101
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Zhang Z, Zhu G, Peuchen EH, Dovichi NJ. Preparation of linear polyacrylamide coating and strong cationic exchange hybrid monolith in a single capillary, and its application as an automated platform for bottom-up proteomics by capillary electrophoresis-mass spectrometry. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2084-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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102
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Chen D, Shen X, Sun L. Capillary zone electrophoresis–mass spectrometry with microliter-scale loading capacity, 140 min separation window and high peak capacity for bottom-up proteomics. Analyst 2017; 142:2118-2127. [DOI: 10.1039/c7an00509a] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CZE–MS can approach a microliter-scale loading capacity and a 140 min separation window for large-scale bottom-up proteomics.
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Affiliation(s)
- Daoyang Chen
- Department of Chemistry
- Michigan State University
- East Lansing
- USA 48824
| | - Xiaojing Shen
- Department of Chemistry
- Michigan State University
- East Lansing
- USA 48824
| | - Liangliang Sun
- Department of Chemistry
- Michigan State University
- East Lansing
- USA 48824
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103
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Zhu G, Sun L, Dovichi NJ. Simplified capillary isoelectric focusing with chemical mobilization for intact protein analysis. J Sep Sci 2016; 40:948-953. [PMID: 27935257 DOI: 10.1002/jssc.201601051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 11/05/2022]
Abstract
We report a capillary isoelectric focusing system based on a sequential injection method for simplified chemical mobilization. This system was coupled to an ion trap mass spectrometer with an electrokinetically pumped nanoelectrospray interface. The nanoelectrospray emitter employed an acidic sheath electrolyte. To simplify focusing and mobilization, a plug of ammonium hydroxide was first injected into the capillary, followed by a section of mixed sample and ampholyte. During focusing, the NH3 H2 O section worked as catholyte. As focusing progressed, the NH3 H2 O section was titrated to lower pH by the acidic sheath electrolyte. Chemical mobilization started automatically once the ammonium hydroxide was consumed by the acidic sheath flow electrolyte, which then acted as the mobilization solution. In this report, the lengths of the NH3 H2 O section and sample were optimized. With a 1 m long capillary, a relative short plug of the NH3 H2 O section (3 cm) produced both fast migration and reasonable separation resolution. The simplified capillary isoelectric focusing mass spectrometry system produced base peak intensity relative standard deviation of 8.5% and migration time relative standard deviation ≤0.6% for myoglobin and cytochrome C in triplicate runs.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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104
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Evaluation of a commercial electro-kinetically pumped sheath-flow nanospray interface coupled to an automated capillary zone electrophoresis system. Anal Bioanal Chem 2016; 409:1789-1795. [PMID: 27981343 DOI: 10.1007/s00216-016-0122-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/10/2016] [Accepted: 11/28/2016] [Indexed: 10/20/2022]
Abstract
Capillary zone electrophoresis-electrospray ionization-mass spectrometry (CZE-ESI-MS) is attracting renewed attention for proteomic and metabolomic analysis. An important reason for this interest is the maturation and commercialization of interfaces for coupling CZE with ESI-MS. One of these interfaces is an electro-kinetically pumped sheath flow nanospray interface developed by the Dovichi group, in which a very low sheath flow is generated based on electroosmosis within a glass emitter. CMP Scientific has commercialized this interface as the EMASS-II ion source. In this work, we compared the performance of the EMASS-II ion source with our in-house system. The performance of the systems is equivalent. We also coupled the EMASS-II ion source with a PrinCE Next|480 capillary electrophoresis autosampler and an Orbitrap mass spectrometer, and analyzed this system's performance in terms of sensitivity, reproducibility, and separation performance for separation of tryptic digests, intact proteins, and amino acids. The system produced reproducible analysis of BSA digest; the RSDs of peptide intensity and migration time across 24 runs were less than 20 and 6%, respectively. The system produced a linear calibration curve of intensity across a 30-fold range of tryptic digest concentration. The combination of a commercial autosampler and electrospray interface efficiently separated amino acids, peptides, and intact proteins, and only required 5 μL of sample for analysis. Graphical Abstract The commercial and locally constructed versions of the interface provide similar numbers of protein identifications from a Xenopus laevis fertilized egg digest.
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105
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Zhang Z, Albanetti T, Linkous T, Larkin CJ, Schoner R, McGivney JB, Dovichi NJ. Comprehensive analysis of host cell impurities in monoclonal antibodies with improved sensitivity by capillary zone electrophoresis mass spectrometry. Electrophoresis 2016; 38:401-407. [DOI: 10.1002/elps.201600390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN USA
| | - Thomas Albanetti
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Travis Linkous
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Christopher J. Larkin
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Ronald Schoner
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - James B. McGivney
- BioPharmaceutical Development, MedImmune LLC; One MedImmune Way; Gaithersburg MD USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN USA
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106
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Zhu G, Sun L, Heidbrink-Thompson J, Kuntumalla S, Lin HY, Larkin CJ, McGivney JB, Dovichi NJ. Capillary zone electrophoresis tandem mass spectrometry detects low concentration host cell impurities in monoclonal antibodies. Electrophoresis 2016; 37:616-22. [PMID: 26530276 DOI: 10.1002/elps.201500301] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/02/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022]
Abstract
We have evaluated CZE-ESI-MS/MS for detection of trace amounts of host cell protein impurities in recombinant therapeutics. Compared to previously published procedures, we have optimized the buffer pH used in the formation of a pH junction to increase injection volume. We also prepared a 5-point calibration curve by spiking 12 standard proteins into a solution of a human mAb. A custom CZE-MS/MS system was used to analyze the tryptic digest of this mixture without depletion of the antibody. CZE generated a ∼70-min separation window (∼90-min total analysis duration) and ∼300-peak capacity. We also analyzed the sample using ultra-performance LC-MS/MS. CZE-MS/MS generated approximately five times higher base peak intensity and more peptide identifications for low-level spiked proteins. Both methods detected all proteins spiked at ∼100 ppm level with respect to the antibody.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Hung-yu Lin
- Department of Analytical Biotechnology, MedImmune, Gaithersburg, MD, USA
| | | | - James B McGivney
- Department of Analytical Biotechnology, MedImmune, Gaithersburg, MD, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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107
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Yuan F, Zhang XH, Nie J, Chen HX, Zhou YL, Zhang XX. Ultrasensitive determination of 5-methylcytosine and 5-hydroxymethylcytosine in genomic DNA by sheathless interfaced capillary electrophoresis-mass spectrometry. Chem Commun (Camb) 2016; 52:2698-700. [PMID: 26753520 DOI: 10.1039/c5cc10155g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A newly developed sheathless interface for capillary electrophoresis-mass spectrometry, using a porous tip sprayer, was first applied for highly sensitive determination of cytosine modifications. The system performed well in identification and quantification of both 5-methylcytosine and 5-hydroxymethylcytosine using only 125 pg (∼20 cells) genomic DNA samples.
