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Yu S, Tan Z, Lai Y, Li Q, Liu J. Nanoparticulate pollutants in the environment: Analytical methods, formation, and transformation. ECO-ENVIRONMENT & HEALTH 2023; 2:61-73. [PMID: 38075291 PMCID: PMC10702925 DOI: 10.1016/j.eehl.2023.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 06/28/2024]
Abstract
The wide application of nanomaterials and plastic products generates a substantial number of nanoparticulate pollutants in the environment. Nanoparticulate pollutants are quite different from their bulk counterparts because of their unique physicochemical properties, which may pose a threat to environmental organisms and human beings. To accurately predict the environmental risks of nanoparticulate pollutants, great efforts have been devoted to developing reliable methods to define their occurrence and track their fate and transformation in the environment. Herein, we summarized representative studies on the preconcentration, separation, formation, and transformation of nanoparticulate pollutants in environmental samples. Finally, some perspectives on future research directions are proposed.
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Affiliation(s)
- Sujuan Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqiang Tan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujian Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qingcun Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfu Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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2
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Cabrera-Orefice A, Potter A, Evers F, Hevler JF, Guerrero-Castillo S. Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. Front Cell Dev Biol 2022; 9:796128. [PMID: 35096826 PMCID: PMC8790184 DOI: 10.3389/fcell.2021.796128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.
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Affiliation(s)
- Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alisa Potter
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Felix Evers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, University of Utrecht, Utrecht, Netherlands.,Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, Netherlands.,Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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3
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Bolze H, Riewe J, Bunjes H, Dietzel A, Burg TP. Protective Filtration for Microfluidic Nanoparticle Precipitation for Pharmaceutical Applications. Chem Eng Technol 2021. [DOI: 10.1002/ceat.202000475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Holger Bolze
- Max Planck Institute for Biophysical Chemistry Research Group Biological Micro- and Nanotechnology Am Fassberg 11 37077 Göttingen Germany
- Technische Universität Darmstadt Department of Electrical Engineering and Information Technology Merckstr. 25 64283 Darmstadt Germany
| | - Juliane Riewe
- Technische Universität Braunschweig Institut für Pharmazeutische Technologie und Biopharmazie Mendelssohnstr. 1 38106 Braunschweig Germany
- Technische Universität Braunschweig PVZ – Center of Pharmaceutical Engineering Franz-Liszt-Str. 35a 38106 Braunschweig Germany
| | - Heike Bunjes
- Technische Universität Braunschweig Institut für Pharmazeutische Technologie und Biopharmazie Mendelssohnstr. 1 38106 Braunschweig Germany
- Technische Universität Braunschweig PVZ – Center of Pharmaceutical Engineering Franz-Liszt-Str. 35a 38106 Braunschweig Germany
| | - Andreas Dietzel
- Technische Universität Braunschweig Institute of Microtechnology Alte Salzdahlumer Str. 203 38124 Braunschweig Germany
- Technische Universität Braunschweig PVZ – Center of Pharmaceutical Engineering Franz-Liszt-Str. 35a 38106 Braunschweig Germany
| | - Thomas P. Burg
- Max Planck Institute for Biophysical Chemistry Research Group Biological Micro- and Nanotechnology Am Fassberg 11 37077 Göttingen Germany
- Technische Universität Darmstadt Department of Electrical Engineering and Information Technology Merckstr. 25 64283 Darmstadt Germany
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4
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Ventouri IK, Malheiro DBA, Voeten RLC, Kok S, Honing M, Somsen GW, Haselberg R. Probing Protein Denaturation during Size-Exclusion Chromatography Using Native Mass Spectrometry. Anal Chem 2020; 92:4292-4300. [PMID: 32107919 PMCID: PMC7081181 DOI: 10.1021/acs.analchem.9b04961] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Size-exclusion chromatography
employing aqueous mobile phases with
volatile salts at neutral pH combined with electrospray-ionization
mass spectrometry (SEC-ESI-MS) is a useful tool to study proteins
in their native state. However, whether the applied eluent conditions
actually prevent protein–stationary phase interactions, and/or
protein denaturation, often is not assessed. In this study, the effects
of volatile mobile phase additives on SEC retention and ESI of proteins
were thoroughly investigated. Myoglobin was used as the main model
protein, and eluents of varying ionic strength and pH were applied.
The degree of interaction between protein and stationary phase was
evaluated by calculating the SEC distribution coefficient. Protein-ion
charge state distributions obtained during offline and online native
ESI-MS were used to monitor alterations in protein structure. Interestingly,
most of the supposedly mild eluent compositions induced nonideal SEC
behavior and/or protein unfolding. SEC experiments revealed that the
nature, ionic strength, and pH of the eluent affected protein retention.
