of bioactive peptides in three hypoallergenic infant milk formulas. An appropriate sample cleanup using a citrate buffer with DTT and urea followed by SPE with Sep-Pack® C18 and StrataX™ cartridges allowed the detection of a large number of low molecular mass bioactive peptides. This preliminary identification was solely based on the measured experimental monoisotopic molecular mass values (M(exp)). Later, we evaluated the classical semiempirical relationships between electrophoretic mobility and charge-to-mass ratio (m(e) vs. q/M(α), α = 1/2 for the classical polymer model) to describe their migration behavior. The assistance of migration prediction proved to be useful to improve reliability of the identification, avoiding misinterpretations and solving some identity conflicts. After revision, the identity of 24, 30, and 38 bioactive peptides was confirmed in each of the three infant milk formulas. A significant number of these peptides were reported as inhibitors of angiotensin-converting enzyme, however, the presence of sequences with other biological activities such as antihypertensive, antithrombotic, hypocholesterolemic, immunomodulation, cytotoxicity, antioxidant, antimicrobial, antigenic, or opioid was also confirmed.
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Affiliation(s)
- Sergio Català-Clariana
- Department of Analytical Chemistry, Nutrition and Food Safety Research Institute-INSA-UB, University of Barcelona, Barcelona, Spain
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13
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Jarvas G, Guttman A. Modeling of cell sorting and rare cell capture with microfabricated biodevices. Trends Biotechnol 2013; 31:696-703. [DOI: 10.1016/j.tibtech.2013.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/30/2013] [Accepted: 10/02/2013] [Indexed: 01/22/2023]
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14
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Zafar MN, Ahmad SA, Butt AM, Qadir MA. Electrochemical Separation of Alanine, Cysteine, and Glycine Using a Digital Thruster. SEP SCI TECHNOL 2013. [DOI: 10.1080/01496395.2013.797467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Miszczak A, Rosłon M, Zbroja G, Brama K, Szalacha E, Gawrońska H, Pawlak K. SEC ICP MS and CZE ICP MS investigation of medium and high molecular weight complexes formed by cadmium ions with phytochelatins. Anal Bioanal Chem 2013; 405:4667-78. [PMID: 23525539 PMCID: PMC3637892 DOI: 10.1007/s00216-013-6868-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/18/2013] [Accepted: 02/24/2013] [Indexed: 11/06/2022]
Abstract
Size-exclusion chromatography (SEC) and capillary zone electrophoresis (CZE) coupled with inductively coupled plasma mass spectrometry were applied to characterize low, medium, and high molecular weight cadmium complexes with glutathione and phytochelatins (PCs). The dominant stoichiometry of the complexes formed in vitro was established as 1:1 using electrospray ionization mass spectrometry. Calculated molecular masses of Cd1L1 complexes were used for calibration of the SEC and CZE methods. The results showed a lower (2 kDa) SEC column exclusion limit for cadmium complexes compared with free peptides (10 kDa), and most of the high molecular weight cadmium species were eluted in the void volume of the column. Moreover, the CZE method based on the semiempirical model of Offord to elucidate peptide migration allowed us to show a high propensity of Cd–PC complexes for polymorphism on complexation, which was also observed for extracts of Arabidopsis thaliana treated with cadmium. All the information presented is vital for understanding the mechanism of metal deactivation in plants. Estimation of molecular mass of Cd-thiopeptide complexes by size electrophoretic mobility ![]()
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Affiliation(s)
- Agata Miszczak
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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16
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Wu HF, Gopal J, Abdelhamid HN, Hasan N. Quantum dot applications endowing novelty to analytical proteomics. Proteomics 2013; 12:2949-61. [PMID: 22930415 DOI: 10.1002/pmic.201200295] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This review surveys all the state-of-art applications of quantum dots (QDs) in conventional and modern analytical methods in proteomic studies. A brief introduction of QDs and their properties is initially presented followed by outlining the application of QDs in fluorescence, MS, imaging, and cancer-based proteomics. The in-depth application of QDs in MALDI-MS and surface assisted laser desorption/ionization-MS has been elaborately discussed, summarizing the speculated mechanism behind the protein-QDs interactions during QD matrix applications leading to enhanced detection sensitivity.
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Affiliation(s)
- Hui-Fen Wu
- Department of Chemistry, National Sun Yat Sen University, Kaohsiung, Taiwan.
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17
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Filipic S, Nikolic K, Vovk I, Krizman M, Agbaba D. Quantitative structure-mobility relationship analysis of imidazoline receptor ligands in CDs-mediated CE. Electrophoresis 2013; 34:471-82. [DOI: 10.1002/elps.201200171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 08/16/2012] [Accepted: 09/15/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Slavica Filipic
- Department of Pharmaceutical Chemistry; Faculty of Pharmacy; University of Belgrade; Belgrade; Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry; Faculty of Pharmacy; University of Belgrade; Belgrade; Serbia
| | | | - Mitja Krizman
- Laboratory of Food Chemistry; National Institute of Chemistry; Ljubljana; Slovenia
| | - Danica Agbaba
- Department of Pharmaceutical Chemistry; Faculty of Pharmacy; University of Belgrade; Belgrade; Serbia
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Predicting retention times of naturally occurring phenolic compounds in reversed-phase liquid chromatography: a Quantitative Structure-Retention Relationship (QSRR) approach. Int J Mol Sci 2012. [PMID: 23203132 PMCID: PMC3509648 DOI: 10.3390/ijms131115387] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Quantitative structure-retention relationships (QSRRs) have successfully been developed for naturally occurring phenolic compounds in a reversed-phase liquid chromatographic (RPLC) system. A total of 1519 descriptors were calculated from the optimized structures of the molecules using MOPAC2009 and DRAGON softwares. The data set of 39 molecules was divided into training and external validation sets. For feature selection and mapping we used step-wise multiple linear regression (SMLR), unsupervised forward selection followed by step-wise multiple linear regression (UFS-SMLR) and artificial neural networks (ANN). Stable and robust models with significant predictive abilities in terms of validation statistics were obtained with negation of any chance correlation. ANN models were found better than remaining two approaches. HNar, IDM, Mp, GATS2v, DISP and 3D-MoRSE (signals 22, 28 and 32) descriptors based on van der Waals volume, electronegativity, mass and polarizability, at atomic level, were found to have significant effects on the retention times. The possible implications of these descriptors in RPLC have been discussed. All the models are proven to be quite able to predict the retention times of phenolic compounds and have shown remarkable validation, robustness, stability and predictive performance.