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Affiliation(s)
- Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Xiao-Hui Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Ji Nie
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Hong-Xu Chen
- Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, Beijing, P. R. China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
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108
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Zhao Y, Sun L, Zhu G, Dovichi NJ. Coupling Capillary Zone Electrophoresis to a Q Exactive HF Mass Spectrometer for Top-down Proteomics: 580 Proteoform Identifications from Yeast. J Proteome Res 2016; 15:3679-3685. [PMID: 27490796 DOI: 10.1021/acs.jproteome.6b00493] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used reversed-phase liquid chromatography to separate the yeast proteome into 23 fractions. These fractions were then analyzed using capillary zone electrophoresis (CZE) coupled to a Q-Exactive HF mass spectrometer using an electrokinetically pumped sheath flow interface. The parameters of the mass spectrometer were first optimized for top-down proteomics using a mixture of seven model proteins; we observed that intact protein mode with a trapping pressure of 0.2 and normalized collision energy of 20% produced the highest intact protein signals and most protein identifications. Then, we applied the optimized parameters for analysis of the fractionated yeast proteome. From this, 580 proteoforms and 180 protein groups were identified via database searching of the MS/MS spectra. This number of proteoform identifications is two times larger than that of previous CZE-MS/MS studies. An additional 3,243 protein species were detected based on the parent ion spectra. Post-translational modifications including N-terminal acetylation, signal peptide removal, and oxidation were identified.
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Affiliation(s)
- Yimeng Zhao
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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109
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Zhu G, Sun L, Dovichi NJ. Dynamic pH junction preconcentration in capillary electrophoresis- electrospray ionization-mass spectrometry for proteomics analysis. Analyst 2016; 141:5216-20. [PMID: 27460877 DOI: 10.1039/c6an01140c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Capillary zone electrophoresis (CZE)-electrospray ionization (ESI)-mass spectrometry (MS) is an interesting complimentary technique to reversed phase liquid chromatography (RPLC)-ESI-MS for proteomics research. However, the low sample loading capacity of CZE (typically a few nL) can limit its application for large-scale proteomics. A number of on-line sample preconcentration methods have been developed to increase sample loading volumes. This review considers the dynamic pH junction as a simple on-line sample preconcentration method; this method is well suited for amphiprotic analytes. In the pH junction, these analytes are suspended in a basic buffer, injected by pressure into the capillary, and separated in an acidic background electrolyte, with no changes in either CZE-MS operations or instrumentation. We have demonstrated that the dynamic pH junction method can improve the sample loading volume to sub-μL volumes without significant loss of separation capacity for bottom-up proteomic analysis. The dynamic pH junction based CZE-ESI-MS system has been applied for a number of complex biological samples, including the E. coli proteome, impurities in recombinant antibody therapeutics, and the characterization of the phosphoproteome from a human cell line.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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110
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Lin L, Liu X, Zhang F, Chi L, Amster IJ, Leach FE, Xia Q, Linhardt RJ. Analysis of heparin oligosaccharides by capillary electrophoresis-negative-ion electrospray ionization mass spectrometry. Anal Bioanal Chem 2016; 409:411-420. [PMID: 27325464 DOI: 10.1007/s00216-016-9662-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/09/2016] [Accepted: 05/20/2016] [Indexed: 11/29/2022]
Abstract
Most hyphenated analytical approaches that rely on liquid chromatography-MS require relatively long separation times, produce incomplete resolution of oligosaccharide mixtures, use eluents that are incompatible with electrospray ionization, or require oligosaccharide derivatization. Here we demonstrate the analysis of heparin oligosaccharides, including disaccharides, ultralow molecular weight heparin, and a low molecular weight heparin, using a novel electrokinetic pump-based CE-MS coupling eletrospray ion source. Reverse polarity CE separation and negative-mode electrospray ionization were optimized using a volatile methanolic ammonium acetate electrolyte and sheath fluid. The online CE hyphenated negative-ion electrospray ionization MS on an LTQ Orbitrap mass spectrometer was useful in disaccharide compositional analysis and bottom-up and top-down analysis of low molecular weight heparin. The application of this CE-MS method to ultralow molecular heparin suggests that a charge state distribution and the low level of sulfate group loss that is achieved make this method useful for online tandem MS analysis of heparins. Graphical abstract Most hyphenated analytical approaches that rely on liquid chromatography-MS require relatively long separation times, produce incomplete resolution of oligosaccharide mixtures, use eluents that are incompatible with electrospray ionization, or require oligosaccharide derivatization. Here we demonstrate the analysis of heparin oligosaccharides, including disaccharides, ultralow molecular weight heparin, and a low molecular weight heparin, using a novel electrokinetic pump-based CE-MS coupling eletrospray ion source. Reverse polarity CE separation and negative-mode electrospray ionization were optimized using a volatile methanolic ammonium acetate electrolyte and sheath fluid. The online CE hyphenated negative-ion electrospray ionization MS on an LTQ Orbitrap mass spectrometer was useful in disaccharide compositional analysis and bottom-up and top-down analysis of low molecular weight heparin. The application of this CE-MS method to ultralow molecular heparin suggests that a charge state distribution and the low level of sulfate group loss that is achieved make this method useful for online tandem MS analysis of heparins.
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Affiliation(s)
- Lei Lin
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA
| | - Xinyue Liu
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,National Glycoengineering Research Center, Shandong University, 44 Wenhuaxi Rd., Jinan, Shandong, 250100, China
| | - Fuming Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.,Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, 44 Wenhuaxi Rd., Jinan, Shandong, 250100, China
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602-2556, USA
| | - Franklyn E Leach
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia, 30602-2556, USA
| | - Qiangwei Xia
- CMP Scientific, Corp., 760 Parkside Ave, Brooklyn, NY, 11226, USA. .,Beijing Proteomics Front Co., Ltd., R&D Building, 29 Shengmingyuan Rd, Changping District, Beijing, 102206, China.
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA. .,Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA. .,Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA. .,Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA.
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111
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Cutting-edge capillary electrophoresis characterization of monoclonal antibodies and related products. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1032:61-78. [PMID: 27265157 DOI: 10.1016/j.jchromb.2016.05.028] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 01/22/2023]
Abstract
Out of all categories, monoclonal antibodies (mAbs), biosimilar, antibody-drug conjugates (ADCs) and Fc-fusion proteins attract the most interest due to their strong therapeutic potency and specificity. Because of their intrinsic complexity due to a large number of micro-heterogeneities, there is a crucial need of analytical methods to provide comprehensive in-depth characterization of these molecules. CE presents some obvious benefits as high resolution separation and miniaturized format to be widely applied to the analysis of biopharmaceuticals. CE is an effective method for the separation of proteins at different levels. capillary gel electrophoresis (CGE), capillary isoelectric focusing (cIEF) and capillary zone electrophoresis (CZE) have been particularly relevant for the characterization of size and charge variants of intact and reduced mAbs, while CE-MS appears to be a promising analytical tool to assess the primary structure of mAbs and related products. This review will be dedicated to detail the current and state-of-the-art CE-based methods for the characterization of mAbs and related products.
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112
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Melani RD, Skinner OS, Fornelli L, Domont GB, Compton PD, Kelleher NL. Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics. Mol Cell Proteomics 2016; 15:2423-34. [PMID: 27178327 DOI: 10.1074/mcp.m115.056523] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Indexed: 11/06/2022] Open
Abstract
Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric l-amino acid oxidase (∼130 kDa) and the multichain toxin cobra venom factor (∼147 kDa). The l-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics.