Protein–stationary phase interactions were effectively avoided
using ammonium acetate at ionic strengths above 0.1 M. Direct-infusion
ESI-MS showed that the tested volatile eluent salts seem to follow
the Hofmeister series: no denaturation was induced using ammonium
acetate (kosmotropic), whereas ammonium formate and bicarbonate (both
chaotropic) caused structural changes. Using a mobile phase of 0.2
M ammonium acetate (pH 6.9), several proteins (i.e., myoglobin, carbonic
anhydrase, and cytochrome c) could be analyzed by SEC-ESI-MS using
different column chemistries without compromising their native state.
Overall, with SEC-ESI-MS, the effect of nonspecific interactions between
protein and stationary phase on the protein structure can be studied,
even revealing gradual structural differences along a peak.
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Affiliation(s)
- Iro K Ventouri
- Division of Bioanalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.,Centre for Analytical Sciences Amsterdam, 1098XH Amsterdam, The Netherlands.,TI-COAST, 1098 XH Amsterdam, The Netherlands.,Analytical Chemistry Group, van't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94720, 1090 GE Amsterdam, The Netherlands
| | - Daniel B A Malheiro
- Division of Bioanalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.,TI-COAST, 1098 XH Amsterdam, The Netherlands
| | - Robert L C Voeten
- Division of Bioanalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.,Centre for Analytical Sciences Amsterdam, 1098XH Amsterdam, The Netherlands.,TI-COAST, 1098 XH Amsterdam, The Netherlands
| | - Sander Kok
- DSM Materials Science Center, 6167 RD Geleen, The Netherlands
| | - Maarten Honing
- Division of Bioanalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.,DSM Materials Science Center, 6167 RD Geleen, The Netherlands
| | - Govert W Somsen
- Division of Bioanalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.,Centre for Analytical Sciences Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Rob Haselberg
- Division of Bioanalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.,Centre for Analytical Sciences Amsterdam, 1098XH Amsterdam, The Netherlands
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5
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Investigation of lipidomic perturbations in oxidatively stressed subcellular organelles and exosomes by asymmetrical flow field–flow fractionation and nanoflow ultrahigh performance liquid chromatography–tandem mass spectrometry. Anal Chim Acta 2019; 1073:79-89. [DOI: 10.1016/j.aca.2019.04.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/22/2022]
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6
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Flow field-flow fractionation: Recent applications for lipidomic and proteomic analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Marassi V, Beretti F, Roda B, Alessandrini A, Facci P, Maraldi T, Zattoni A, Reschiglian P, Portolani M. A new approach for the separation, characterization and testing of potential prionoid protein aggregates through hollow-fiber flow field-flow fractionation and multi-angle light scattering. Anal Chim Acta 2019; 1087:121-130. [PMID: 31585560 DOI: 10.1016/j.aca.2019.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/27/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022]
Abstract
Protein misfolding and aggregation are the common mechanisms in a variety of aggregation-dependent diseases. The compromised proteins often assemble into toxic, accumulating amyloid-like structures of various lengths and their toxicity can also be transferred both in vivo and in vitro a prion-like behavior. The characterization of protein interactions, degradation and conformational dynamics in biological systems still represents an analytical challenge in the prion-like protein comprehension. In our work, we investigated the nature of a transferable cytotoxic agent, presumably a misfolded protein, through the coupling of a multi-detector, non-destructive separation platform based on hollow-fiber flow field-flow fractionation with imaging and downstream in vitro tests. After purification with ion exchange chromatography, the transferable cytotoxic agentwas analyzed with Atomic Force Microscopy and statistical analysis, showing that the concentration of protein dimers and low n-oligomer forms was higher in the cytotoxic sample than in the control preparation. To assess whether the presence of these species was the actual toxic and/or self-propagating factor, we employed HF5 fractionation, with UV and Multi-Angle Light Scattering detection, to define proteins molar mass distribution and abundance, and fractionate the sample into size-homogeneous fractions. These fractions were then tested individually in vitro to investigate the direct correlation with cytotoxicity. Only the later-eluted fraction, which contains high-molar mass aggregates, proved to be toxic onto cell cultures. Moreover, it was observed that the selective transfer of toxicity also occurs for one lower-mass fraction, suggesting that two different mechanisms, acute and later induced toxicity, are in place. These results strongly encourage the efficacy of this platform to enable the identification of protein toxicants.