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Akbar J, Iqbal MS, Chaudhary MT, Yasin T, Massey S. A QSPR study of drug release from an arabinoxylan using ab initio optimization and neural networks. Carbohydr Polym 2012. [DOI: 10.1016/j.carbpol.2012.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mittermayr S, Guttman A. Influence of molecular configuration and conformation on the electromigration of oligosaccharides in narrow bore capillaries. Electrophoresis 2012; 33:1000-7. [DOI: 10.1002/elps.201100681] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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21
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The design and synthesis of alanine-based indolicidin derivatives with identical physicochemical properties and their separation using capillary electrophoresis. Anal Bioanal Chem 2010; 398:3073-9. [PMID: 20924563 DOI: 10.1007/s00216-010-4249-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 09/16/2010] [Accepted: 09/22/2010] [Indexed: 10/19/2022]
Abstract
Four novel alanine-based indolicidin peptide derivatives were designed containing one WPW motif and two alanine residues, resulting in peptides of similar sequence. The separation of these peptides with identical physicochemical properties including molar mass, charge, and secondary structure as characterized by circular dichroism spectroscopy is very difficult; and the separation of peptides with differing physicochemical properties has only previously been reported. Capillary electrophoresis parameters such as separation buffer concentration, separation buffer pH, capillary length, and separation voltage were investigated to optimize the analysis. Using optimized conditions of a background electrolyte containing 5 mM formic acid of pH 2.0, total capillary length of 51 cm and a voltage of 10 kV enabled a baseline separation of the four peptides. The relative standard deviation of the peak areas and migration times for method repeatability (n = 3) were found to be lower than 8% and 3%, respectively. In addition, reasoning for the separation of these peptides is proposed based on the acidity of the formic acid buffer and the hydrophobic grouping of the tryptophan residues in the peptide primary sequence.
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Jiao L. QSPR studies on soot-water partition coefficients of persistent organic pollutants by using artificial neural network. CHEMOSPHERE 2010; 80:671-675. [PMID: 20452639 DOI: 10.1016/j.chemosphere.2010.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 03/08/2010] [Accepted: 04/02/2010] [Indexed: 05/29/2023]
Abstract
Two quantitative structure property relationship (QSPR) models for predicting soot-water partition coefficients (K(sc)) of 25 persistent organic pollutants (POPs) were developed. One model was established with linear artificial neural network (L-ANN), the other model was developed by using back propagation artificial neural network (BP-ANN). Leave one out cross validation was adopted to assess the predictive ability of the developed models. For the L-ANN model, the square of correlation coefficient (R(2)) between the predicted and experimental log K(SC) is 0.8358 and the RMS%RE is 6.32 for all the compounds. For the BP-ANN model, R(2) is 0.9628 and the RMS%RE is 4.12 for all the compounds. The result of leave one out cross validation demonstrates that both L-ANN and BP-ANN are practicable for developing the QSPR model for K(SC) of the investigated POPs. However, the model established with BP-ANN is better than the model established with L-ANN in prediction accuracy. It is shown that BP-ANN is a promising method for developing QSPR models for K(SC) of POPs.
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Affiliation(s)
- Long Jiao
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, PR China.
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Piaggio MV, Peirotti MB, Deiber JA. Estimation of global structural and transport properties of peptides through the modeling of their CZE mobility data. J Sep Sci 2010; 33:2423-9. [DOI: 10.1002/jssc.201000134] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Benavente F, Giménez E, Barrón D, Barbosa J, Sanz-Nebot V. Modeling the electrophoretic behavior of quinolones in aqueous and hydroorganic media. Electrophoresis 2010; 31:965-72. [DOI: 10.1002/elps.200900344] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Jing J, Liang G, Mei H, Xiao S, Xia Z, Li Z. Quantitative structure–mobility relationship studies of dipeptides in capillary zone electrophoresis using three-dimensional holographic vector of atomic interaction field. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020802512203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Mittermayr S, Chovan T, Guttman A. Two variable semi-empirical and artificial neural-network-based modeling of peptide mobilities in CZE: The effect of temperature and organic modifier concentration. Electrophoresis 2009; 30:890-6. [DOI: 10.1002/elps.200800748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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The free solution electrophoretic mobility of peptides by a bead modeling methodology. J Chromatogr A 2009; 1216:1908-16. [DOI: 10.1016/j.chroma.2008.09.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 09/02/2008] [Accepted: 09/04/2008] [Indexed: 11/24/2022]
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