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Affiliation(s)
- Rafael D Melani
- From the ‡Proteomics Unit, Rio de Janeiro Proteomics Network, Departamento de Bioquímica. Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil; §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Owen S Skinner
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Luca Fornelli
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Gilberto B Domont
- From the ‡Proteomics Unit, Rio de Janeiro Proteomics Network, Departamento de Bioquímica. Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil;
| | - Philip D Compton
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Neil L Kelleher
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
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113
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Guo X, Fillmore TL, Gao Y, Tang K. Capillary Electrophoresis-Nanoelectrospray Ionization-Selected Reaction Monitoring Mass Spectrometry via a True Sheathless Metal-Coated Emitter Interface for Robust and High-Sensitivity Sample Quantification. Anal Chem 2016; 88:4418-25. [PMID: 27028594 DOI: 10.1021/acs.analchem.5b04912] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A new sheathless transient capillary isotachophoresis (CITP)/capillary zone electrophoresis (CZE)-MS interface, based on a commercially available capillary with an integrated metal-coated ESI emitter, was developed in this study aiming at overcoming the reproducibility and ruggedness problems suffered to a certain degree by almost all the available CE-MS interfaces, and pushing the CE-MS technology suitable for routine sample analysis with high sensitivity. The new CITP/CZE-MS interface allows the electric contact between ESI voltage power supply and the CE separation liquid by using a conductive liquid that comes in contact with the metal-coated surface of the ESI emitter, making it a true sheathless CE-MS interface. Stable electrospray was established by avoiding the formation of gas bubbles from electrochemical reaction inside the CE capillary. Crucial operating parameters, such as sample loading volume, flow rate, and separation voltage, were systematically evaluated for their effects on both CITP/CZE separation efficiency and MS detection sensitivity. Around one hundred CITP/CZE-MS analyses can be easily achieved by using the new sheathless CITP/CZE interface without a noticeable loss of metal coating on the ESI emitter surface, or degrading of the ESI emitter performance. The reproducibility in analyte migration time and quantitative performance of the new interface was experimentally evaluated to demonstrate a LOQ below 5 attomole.
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Affiliation(s)
- Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University , Nanjing 210029, China
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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114
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Ibrahim M, Gahoual R, Enkler L, Becker HD, Chicher J, Hammann P, François YN, Kuhn L, Leize-Wagner E. Improvement of Mitochondria Extract from Saccharomyces cerevisiae Characterization in Shotgun Proteomics Using Sheathless Capillary Electrophoresis Coupled to Tandem Mass Spectrometry. J Chromatogr Sci 2016; 54:653-63. [PMID: 26860395 PMCID: PMC4885408 DOI: 10.1093/chromsci/bmw005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/11/2015] [Indexed: 12/16/2022]
Abstract
In this work, we describe the characterization of a quantity-limited sample (100 ng) of yeast mitochondria by shotgun bottom-up proteomics. Sample characterization was carried out by sheathless capillary electrophoresis, equipped with a high sensitivity porous tip and coupled to tandem mass spectrometry (CESI-MS-MS) and concomitantly with a state-of-art nano flow liquid chromatography coupled to a similar mass spectrometry (MS) system (nanoLC-MS-MS). With single injections, both nanoLC-MS-MS and CESI-MS-MS 60 min-long separation experiments allowed us to identify 271 proteins (976 unique peptides) and 300 proteins (1,765 unique peptides) respectively, demonstrating a significant specificity and complementarity in identification depending on the physicochemical separation employed. Such complementary, maximizing the number of analytes detected, presents a powerful tool to deepen a biological sample's proteomic characterization. A comprehensive study of the specificity provided by each separating technique was also performed using the different properties of the identified peptides: molecular weight, mass-to-charge ratio (m/z), isoelectric point (pI), sequence coverage or MS-MS spectral quality enabled to determine the contribution of each separation. For example, CESI-MS-MS enables to identify larger peptides and eases the detection of those having extreme pI without impairing spectral quality. The addition of peptides, and therefore proteins identified by both techniques allowed us to increase significantly the sequence coverages and then the confidence of characterization. In this study, we also demonstrated that the two yeast enolase isoenzymes were both characterized in the CESI-MS-MS data set. The observation of discriminant proteotypic peptides is facilitated when a high number of precursors with high-quality MS-MS spectra are generated.
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Affiliation(s)
- Marianne Ibrahim
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
| | - Rabah Gahoual
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
| | - Ludovic Enkler
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Hubert Dominique Becker
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Johana Chicher
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FRC 1589, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FRC 1589, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FRC 1589, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
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115
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Gulersonmez MC, Lock S, Hankemeier T, Ramautar R. Sheathless capillary electrophoresis-mass spectrometry for anionic metabolic profiling. Electrophoresis 2016; 37:1007-14. [PMID: 26593113 PMCID: PMC5064653 DOI: 10.1002/elps.201500435] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 12/23/2022]
Abstract
The performance of CE coupled on-line to MS via a sheathless porous tip sprayer was evaluated for anionic metabolic profiling. A representative metabolite mixture and biological samples were used for the evaluation of various analytical parameters, such as peak efficiency (plate numbers), migration time and peak area repeatability, and LODs. The BGE, i.e. 10% acetic acid (pH 2.2), previously used for cationic metabolic profiling was now assessed for anionic metabolic profiling by using MS detection in negative ion mode. For test compounds, RSDs for migration times and peak areas were below 2 and 11%, respectively, and plate numbers ranged from 60 000 to 40 0000 demonstrating a high separation efficiency. Critical metabolites with low or no retention on reversed-phase LC could be efficiently separated and selectively analyzed by the sheathless CE-MS method. An injection volume of only circa 20 nL resulted in LODs between 10 and 200 nM (corresponding to an amount of 0.4-4 fmol), which was an at least tenfold improvement as compared to LODs obtained by conventional CE-MS approaches for these analytes. The methodology was applied to anionic metabolic profiling of glioblastoma cell line extracts. Overall, a sheathless CE-MS method has been developed for highly efficient and sensitive anionic metabolic profiling studies, which can also be used for cationic metabolic profiling studies by only switching the MS detection and separation voltage polarity.