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Affiliation(s)
- Valentina Marassi
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy
| | - Francesca Beretti
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124, Modena, Italy
| | - Barbara Roda
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy.
| | - Andrea Alessandrini
- CNR-Istituto Nanoscienze, S3, Via Campi 213/A, 41125, Modena, Italy; Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A, 41125, Modena, Italy
| | - Paolo Facci
- CNR-Istituto Nanoscienze, S3, Via Campi 213/A, 41125, Modena, Italy; Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A, 41125, Modena, Italy
| | - Tullia Maraldi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124, Modena, Italy
| | - Andrea Zattoni
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy
| | - Pierluigi Reschiglian
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy
| | - Marinella Portolani
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124, Modena, Italy
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8
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Analysis of lipoprotein-specific lipids in patients with acute coronary syndrome by asymmetrical flow field-flow fractionation and nanoflow liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1099:56-63. [PMID: 30243114 DOI: 10.1016/j.jchromb.2018.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/07/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023]
Abstract
A comprehensive lipid analysis was performed at the plasma lipoprotein level in patients with acute coronary syndrome (ACS) and stable coronary artery disease (CAD). Because the lipids in lipoproteins are related to the pathology of the cardiovascular system, lipoprotein-specific lipid analysis can be useful for understanding the mechanism of lipid-associated cardiovascular diseases. Lipoproteins were size-sorted into high density lipoproteins (HDL) and low density lipoproteins (LDL) using asymmetrical flow field-flow fractionation, then lipids of each lipoprotein were analysed using nanoflow ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry. A total of 365 lipids were structurally identified and quantified by selected reaction monitoring method. Two high abundance lysophosphatidylcholines (16:0 and 18:0) were significantly increased only in the HDL of the ACS group (vs. the stable CAD group). Phosphatidylethanolamines (38:5 and 40:5) significantly increased in ACS by >2-fold in both lipoproteins. (18:0, 22:6)-diacylglycerol increased in ACS by 3.5-fold only in LDL; however, most high abundance triacylglycerols decreased 2-fold in both lipoproteins. The present study revealed the usefulness of lipoprotein-specific analysis of lipids in distinguishing ACS from stable CAD, and the selected lipids analysed in this study may be useful in the development of lipid markers for the early detection of ACS.
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9
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Kuklenyik Z, Jones JI, Gardner MS, Schieltz DM, Parks BA, Toth CA, Rees JC, Andrews ML, Carter K, Lehtikoski AK, McWilliams LG, Williamson YM, Bierbaum KP, Pirkle JL, Barr JR. Core lipid, surface lipid and apolipoprotein composition analysis of lipoprotein particles as a function of particle size in one workflow integrating asymmetric flow field-flow fractionation and liquid chromatography-tandem mass spectrometry. PLoS One 2018; 13:e0194797. [PMID: 29634782 PMCID: PMC5892890 DOI: 10.1371/journal.pone.0194797] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/09/2018] [Indexed: 12/18/2022] Open
Abstract
Lipoproteins are complex molecular assemblies that are key participants in the intricate cascade of extracellular lipid metabolism with important consequences in the formation of atherosclerotic lesions and the development of cardiovascular disease. Multiplexed mass spectrometry (MS) techniques have substantially improved the ability to characterize the composition of lipoproteins. However, these advanced MS techniques are limited by traditional pre-analytical fractionation techniques that compromise the structural integrity of lipoprotein particles during separation from serum or plasma. In this work, we applied a highly effective and gentle hydrodynamic size based fractionation technique, asymmetric flow field-flow fractionation (AF4), and integrated it into a comprehensive tandem mass spectrometry based workflow that was used for the measurement of apolipoproteins (apos A-I, A-II, A-IV, B, C-I, C-II, C-III and E), free cholesterol (FC), cholesterol esters (CE), triglycerides (TG), and phospholipids (PL) (phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylethanolamine (PE), phosphatidylinositol (PI) and lysophosphatidylcholine (LPC)). Hydrodynamic size in each of 40 size fractions separated by AF4 was measured by dynamic light scattering. Measuring all major lipids and apolipoproteins in each size fraction and in the whole serum, using total of 0.1 ml, allowed the volumetric calculation of lipoprotein particle numbers and expression of composition in molar analyte per particle number ratios. Measurements in 110 serum samples showed substantive differences between size fractions of HDL and LDL. Lipoprotein composition within size fractions was expressed in molar ratios of analytes (A-I/A-II, C-II/C-I, C-II/C-III. E/C-III, FC/PL, SM/PL, PE/PL, and PI/PL), showing differences in sample categories with combinations of normal and high levels of Total-C and/or Total-TG. The agreement with previous studies indirectly validates the AF4-LC-MS/MS approach and demonstrates the potential of this workflow for characterization of lipoprotein composition in clinical studies using small volumes of archived frozen samples.