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Affiliation(s)
- Mehmet Can Gulersonmez
- Leiden Academic Center for Drug Research, Division of Analytical Biosciences, Leiden University, Leiden, The Netherlands
| | - Stephen Lock
- Sciex, Phoenix House, Center Park, Warrington, UK
| | - Thomas Hankemeier
- Leiden Academic Center for Drug Research, Division of Analytical Biosciences, Leiden University, Leiden, The Netherlands
| | - Rawi Ramautar
- Leiden Academic Center for Drug Research, Division of Analytical Biosciences, Leiden University, Leiden, The Netherlands
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116
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González-Ruiz V, Codesido S, Far J, Rudaz S, Schappler J. Evaluation of a new low sheath-flow interface for CE-MS. Electrophoresis 2016; 37:936-46. [DOI: 10.1002/elps.201500523] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Víctor González-Ruiz
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva 4 Switzerland
| | | | - Johann Far
- Laboratory of Mass Spectrometry, Chemistry Institute; University of Liège; Liège Belgium
- Analis; Suarlee Belgium
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva 4 Switzerland
| | - Julie Schappler
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva 4 Switzerland
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117
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Heemskerk AAM, Deelder AM, Mayboroda OA. CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications. MASS SPECTROMETRY REVIEWS 2016; 35:259-271. [PMID: 24852088 DOI: 10.1002/mas.21432] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
With the development of more sensitive hyphenation strategies for capillary electrophoresis-electrospray-mass spectrometry the technique has reemerged as technique with high separation power combined with high sensitivity in the analysis of peptides and protein digests. This review will discuss the newly developed hyphenation strategies for CE-ESI-MS and their application in bottom-up proteomics as well as the applications in the same time span, 2009 to present, using co-axial sheathliquid. Subsequently all separate aspects in the development of a CE-ESI-MS method for bottom-up proteomics shall be discussed, highlighting certain applications and discussing pros and cons of the various choices. The separation of peptides in a capillary electrophoresis system is discussed including the great potential for modeling of this migration of peptides due to the simple electrophoretic separation process. Furthermore, the technical aspects of method development are discussed, namely; background electrolyte choice, coating of the separation capillary and chosen loading method. Finally, conclusions and an outlook on future developments in the field of bottom-up proteomics by CE-ESI-MS will be provided.
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Affiliation(s)
- Anthonius A M Heemskerk
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
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118
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119
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Savaryn JP, Skinner OS, Fornelli L, Fellers RT, Compton PD, Terhune SS, Abecassis MM, Kelleher NL. Targeted analysis of recombinant NF kappa B (RelA/p65) by denaturing and native top down mass spectrometry. J Proteomics 2016; 134:76-84. [PMID: 25952688 PMCID: PMC4633404 DOI: 10.1016/j.jprot.2015.04.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/06/2015] [Accepted: 04/24/2015] [Indexed: 02/03/2023]
Abstract
Measuring post-translational modifications on transcription factors by targeted mass spectrometry is hampered by low protein abundance and inefficient isolation. Here, we utilized HaloTag technology to overcome these limitations and evaluate various top down mass spectrometry approaches for measuring NF-κB p65 proteoforms isolated from human cells. We show isotopic resolution of N-terminally acetylated p65 and determined it is the most abundant proteoform expressed following transfection in 293T cells. We also show MS(1) evidence for monophosphorylation of p65 under similar culture conditions and describe a high propensity for p65 proteoforms to fragment internally during beam-style MS(2) fragmentation; up to 71% of the fragment ions could be matched as internals in some fragmentation spectra. Finally, we used native spray mass spectrometry to measure proteins copurifying with p65 and present evidence for the native detection of p65, 71kDa heat shock protein, and p65 homodimer. Collectively, our work demonstrates the efficient isolation and top down mass spectrometry analysis of p65 from human cells, and we discuss the perturbations of overexpressing tagged proteins to study their biochemistry. This article is part of a Special Issue entitled: Protein Species. BIOLOGICAL SIGNIFICANCE Characterizing transcription factor proteoforms in human cells is of high value to the field of molecular biology; many agree that post-translational modifications and combinations thereof play a critical role in modulating transcription factor activity. Thus, measuring these modifications promises increased understanding of molecular mechanisms governing the regulation of complex gene expression outcomes. To date, comprehensive characterization of transcription factor proteoforms within human cells has eluded measurement, owing primarily-with regard to top down mass spectrometry-to large protein size and low relative abundance. Here, we utilized HaloTag technology and recombinant protein expression to overcome these limitations and show top down mass spectrometry characterization of proteoforms of the 60kDa NF-kB protein, p65. By optimizing the analytical procedure (i.e. purification, MS(1), and MS(2)), our results make important progress toward the ultimate goal of targeted transcription factor characterization from endogenous loci.
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Affiliation(s)
- John Paul Savaryn
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA; Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Owen S Skinner
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Philip D Compton
- Department of Chemistry, Northwestern University, Evanston, IL, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Scott S Terhune
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mike M Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
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120
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Zhao Y, Sun L, Knierman MD, Dovichi NJ. Fast separation and analysis of reduced monoclonal antibodies with capillary zone electrophoresis coupled to mass spectrometry. Talanta 2016; 148:529-33. [DOI: 10.1016/j.talanta.2015.11.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 12/18/2022]
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121
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Han M, Rock BM, Pearson JT, Rock DA. Intact mass analysis of monoclonal antibodies by capillary electrophoresis—Mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1011:24-32. [DOI: 10.1016/j.jchromb.2015.12.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/17/2015] [Accepted: 12/20/2015] [Indexed: 12/23/2022]
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122
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Sun X, Lin L, Liu X, Zhang F, Chi L, Xia Q, Linhardt RJ. Capillary Electrophoresis-Mass Spectrometry for the Analysis of Heparin Oligosaccharides and Low Molecular Weight Heparin. Anal Chem 2016; 88:1937-43. [PMID: 26714061 DOI: 10.1021/acs.analchem.5b04405] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Heparins, highly sulfated, linear polysaccharides also known as glycosaminoglycans, are among the most challenging biopolymers to analyze. Hyphenated techniques in conjunction with mass spectrometry (MS) offer rapid analysis of complex glycosaminoglycan mixtures, providing detailed structural and quantitative data. Previous analytical approaches have often relied on liquid chromatography (LC)-MS, and some have limitations including long separation times, low resolution of oligosaccharide mixtures, incompatibility of eluents, and often require oligosaccharide derivatization. This study examines the analysis of glycosaminoglycan oligosaccharides using a novel electrokinetic pump-based capillary electrophoresis (CE)-MS interface. CE separation and electrospray were optimized using a volatile ammonium bicarbonate electrolyte and a methanol-formic acid sheath fluid. The online analyses of highly sulfated heparin oligosaccharides, ranging from disaccharides to low molecular weight heparins, were performed within a 10 min time frame, offering an opportunity for higher-throughput analysis. Disaccharide compositional analysis as well as top-down analysis of low molecular weight heparin was demonstrated. Using normal polarity CE separation and positive-ion electrospray ionization MS, excellent run-to-run reproducibility (relative standard deviation of 3.6-5.1% for peak area and 0.2-0.4% for peak migration time) and sensitivity (limit of quantification of 2.0-5.9 ng/mL and limit of detection of 0.6-1.8 ng/mL) could be achieved.