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Affiliation(s)
- Zsuzsanna Kuklenyik
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jeffery I. Jones
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Michael S. Gardner
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - David M. Schieltz
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bryan A. Parks
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Christopher A. Toth
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jon C. Rees
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Michael L. Andrews
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kayla Carter
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Antony K. Lehtikoski
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lisa G. McWilliams
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Yulanda M. Williamson
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kevin P. Bierbaum
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James L. Pirkle
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John R. Barr
- Clinical Chemistry Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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10
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Flow Field-Flow Fractionation with Mass Spectrometry for Top-Down and Bottom-Up Lipidomics. JOURNAL OF ANALYSIS AND TESTING 2017. [DOI: 10.1007/s41664-017-0027-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Frit inlet field-flow fractionation techniques for the characterization of polyion complex self-assemblies. J Chromatogr A 2017; 1481:101-110. [DOI: 10.1016/j.chroma.2016.12.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/15/2023]
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12
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13
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Lee ST, Yang B, Kim JY, Park JH, Moon MH. Combining asymmetrical flow field-flow fractionation with on- and off-line fluorescence detection to examine biodegradation of riverine dissolved and particulate organic matter. J Chromatogr A 2015; 1409:218-25. [DOI: 10.1016/j.chroma.2015.07.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 07/15/2015] [Accepted: 07/18/2015] [Indexed: 11/26/2022]
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14
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Kim KH, Compton PD, Tran JC, Kelleher NL. Online matrix removal platform for coupling gel-based separations to whole protein electrospray ionization mass spectrometry. J Proteome Res 2015; 14:2199-206. [PMID: 25836738 DOI: 10.1021/pr501331q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A fractionation method called gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) has been used to dramatically increase the number of proteins identified in top-down proteomic workflows; however, the technique involves the use of sodium dodecyl sulfate (SDS), a surfactant that interferes with electrospray ionization. Therefore, an efficient removal of SDS is absolutely required prior to mass analysis. Traditionally, methanol/chloroform precipitation and spin columns have been used, but they lack reproducibility and are difficult to automate. Therefore, we developed an in-line matrix removal platform to enable the direct analysis of samples containing SDS and salts. Only small molecules like SDS permeate a porous membrane and are removed in a manner similar to cross-flow filtration. With this device, near-complete removal of SDS is accomplished within 5 min and proteins are subsequently mobilized into a mass spectrometer. The new platform was optimized for the analysis of GELFrEE fractions enriched for histones extracted from human HeLa cells. All four core histones and their proteoforms were detected in a single spectrum by high-resolution mass spectrometry. The new method versus protein precipitation/resuspension showed 2- to 10-fold improved signal intensities, offering a clear path forward to improve proteome coverage and the efficiency of top-down proteomics.
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Affiliation(s)
- Ki Hun Kim
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - John C Tran
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2145 North Sheridan Road, Evanston, Illinois 60208, United States
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15
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Multivariate DoE Optimization of Asymmetric Flow Field Flow Fractionation Coupled to Quantitative LC-MS/MS for Analysis of Lipoprotein Subclasses. CHROMATOGRAPHY 2015. [DOI: 10.3390/chromatography2010096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Meermann B. Field-flow fractionation coupled to ICP–MS: separation at the nanoscale, previous and recent application trends. Anal Bioanal Chem 2015; 407:2665-74. [DOI: 10.1007/s00216-014-8416-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/27/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
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17
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Hydrodynamic size-based separation and characterization of protein aggregates from total cell lysates. Nat Protoc 2014; 10:134-48. [PMID: 25521790 DOI: 10.1038/nprot.2015.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herein we describe a protocol that uses hollow-fiber flow field-flow fractionation (FFF) coupled with multiangle light scattering (MALS) for hydrodynamic size-based separation and characterization of complex protein aggregates. The fractionation method, which requires 1.5 h to run, was successfully modified from the analysis of protein aggregates, as found in simple protein mixtures, to complex aggregates, as found in total cell lysates. In contrast to other related methods (filter assay, analytical ultracentrifugation, gel electrophoresis and size-exclusion chromatography), hollow-fiber flow FFF coupled with MALS allows a flow-based fractionation of highly purified protein aggregates and simultaneous measurement of their molecular weight, r.m.s. radius and molecular conformation (e.g., round, rod-shaped, compact or relaxed). The polyethersulfone hollow fibers used, which have a 0.8-mm inner diameter, allow separation of as little as 20 μg of total cell lysates. In addition, the ability to run the samples in different denaturing and nondenaturing buffer allows defining true aggregates from artifacts, which can form during sample preparation. The protocol was set up using Paraquat-induced carbonylation, a model that induces protein aggregation in cultured cells. This technique will advance the biochemical, proteomic and biophysical characterization of molecular-weight aggregates associated with protein mutations, as found in many CNS degenerative diseases, or chronic oxidative stress, as found in aging, and chronic metabolic and inflammatory conditions.
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18
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Marassi V, Roda B, Zattoni A, Tanase M, Reschiglian P. Hollow fiber flow field-flow fractionation and size-exclusion chromatography with multi-angle light scattering detection: A complementary approach in biopharmaceutical industry. J Chromatogr A 2014; 1372C:196-203. [DOI: 10.1016/j.chroma.2014.10.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 12/29/2022]
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Scientific Opinion on the evaluation of allergenic foods and food ingredients for labelling purposes. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3894] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Till U, Gaucher-Delmas M, Saint-Aguet P, Hamon G, Marty JD, Chassenieux C, Payré B, Goudounèche D, Mingotaud AF, Violleau F. Asymmetrical flow field-flow fractionation with multi-angle light scattering and quasi-elastic light scattering for characterization of polymersomes: comparison with classical techniques. Anal Bioanal Chem 2014; 406:7841-53. [PMID: 24951132 DOI: 10.1007/s00216-014-7891-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/17/2014] [Accepted: 05/13/2014] [Indexed: 11/24/2022]
Abstract
Polymersomes formed from amphiphilic block copolymers, such as poly(ethyleneoxide-b-ε-caprolactone) (PEO-b-PCL) or poly(ethyleneoxide-b-methylmethacrylate), were characterized by asymmetrical flow field-flow fractionation coupled with quasi-elastic light scattering (QELS), multi-angle light scattering (MALS), and refractive index detection, leading to the determination of their size, shape, and molecular weight. The method was cross-examined with more classical ones, like batch dynamic and static light scattering, electron microscopy, and atomic force microscopy. The results show good complementarities between all the techniques; asymmetrical flow field-flow fractionation being the most pertinent one when the sample exhibits several different types of population.
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Affiliation(s)
- Ugo Till
- Université de Toulouse, UPS/CNRS, IMRCP, 118 route de Narbonne, 31062, Toulouse Cedex 9, France
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Yang I, Kim KH, Lee JY, Moon MH. On-line miniaturized asymmetrical flow field-flow fractionation-electrospray ionization-tandem mass spectrometry with selected reaction monitoring for quantitative analysis of phospholipids in plasma lipoproteins. J Chromatogr A 2014; 1324:224-30. [DOI: 10.1016/j.chroma.2013.11.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/14/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
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22
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Mitais N, Bessette B, Gobron S, Cardot P, Jauberteau MO, Battu S, Lalloué F. Kinetics of chemically mediated neurodegeneration/neuroregeneration of mouse olfactory epithelium: monitoring by hyperlayer sedimentation field flow fractionation. Anal Bioanal Chem 2013; 406:1671-81. [PMID: 24337138 DOI: 10.1007/s00216-013-7526-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 11/17/2013] [Accepted: 11/20/2013] [Indexed: 12/17/2022]
Abstract
The increase in the incidence of neurodegenerative diseases linked to aging or injury needs to be addressed in research into neuroprotective or neuroregenerative therapies, and requires the development of specific biological models. To achieve this goal we propose (1) the use of the mouse olfactory epithelium as a biological support which specifically exhibits a regenerative or a self-renewing capacity and during the lifetime necessitates the presence of neural stem cells, and (2) the use of an intraperitoneal injection of 2,6-dichlorobenzonitrile (diclobenil) as a chemical inducer of neurodegeneration in olfactory epithelium by selectively killing mature cells. We developed a biological model to follow the processes of neurodegeneration (chemically induced) and neuroregeneration (self-renewal of olfactory epithelium). The purpose of this study was to develop a method to monitor quickly neurodegeneration/neuroregeneration processes in order to further screen protective and regenerative therapies. For this purpose, we used the sedimentation field flow fractionation elution of olfactory epithelium. We obtained specific elution profiles and retention parameters allowing the monitoring of the induction and kinetics of biological processes. The use of insulin-like growth factor 1α as a neuroprotective agent in an innovative nebulization protocol showed sedimentation field flow fractionation to be a simple, fast and low-cost method to monitor such a biological event on the scale of an entire organism.