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Affiliation(s)
- Xiaojun Sun
- National Glycoengineering Research Center, Shandong University , Jinan 250100, China
| | | | - Xinyue Liu
- National Glycoengineering Research Center, Shandong University , Jinan 250100, China
| | | | - Lianli Chi
- National Glycoengineering Research Center, Shandong University , Jinan 250100, China
| | - Qiangwei Xia
- CMP Scientific, Corporation, 760 Parkside Avenue, Brooklyn, New York 11226, United States.,Beijing Proteomics Front Company, Limited, R&D Building, 29 Shengmingyuan Road, Changping District, Beijing 102206, China
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123
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Zhu G, Sun L, Dovichi NJ. Thermally-initiated free radical polymerization for reproducible production of stable linear polyacrylamide coated capillaries, and their application to proteomic analysis using capillary zone electrophoresis-mass spectrometry. Talanta 2016; 146:839-43. [PMID: 26695337 PMCID: PMC4690009 DOI: 10.1016/j.talanta.2015.06.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 02/03/2023]
Abstract
Proteomic analysis using capillary zone electrophoresis (CZE) typically is performed with linear polyacrylamide (LPA) coated capillaries. These capillaries both minimize the adsorption of peptides and proteins to the inner wall of the capillary and decrease electroosmosis, which increases the separation capacity. LPA coating protocols were first reported by Hjerten in 1985. Conventional LPA production is based on the use of tetramethylethylenediamine (TEMED) to catalyze the free-radical polymerization that couples acrylamide to a capillary wall that has been pretreated with γ-methacryloxypropyltrimethoxysilane. The treated capillary is filled with a mixture of monomer, TEMED, and ammonium persulfate; free radical polymerization forms the LPA coating. Over many years, we have observed significant variation in the electroosmotic properties of commercial LPA coated capillaries both along the capillary length and between lots. We believe this variation is due to differences in the time between initiation of the reaction and the filling of the capillary. Here, we report a simple method for the generation of very stable and reproducible coatings. In this protocol, the monomer mixture and an ammonium persulfate initiator are introduced into the capillary without TEMED initiator. The mixture is stable and does not begin polymerization at room temperature. The filled capillary is then heated in a water bath to initiate polymerization in a well-controlled manner. A mixture of four standard proteins was used to evaluate the coating performance. Compared with commercialized LPA capillaries, our LPA capillaries generate much better separation performance and superior protein peak shape in CZE analysis. We also analyzed an intact antibody (MW 150K) by CZE-MS with the new LPA capillary in triplicate runs. The intact antibody generated a Gaussian-shaped electrophoresis peak with 1.2% relative standard deviation in migration time and 8.5% in base peak intensity. An automated CZE-MS system was used to generate 97 successive separations of a BSA tryptic digest over a 145-h period. Separation efficiency averaged over 100,000 theoretical plates across this period with no systematic variation. The LPA coating protocol had excellent batch-to-batch reproducibility with relative standard deviation in migration time<7%, and in separation window<1%.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556, USA
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124
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Bush DR, Zang L, Belov AM, Ivanov AR, Karger BL. High Resolution CZE-MS Quantitative Characterization of Intact Biopharmaceutical Proteins: Proteoforms of Interferon-β1. Anal Chem 2015; 88:1138-46. [DOI: 10.1021/acs.analchem.5b03218] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- David R. Bush
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Li Zang
- Analytical
Development Department, Biogen, Cambridge, Massachusetts 02142, United States
| | - Arseniy M. Belov
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Alexander R. Ivanov
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Barry L. Karger
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
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125
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Sun L, Zhu G, Yan X, Zhang Z, Wojcik R, Champion MM, Dovichi NJ. Capillary zone electrophoresis for bottom-up analysis of complex proteomes. Proteomics 2015; 16:188-96. [PMID: 26508368 DOI: 10.1002/pmic.201500339] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/30/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Capillary zone electrophoresis (CZE) is emerging as a useful tool in proteomic analysis. Interest arises from dramatic improvements in performance that result from improvements in the background electrolyte used for the separation, the incorporation of advanced sample injection methods, the development of robust and sensitive electrospray interfaces, and the coupling with Orbitrap mass spectrometers with high resolution and sensitivity. The combination of these technologies produces performance that is rapidly approaching the performance of UPLC-based methods for microgram samples and exceeds the performance of UPLC-based methods for mid- to low nanogram samples. These systems now produce over 10 000 peptide IDs in a single 100-min analysis of the HeLa proteome.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Roza Wojcik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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126
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Zhang Z, Sun L, Zhu G, Cox OF, Huber PW, Dovichi NJ. Nearly 1000 Protein Identifications from 50 ng of Xenopus laevis Zygote Homogenate Using Online Sample Preparation on a Strong Cation Exchange Monolith Based Microreactor Coupled with Capillary Zone Electrophoresis. Anal Chem 2015; 88:877-82. [PMID: 26670623 DOI: 10.1021/acs.analchem.5b03496] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A sulfonate-silica hybrid strong cation exchange monolith microreactor was synthesized and coupled to a linear polyacrylamide coated capillary for online sample preparation and capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) bottom-up proteomic analysis. The protein sample was loaded onto the microreactor in an acidic buffer. After online reduction, alkylation, and digestion with trypsin, the digests were eluted with 200 mM ammonium bicarbonate at pH 8.2 for CZE-MS/MS analysis using 1 M acetic acid as the background electrolyte. This combination of basic elution and acidic background electrolytes results in both sample stacking and formation of a dynamic pH junction. 369 protein groups and 1274 peptides were identified from 50 ng of Xenopus laevis zygote homogenate, which is comparable with an offline sample preparation method, but the time required for sample preparation was decreased from over 24 h to less than 40 min. Dramatically improved performance was produced by coupling the reactor to a longer separation capillary (∼100 cm) and a Q Exactive HF mass spectrometer. 975 protein groups and 3749 peptides were identified from 50 ng of Xenopus protein using the online sample preparation method.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Olivia F Cox
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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127
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2013-middle 2015). Electrophoresis 2015; 37:162-88. [DOI: 10.1002/elps.201500329] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, v.v.i; The Czech Academy of Sciences; Prague Czech Republic
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128
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129
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Ludwig KR, Sun L, Zhu G, Dovichi NJ, Hummon AB. Over 2300 phosphorylated peptide identifications with single-shot capillary zone electrophoresis-tandem mass spectrometry in a 100 min separation. Anal Chem 2015; 87:9532-7. [PMID: 26399161 PMCID: PMC4605816 DOI: 10.1021/acs.analchem.5b02457] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ultraperformance liquid chromatography (UPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) is typically employed for phosphoproteome analysis. Alternatively, capillary zone electrophoresis (CZE)-ESI-MS/MS has great potential for phosphoproteome analysis due to the significantly different migration times of phosphorylated and unphosphorylated forms of peptides. In this work, we systematically compared UPLC-MS/MS and CZE-MS/MS for phosphorylated peptide identifications (IDs) using an enriched phosphoproteome from the MCF-10A cell line. When the sample loading amount of UPLC was 10 times higher than that of CZE (2 μg vs 200 ng), UPLC generated more phosphorylated peptide IDs than CZE (3313 vs 1783). However, when the same sample loading amounts were used for CZE and UPLC (2-200 ng), CZE-MS/MS consistently and significantly outperformed UPLC-MS/MS in terms of phosphorylated peptide and total peptide IDs. This superior performance is most likely due to the higher peptide intensity generated by CZE-MS/MS. More importantly, compared with UPLC data from a 2 μg sample, CZE-MS/MS can identify over 500 unique phosphorylated peptides from a 200 ng sample, suggesting that CZE and UPLC are complementary for phosphorylated peptide IDs. With further improved loading capacity via a dynamic pH junction method, 2313 phosphorylated peptides were identified with single-shot CZE-MS/MS in a 100 min analysis. This number of phosphorylated peptide IDs is over 1 order of magnitude higher than the number of phosphorylated peptide IDs previously reported by single-shot CZE-MS/MS.