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Affiliation(s)
- N Mitais
- Laboratoire d'Immunologie, EA 3842, "Homéostasie Cellulaire et Pathologies", Faculté de Médecine, Université de Limoges, 2 rue du Docteur Marcland, 87025, Limoges Cedex, France
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Top–down lipidomic analysis of human lipoproteins by chip-type asymmetrical flow field-flow fractionation–electrospray ionization-tandem mass spectrometry. J Chromatogr A 2013; 1280:92-7. [DOI: 10.1016/j.chroma.2013.01.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/24/2012] [Accepted: 01/10/2013] [Indexed: 11/19/2022]
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25
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Discovery of candidate phospholipid biomarkers in human lipoproteins with coronary artery disease by flow field-flow fractionation and nanoflow liquid chromatography–tandem mass spectrometry. J Chromatogr A 2012. [DOI: 10.1016/j.chroma.2012.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ibrahim T, Battu S, Cook-Moreau J, Cardot P. Instrumentation of hollow fiber flow field flow fractionation for selective cell elution. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 901:59-66. [DOI: 10.1016/j.jchromb.2012.05.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/02/2012] [Accepted: 05/04/2012] [Indexed: 12/24/2022]
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Kim JY, Kim SK, Kang D, Moon MH. Dual lectin-based size sorting strategy to enrich targeted N-glycopeptides by asymmetrical flow field-flow fractionation: profiling lung cancer biomarkers. Anal Chem 2012; 84:5343-50. [PMID: 22616828 DOI: 10.1021/ac300772w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A dual lectin-based size sorting and simultaneous enrichment strategy for selectively isolating N-linked glycopeptides was developed using asymmetrical flow field-flow fractionation (AF4). AF4 is an elution-based method for separating biological macromolecules that has been utilized for the separation of lectin-glycopeptide complexes formed by mixing serum peptides with lectin cocktails according to the difference in diffusion coefficients. It has also been used for simultaneous depletion of nonglycosylated peptides. The dual lectin-based enrichment method was applied to proteolytic peptides from lung cancer serum samples with two lectins (WGA, GlcNAc-specific, and SNA, Sia-specific), and the whole mixture was separated by AF4. The lectin-glycopeptide complex fractions collected during AF4 separation were endoglycosidically digested with PNGase F. The resulting deamidated glycopeptides were analyzed by nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS) to semiquantitatively profile the N-linked glycopeptides from the sera of lung cancer patients and healthy controls. The AF4 enrichment strategy coupled with nLC-ESI-MS-MS identified 16/24 (up/down-regulated by at least 10-fold compared to normal sera) N-linked glycopeptides from a WGA complex fraction of lung cancer sera and 18/3 from a SNA fraction.
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Affiliation(s)
- Jin Yong Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
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Schachermeyer S, Ashby J, Zhong W. Advances in field-flow fractionation for the analysis of biomolecules: instrument design and hyphenation. Anal Bioanal Chem 2012; 404:1151-8. [DOI: 10.1007/s00216-012-6069-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 04/02/2012] [Accepted: 04/21/2012] [Indexed: 10/28/2022]
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Two dimensional (pI & ds) separation of phosphorylated proteins by isoelectric focusing/asymmetrical flow field-flow fractionation: Application to prostatic cancer cell line. J Proteomics 2012; 75:2297-305. [DOI: 10.1016/j.jprot.2012.01.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 01/26/2012] [Accepted: 01/29/2012] [Indexed: 11/18/2022]
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Guerrier L, Fortis F, Boschetti E. Solid-phase fractionation strategies applied to proteomics investigations. Methods Mol Biol 2012; 818:11-33. [PMID: 22083813 DOI: 10.1007/978-1-61779-418-6_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methods for protein fractionation in the proteomics investigation field are relatively numerous. They apply to the prefractionation of the sample to obtain less complex protein mixtures for an easier analysis; they are also used as a means to evidence specific proteins or protein classes otherwise impossible to detect. They involve depletion of high-abundance proteins suppressing the signal of dilute species; they are also capable to enhance the detectability of low-abundance species while concomitantly decreasing the concentration of abundant proteins such as albumin in serum and hemoglobin in red blood cell lysates. Fractionation of proteomes is also used for the isolation of targeted species that are selected for their different expression under certain pathological conditions and that are detected by mass spectrometry. Two unconventional methods of large interest in proteomics due to the low level of protein redundancy between fractions are also reported.All these methods are reviewed and detailed method given to allow specialists of proteomics investigation to access selected separation methods generally dispersed on different technical reviews or books.