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Affiliation(s)
- Katelyn R. Ludwig
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
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130
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Jarvas G, Guttman A, Foret F. Numerical modeling of capillary electrophoresis - electrospray mass spectrometry interface design. MASS SPECTROMETRY REVIEWS 2015; 34:558-569. [PMID: 24676884 DOI: 10.1002/mas.21423] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 06/03/2023]
Abstract
Capillary electrophoresis hyphenated with electrospray mass spectrometry (CE-ESI-MS) has emerged in the past decade as one of the most powerful bioanalytical techniques. As the sensitivity and efficiency of new CE-ESI-MS interface designs are continuously improving, numerical modeling can play important role during their development. In this review, different aspects of computer modeling and simulation of CE-ESI-MS interfaces are comprehensively discussed. Relevant essentials of hydrodynamics as well as state-of-the-art modeling techniques are critically evaluated. Sheath liquid-, sheathless-, and liquid-junction interfaces are reviewed from the viewpoint of multidisciplinary numerical modeling along with details of single and multiphase models together with electric field mediated flows, electrohydrodynamics, and free fluid-surface methods. Practical examples are given to help non-specialists to understand the basic principles and applications. Finally, alternative approaches like air amplifiers are also included. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 558-569, 2015.
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Affiliation(s)
- Gabor Jarvas
- CEITEC-Central European Institute of Technology, Brno, Czech Republic
- MTA-PE Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprem, Hungary
| | - Andras Guttman
- MTA-PE Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprem, Hungary
| | - Frantisek Foret
- CEITEC-Central European Institute of Technology, Brno, Czech Republic
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic, Brno, Czech Republic
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131
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Wenz C, Barbas C, López-Gonzálvez Á, Garcia A, Benavente F, Sanz-Nebot V, Blanc T, Freckleton G, Britz-McKibbin P, Shanmuganathan M, de l'Escaille F, Far J, Haselberg R, Huang S, Huhn C, Pattky M, Michels D, Mou S, Yang F, Neusuess C, Tromsdorf N, Baidoo EE, Keasling JD, Park SS. Interlaboratory study to evaluate the robustness of capillary electrophoresis-mass spectrometry for peptide mapping. J Sep Sci 2015; 38:3262-3270. [DOI: 10.1002/jssc.201500551] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/19/2015] [Accepted: 06/21/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Christian Wenz
- Agilent Technologies R&D and Marketing GmbH & Co. KG; Waldbronn Germany
| | | | | | | | | | | | - Tim Blanc
- Eli Lilly and Company; Bioanalytical Science; Branchburg NJ USA
| | | | | | | | | | - Johann Far
- University of Liege, Department of Chemistry; Mass Spectrometry Laboratory; Liege Belgium
| | - Rob Haselberg
- VU University Amsterdam; Division of BioAnalytical Chemistry; Amsterdam the Netherlands
- University of Tasmania; School of Chemistry; Hobart Australia
| | | | - Carolin Huhn
- University of Tuebingen; Institute for Physical and Theoretical Chemistry; Tuebingen Germany
| | - Martin Pattky
- University of Tuebingen; Institute for Physical and Theoretical Chemistry; Tuebingen Germany
| | - David Michels
- Genentech, Inc; Protein Analytical Chemistry Department; San Francisco CA USA
| | - Si Mou
- Genentech, Inc; Protein Analytical Chemistry Department; San Francisco CA USA
| | - Feng Yang
- Genentech, Inc; Protein Analytical Chemistry Department; San Francisco CA USA
| | | | | | - Edward E.K. Baidoo
- Joint BioEnergy Institute; Lawrence Berkeley National Laboratory; Emeryville CA USA
| | - Jay D. Keasling
- Joint BioEnergy Institute; Lawrence Berkeley National Laboratory; Emeryville CA USA
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132
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Zhang Z, Sun L, Zhu G, Yan X, Dovichi NJ. Integrated strong cation-exchange hybrid monolith coupled with capillary zone electrophoresis and simultaneous dynamic pH junction for large-volume proteomic analysis by mass spectrometry. Talanta 2015; 138:117-122. [PMID: 25863379 PMCID: PMC4394190 DOI: 10.1016/j.talanta.2015.01.040] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 10/24/2022]
Abstract
A sulfonate-silica hybrid strong cation-exchange (SCX) monolith was synthesized at the proximal end of a capillary zone electrophoresis column and used for on-line solid-phase extraction (SPE) sample preconcentration. Sample was prepared in an acidic buffer and deposited onto the SCX-SPE monolith and eluted using a basic buffer. Electrophoresis was performed in an acidic buffer. This combination of buffers results in formation of a dynamic pH junction, which allows use of relatively large elution buffer volume while maintaining peak efficiency and resolution. All experiments were performed with a 50 µm ID capillary, a 1cm long SCX-SPE monolith, a 60cm long separation capillary, and a electrokinetically pumped nanospray interface. The volume of the capillary is 1.1 µL. By loading 21 µL of a 1×10(-7) M angiotensin II solution, an enrichment factor of 3000 compared to standard electrokinetic injection was achieved on this platform while retaining efficient electrophoretic performance (N=44,000 plates). The loading capacity of the sulfonate SCX hybrid monolith was determined to be ~15 pmol by frontal analysis with 10(-5) M angiotensin II. The system was also applied to the analysis of a 10(-4) mg/mL bovine serum albumin tryptic digest; the protein coverage was 12% and 11 peptides were identified. Finally, by loading 5.5 µL of a 10(-3) mg/mL E. coli digest, 109 proteins and 271 peptides were identified in a 20 min separation; the median separation efficiency generated by these peptides was 25,000 theoretical plates.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA.
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133
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Zhao Y, Riley NM, Sun L, Hebert AS, Yan X, Westphall MS, Rush MJP, Zhu G, Champion MM, Medie FM, DiGiuseppe Champion PA, Coon JJ, Dovichi NJ. Coupling capillary zone electrophoresis with electron transfer dissociation and activated ion electron transfer dissociation for top-down proteomics. Anal Chem 2015; 87:5422-9. [PMID: 25893372 PMCID: PMC4439324 DOI: 10.1021/acs.analchem.5b00883] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Top-down proteomics offers the potential for full protein characterization, but many challenges remain for this approach, including efficient protein separations and effective fragmentation of intact proteins. Capillary zone electrophoresis (CZE) has shown great potential for separation of intact proteins, especially for differentially modified proteoforms of the same gene product. To date, however, CZE has been used only with collision-based fragmentation methods. Here we report the first implementation of electron transfer dissociation (ETD) with online CZE separations for top-down proteomics, analyzing a mixture of four standard proteins and a complex protein mixture from the Mycobacterium marinum bacterial secretome. Using a multipurpose dissociation cell on an Orbitrap Elite system, we demonstrate that CZE is fully compatible with ETD as well as higher energy collisional dissociation (HCD), and that the two complementary fragmentation methods can be used in tandem on the electrophoretic time scale for improved protein characterization. Furthermore, we show that activated ion electron transfer dissociation (AI-ETD), a recently introduced method for enhanced ETD fragmentation, provides useful performance with CZE separations to greatly increase protein characterization. When combined with HCD, AI-ETD improved the protein sequence coverage by more than 200% for proteins from both standard and complex mixtures, highlighting the benefits electron-driven dissociation methods can add to CZE separations.
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Affiliation(s)
- Yimeng Zhao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Nicholas M. Riley
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Alexander S. Hebert
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael S. Westphall
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Matthew J. P. Rush
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Felix Mba Medie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Joshua J. Coon
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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134
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Faserl K, Kremser L, Müller M, Teis D, Lindner HH. Quantitative proteomics using ultralow flow capillary electrophoresis-mass spectrometry. Anal Chem 2015; 87:4633-40. [PMID: 25839223 PMCID: PMC4423236 DOI: 10.1021/acs.analchem.5b00312] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
In this work, we evaluate the incorporation
of an ultralow flow
interface for coupling capillary electrophoresis (CE) and mass spectrometry
(MS), in combination with reversed-phase high-pressure liquid chromatography
(HPLC) fractionation as an alternate workflow for quantitative proteomics.
Proteins, extracted from a SILAC (stable isotope labeling by amino
acids in cell culture) labeled and an unlabeled yeast strain were
mixed and digested enzymatically in solution. The resulting peptides
were fractionated using RP-HPLC and analyzed by CE–MS yielding
a total of 28 538 quantified peptides that correspond to 3 272
quantified proteins. CE–MS analysis was performed using a neutral
capillary coating, providing the highest separation efficiency at
ultralow flow conditions (<10 nL/min). Moreover, we were able to
demonstrate that CE–MS is a powerful method for the identification
of low-abundance modified peptides within the same sample. Without
any further enrichment strategies, we succeeded in quantifying 1 371
phosphopeptides present in the CE–MS data set and found 49
phosphopeptides to be differentially regulated in the two yeast strains.
Including acetylation, phosphorylation, deamidation, and oxidized
forms, a total of 8 106 modified peptides could be identified
in addition to 33 854 unique peptide sequences found. The work
presented here shows the first quantitative proteomics approach that
combines SILAC labeling with CE–MS analysis.
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Affiliation(s)
- Klaus Faserl
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Leopold Kremser
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Martin Müller
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - David Teis
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Herbert H Lindner
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
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135
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Zhang Z, Yan X, Sun L, Zhu G, Dovichi NJ. Detachable strong cation exchange monolith, integrated with capillary zone electrophoresis and coupled with pH gradient elution, produces improved sensitivity and numbers of peptide identifications during bottom-up analysis of complex proteomes. Anal Chem 2015; 87:4572-7. [PMID: 25822566 DOI: 10.1021/acs.analchem.5b00789] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A detachable sulfonate-silica hybrid strong cation-exchange monolith was synthesized in a fused silica capillary, and used for solid phase extraction with online pH gradient elution during capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) proteomic analysis. Tryptic digests were prepared in 50 mM formic acid and loaded onto the strong cation-exchange monolith. Fractions were eluted using a series of buffers with lower concentration but higher pH values than the 50 mM formic acid background electrolyte. This combination of elution and background electrolytes results in both sample stacking and formation of a dynamic pH junction and allows use of relatively large elution buffer volumes while maintaining reasonable peak efficiency and resolution. A series of five pH bumps were applied to elute E. coli tryptic peptides from the monolith, followed by analysis using CZE coupled to an LTQ-Orbitrap Velos mass spectrometer; 799 protein groups and 3381 peptides were identified from 50 ng of the digest in a 2.5 h analysis, which approaches the identification rate for this organism that was obtained with an Orbitrap Fusion. We attribute the improved numbers of peptide and protein identifications to the efficient fractionation by the online pH gradient elution, which decreased the complexity of the sample in each elution step and improved the signal intensity of low abundance peptides. We also performed a comparative analysis using a nanoACQUITY UltraPerformance LCH system. Similar numbers of protein and peptide identifications were produced by the two methods. Protein identifications showed significant overlap between the two methods, whereas peptide identifications were complementary.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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136
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Schiavone NM, Sarver SA, Sun L, Wojcik R, Dovichi NJ. High speed capillary zone electrophoresis-mass spectrometry via an electrokinetically pumped sheath flow interface for rapid analysis of amino acids and a protein digest. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 991:53-8. [PMID: 25913424 DOI: 10.1016/j.jchromb.2015.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 12/22/2022]
Abstract
While capillary zone electrophoresis (CZE) has been used to produce very rapid and efficient separations, coupling these high-speed separations with mass spectrometry (MS) has been challenging. Now, with much faster and sensitive mass spectrometers, it is possible to take full advantage of the CZE speed and reconstruct the fast migrating peaks. Here are three high-speed CZE-MS analyses via an electrokinetically pumped sheath-flow interface. The first separation demonstrates CZE-ESI-MS of an amino acid mixture with a 2-min separation, >50,000 theoretical plates, low micromolar concentration detection limits, and subfemtomole mass detection limits (LTQ XL mass spectrometer). The second separation with our recently improved third-generation CE-MS interface illustrates a 20 amino acid separation in ∼7min with an average over 200,000 plate counts, and results in almost-baseline resolution of structural isomers, leucine and isoleucine. The third separation is of a BSA digest with a reproducible CZE separation and mass spectrometry detection in 2min. CZE-MS/MS analysis of the BSA digest identified 31 peptides, produced 52% sequence coverage, and generated a peak capacity of ∼40 across the 1-min separation window (Q-Exactive mass spectrometer).