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Affiliation(s)
- Luc Guerrier
- Bio-Rad Laboratories, Marnes la Coquette, France
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Kim KH, Moon MH. Chip-Type Asymmetrical Flow Field-Flow Fractionation Channel Coupled with Mass Spectrometry for Top-Down Protein Identification. Anal Chem 2011; 83:8652-8. [DOI: 10.1021/ac202098b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ki Hun Kim
- Department of Chemistry, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul 120-749, Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul 120-749, Korea
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Yohannes G, Jussila M, Hartonen K, Riekkola ML. Asymmetrical flow field-flow fractionation technique for separation and characterization of biopolymers and bioparticles. J Chromatogr A 2011; 1218:4104-16. [DOI: 10.1016/j.chroma.2010.12.110] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/20/2010] [Accepted: 12/26/2010] [Indexed: 12/17/2022]
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Kang D, Ji ES, Moon MH, Yoo JS. Lectin-based enrichment method for glycoproteomics using hollow fiber flow field-flow fractionation: application to Streptococcus pyogenes. J Proteome Res 2010; 9:2855-62. [PMID: 20377246 DOI: 10.1021/pr900937w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This paper presents a new application of hollow fiber flow field-flow fractionation (HF5) as a preparative method to preconcentrate high mannose type N-linked glycoproteins from Streptococcus pyogenes by means of the mannose-specific binding affinity between concanavalian A (ConA) and N-linked glycosylated proteins. Prior to fractionation of N-linked glycoproteins from bacterial lysates, it was examined that ConA formed several types of multimers depending on the pH values (4, 6, and 8) of the carrier solution and it was confirmed that the molecular weight (MW) of ConA, spiked with alpha-1 acid glycoprotein (AGP) as a standard glycoprotein, increased due to binding with the mannose moiety of AGP. After adding ConA to bacterial lysates, mannose type N-linked glycoproteins were found to be enriched when the ConA fraction was isolated from whole bacterial lysates through HF5 run. For the identification of glycoproteins, the ConA fraction of HF5 was tryptically digested and followed by two-dimensional nanoflow strong cation exchange-reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry (2D SCX-RPLC-ESI-MS-MS) analysis to identify the N-linked glycoprotein species. From two-dimensional shotgun analyses, 45 proteins that exist on the Asn-Xaa-Ser/Thr sequence were identified as high mannose type N-linked glycoprotein. As a result, it was first demonstrated that HF5 is an alternative tool to enrich high mannose type N-linked glycoproteins using ConA-specific binding affinity.
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Affiliation(s)
- Dukjin Kang
- Mass Spectrometry Research Center, Korea Basic Science Institute, Chungcheongbuk-Do, Korea
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35
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Rambaldi DC, Reschiglian P, Zattoni A. Flow field-flow fractionation: recent trends in protein analysis. Anal Bioanal Chem 2010; 399:1439-47. [DOI: 10.1007/s00216-010-4312-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 11/29/2022]
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Kim KH, Lee JY, Moon MH. Effect of sodium dodecyl sulfate on protein separation by hollow fiber flow field-flow fractionation. Analyst 2010; 136:388-92. [PMID: 20963232 DOI: 10.1039/c0an00172d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Effects of protein denaturation and formation of protein-sodium dodecyl sulfate (SDS) complexes on protein separation and identification were investigated using hollow fiber flow field-flow fractionation (HF5) and nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS). Denaturation and formation of protein-SDS complexes prior to HF5 separation resulted an increase in the retention of few protein standards due to unfolding of the protein structures and complexation, yielding ~30% increase in hydrodynamic diameter. In addition, low molecular weight proteins which could be lost from the HF membrane due to the pore size limitation showed an increase of peak recovery about 2-6 folds for cytochrome C and carbonic anhydrase. In the case of proteins composed of a number of subunits, denaturation resulted in a decrease in retention due to dissociation of protein subunits. A serum proteome sample, denatured with dithiothreitol and SDS, was fractionated by HF5, and the eluting protein fractions after tryptic digestion were analyzed for protein identification using nLC-ESI-MS-MS. The resulting pools of identified proteins were found to depend on whether the serum sample was treated with or without denaturation prior to the HF5 run due to differences in the aqueous solubility of the proteins. The enhancement of protein solubility by SDS also increased the number of identified membrane proteins (54 vs. 31).
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Affiliation(s)
- Ki Hun Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, South Korea
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37
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Moon MH. Flow field-flow fractionation and multiangle light scattering for ultrahigh molecular weight sodium hyaluronate characterization. J Sep Sci 2010; 33:3519-29. [DOI: 10.1002/jssc.201000414] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/17/2010] [Accepted: 08/18/2010] [Indexed: 11/11/2022]
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Investigating the relationship between cell cycle stage and diosgenin-induced megakaryocytic differentiation of HEL cells using sedimentation field-flow fractionation. Anal Bioanal Chem 2010; 398:1273-83. [PMID: 20714892 DOI: 10.1007/s00216-010-4062-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
Differentiation therapy could be one strategy for stopping cancer cell proliferation. A plant steroid, diosgenin, is known to induce megakaryocytic differentiation in human erythroleukemia (HEL) cells. In recent studies, the use of sedimentation field-flow fractionation (SdFFF) allowed the preparation of subpopulations that may differ in regard to sensitivity to differentiation induction. The specific goal of this study was to determine the relationship between cell cycle stage and sensitivity to megakaryocytic differentiation induction of HEL cells. After first confirming the capacity of diosgenin to specifically select targets, hyperlayer SdFFF cell sorting was used to prepare fractions according to cell cycle position from crude HEL cells. The sensitivities of these fractions to diosgenin-induced differentiation were then tested. The coupling of SdFFF cell separation to imaging flow cytometry showed that G1-phase cells were more sensitive to differentiation induction than S/G2M-phase cells, confirming the relationship between cell status at the start of induction, the extent of the biological event, and the potential of SdFFF in cancer research.
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Effect of asymmetrical flow field-flow fractionation channel geometry on separation efficiency. J Chromatogr A 2010; 1217:3876-80. [DOI: 10.1016/j.chroma.2010.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 03/30/2010] [Accepted: 04/09/2010] [Indexed: 11/20/2022]
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40
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Sedimentation field-flow fractionation separation of proliferative and differentiated subpopulations during Ca2+-induced differentiation in HaCaT cells. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1051-8. [DOI: 10.1016/j.jchromb.2010.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 03/05/2010] [Accepted: 03/09/2010] [Indexed: 11/22/2022]
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Horvatovich PL, Bischoff R. Current technological challenges in biomarker discovery and validation. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:101-121. [PMID: 20065518 DOI: 10.1255/ejms.1050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this review we will give an overview of the issues related to biomarker discovery studies with a focus on liquid chromatography-mass spectrometry (LC-MS) methods. Biomarker discovery is based on a close collaboration between clinicians, analytical scientists and chemometritians/statisticians. It is critical to define the final purpose of a biomarker or biomarker pattern at the onset of the study and to select case and control samples accordingly. This is followed by designing the experiment, starting with the sampling strategy, sample collection, storage and separation protocols, choice and validation of the quantitative profiling platform followed by data processing, statistical analysis and validation workflows. Biomarker candidates that result after statistical validation should be submitted for further validation and, ideally, be connected to the disease mechanism after their identification. Since most discovery studies work with a relatively small number of samples, it is necessary to assess the specificity and sensitivity of a given biomarker-based assay in a larger set of independent samples, preferably analyzed at another clinical center. Targeted analytical methods of higher throughput than the original discovery method are needed at this point and LC-tandem mass spectrometry is gaining acceptance in this field. Throughout this review, we will focus on possible sources of variance and how they can be assessed and reduced in order to avoid false positives and to reduce the number of false negatives in biomarker discovery research.
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Affiliation(s)
- Peter L Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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Qureshi RN, Kok WT, Schoenmakers PJ. Fractionation of human serum lipoproteins and simultaneous enzymatic determination of cholesterol and triglycerides. Anal Chim Acta 2009; 654:85-91. [DOI: 10.1016/j.aca.2009.06.060] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 06/24/2009] [Accepted: 06/25/2009] [Indexed: 11/27/2022]
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43
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Lee JY, Kim KH, Moon MH. Evaluation of multiplexed hollow fiber flow field-flow fractionation for semi-preparative purposes. J Chromatogr A 2009; 1216:6539-42. [DOI: 10.1016/j.chroma.2009.07.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/16/2009] [Accepted: 07/27/2009] [Indexed: 11/28/2022]
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Kim KH, Moon MH. High Speed Two-Dimensional Protein Separation without Gel by Isoelectric Focusing−Asymmetrical Flow Field Flow Fractionation: Application to Urinary Proteome. J Proteome Res 2009; 8:4272-8. [DOI: 10.1021/pr900363s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ki Hun Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
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Rambaldi DC, Zattoni A, Reschiglian P, Colombo R, De Lorenzi E. In vitro amyloid Aβ1-42 peptide aggregation monitoring by asymmetrical flow field-flow fractionation with multi-angle light scattering detection. Anal Bioanal Chem 2009; 394:2145-9. [DOI: 10.1007/s00216-009-2899-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/04/2009] [Accepted: 06/09/2009] [Indexed: 02/02/2023]
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46
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Monaci L, Visconti A. Mass spectrometry-based proteomics methods for analysis of food allergens. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2009.02.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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47
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Field-flow fractionation in bioanalysis: A review of recent trends. Anal Chim Acta 2009; 635:132-43. [DOI: 10.1016/j.aca.2009.01.015] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 01/08/2009] [Accepted: 01/09/2009] [Indexed: 11/23/2022]
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