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Affiliation(s)
- Nicole M Schiavone
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Scott A Sarver
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Roza Wojcik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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137
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Sun L, Zhu G, Zhang Z, Mou S, Dovichi NJ. Third-generation electrokinetically pumped sheath-flow nanospray interface with improved stability and sensitivity for automated capillary zone electrophoresis-mass spectrometry analysis of complex proteome digests. J Proteome Res 2015; 14:2312-21. [PMID: 25786131 DOI: 10.1021/acs.jproteome.5b00100] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have reported a set of electrokinetically pumped sheath flow nanoelectrospray interfaces to couple capillary zone electrophoresis with mass spectrometry. A separation capillary is threaded through a cross into a glass emitter. A side arm provides fluidic contact with a sheath buffer reservoir that is connected to a power supply. The potential applied to the sheath buffer drives electro-osmosis in the emitter to pump the sheath fluid at nanoliter per minute rates. Our first-generation interface placed a flat-tipped capillary in the emitter. Sensitivity was inversely related to orifice size and to the distance from the capillary tip to the emitter orifice. A second-generation interface used a capillary with an etched tip that allowed the capillary exit to approach within a few hundred micrometers of the emitter orifice, resulting in a significant increase in sensitivity. In both the first- and second-generation interfaces, the emitter diameter was typically 8 μm; these narrow orifices were susceptible to plugging and tended to have limited lifetime. We now report a third-generation interface that employs a larger diameter emitter orifice with very short distance between the capillary tip and the emitter orifice. This modified interface is much more robust and produces much longer lifetime than our previous designs with no loss in sensitivity. We evaluated the third-generation interface for a 5000 min (127 runs, 3.5 days) repetitive analysis of bovine serum albumin digest using an uncoated capillary. We observed a 10% relative standard deviation in peak area, an average of 160,000 theoretical plates, and very low carry-over (much less than 1%). We employed a linear-polyacrylamide (LPA)-coated capillary for single-shot, bottom-up proteomic analysis of 300 ng of Xenopus laevis fertilized egg proteome digest and identified 1249 protein groups and 4038 peptides in a 110 min separation using an LTQ-Orbitrap Velos mass spectrometer; peak capacity was ∼330. The proteome data set using this third-generation interface-based CZE-MS/MS is similar in size to that generated using a commercial ultraperformance liquid chromatographic analysis of the same sample with the same mass spectrometer and similar analysis time.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Si Mou
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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138
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Skinner OS, Do Vale LHF, Catherman AD, Havugimana PC, de Sousa MV, Compton PD, Kelleher NL. Native GELFrEE: a new separation technique for biomolecular assemblies. Anal Chem 2015; 87:3032-8. [PMID: 25664979 DOI: 10.1021/ac504678d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The cadre of protein complexes in cells performs an array of functions necessary for life. Their varied structures are foundational to their ability to perform biological functions, lending great import to the elucidation of complex composition and dynamics. Native separation techniques that are operative on low sample amounts and provide high resolution are necessary to gain valuable data on endogenous complexes. Here, we detail and optimize the use of tube gel separations to produce samples proven compatible with native, multistage mass spectrometry (nMS/MS). We find that a continuous system (i.e., no stacking gel) with a gradient in its extent of cross-linking and use of the clear native buffer system performs well for both fractionation and native mass spectrometry of heart extracts and a fungal secretome. This integrated advance in separations and nMS/MS offers the prospect of untargeted proteomics at the next hierarchical level of protein organization in biology.
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Affiliation(s)
- Owen S Skinner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University , Evanston, Illinois 60208, United States
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139
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He M, Xue Z, Zhang Y, Huang Z, Fang X, Qu F, Ouyang Z, Xu W. Development and Characterizations of a Miniature Capillary Electrophoresis Mass Spectrometry System. Anal Chem 2015; 87:2236-41. [PMID: 25597704 DOI: 10.1021/ac504868w] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Muyi He
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zhenhua Xue
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yinna Zhang
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zejian Huang
- National Institute of Metrology, Beijing 100013, China
| | - Xiang Fang
- National Institute of Metrology, Beijing 100013, China
| | - Feng Qu
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zheng Ouyang
- Biomedical
Engineering Department, Purdue University, West Lafayette, Indiana 47907, United States
| | - Wei Xu
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
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140
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Han X, Wang Y, Aslanian A, Fonslow B, Graczyk B, Davis TN, Yates JR. In-line separation by capillary electrophoresis prior to analysis by top-down mass spectrometry enables sensitive characterization of protein complexes. J Proteome Res 2014; 13:6078-86. [PMID: 25382489 PMCID: PMC4262260 DOI: 10.1021/pr500971h] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Intact
protein analysis via top-down mass spectrometry (MS) provides
a bird’s eye view over the protein complexes and complex protein
mixtures with the unique capability of characterizing protein variants,
splice isoforms, and combinatorial post-translational modifications
(PTMs). Here we applied capillary electrophoresis (CE) through a sheathless
CE–electrospray ionization interface coupled to an LTQ Velos
Orbitrap Elite mass spectrometer to analyze the Dam1 complex from Saccharomyces cerevisiae. We achieved a 100-fold
increase in sensitivity compared to a reversed-phase liquid chromatography
coupled MS analysis of recombinant Dam1 complex with a total loading
of 2.5 ng (12 amol). N-terminal processing forms of individual subunits
of the Dam1 complex were observed as well as their phosphorylation
stoichiometry upon Mps1p kinase treatment.
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Affiliation(s)
- Xuemei Han
- Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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141
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Ramautar R, Somsen GW, de Jong GJ. CE-MS for metabolomics: Developments and applications in the period 2012-2014. Electrophoresis 2014; 36:212-24. [DOI: 10.1002/elps.201400388] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Rawi Ramautar
- Division of Analytical Biosciences; LACDR; Leiden University; Leiden The Netherlands
| | - Govert W. Somsen
- AIMMS research group BioMolecular Analysis; Division of BioAnalytical Chemistry; VU University Amsterdam; Amsterdam The Netherlands
| | - Gerhardus J. de Jong
- Biomolecular Analysis; Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht The Netherlands
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142
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Lindenburg PW, Haselberg R, Rozing G, Ramautar R. Developments in Interfacing Designs for CE–MS: Towards Enabling Tools for Proteomics and Metabolomics. Chromatographia 2014. [DOI: 10.1007/s10337-014-2795-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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143
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Han X, Wang Y, Aslanian A, Bern M, Lavallée-Adam M, Yates JR. Sheathless capillary electrophoresis-tandem mass spectrometry for top-down characterization of Pyrococcus furiosus proteins on a proteome scale. Anal Chem 2014; 86:11006-12. [PMID: 25346219 PMCID: PMC4238646 DOI: 10.1021/ac503439n] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
Intact protein analysis via top-down
mass spectrometry (MS) provides
the unique capability of fully characterizing protein isoforms and
combinatorial post-translational modifications (PTMs) compared to
the bottom-up MS approach. Front-end protein separation poses a challenge
for analyzing complex mixtures of intact proteins on a proteomic scale.
Here we applied capillary electrophoresis (CE) through a sheathless
capillary electrophoresis-electrospray ionization (CESI) interface
coupled to an Orbitrap Elite mass spectrometer to profile the proteome
from Pyrococcus furiosus. CESI-top-down MS analysis
of Pyrococcus furiosus cell lysate identified 134
proteins and 291 proteoforms with a total sample consumption of 270
ng in 120 min of total analysis time. Truncations and various PTMs
were detected, including acetylation, disulfide bonds, oxidation,
glycosylation, and hypusine. This is the largest scale analysis of
intact proteins by CE-top-down MS to date.
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Affiliation(s)
- Xuemei Han
- Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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144
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Sun L, Hebert AS, Yan X, Zhao Y, Westphall MS, Rush MJP, Zhu G, Champion MM, Coon JJ, Dovichi NJ. Over 10,000 peptide identifications from the HeLa proteome by using single-shot capillary zone electrophoresis combined with tandem mass spectrometry. Angew Chem Int Ed Engl 2014; 53:13931-3. [PMID: 25346227 DOI: 10.1002/anie.201409075] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 09/26/2014] [Indexed: 01/14/2023]
Abstract
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has recently attracted attention as a tool for shotgun proteomics. However, its performance for this analysis has so far fallen far below that of reversed-phase liquid chromatography (RPLC)-MS/MS. The use of a CZE method with a wide separation window (up to 90 min) and high peak capacity (ca. 300) is reported. This method was coupled to an Orbitrap Fusion mass spectrometer through an electrokinetically pumped sheath-flow interface for the analysis of complex proteome digests. Single-shot CZE-MS/MS lead to the identification of over 10 000 peptides and 2100 proteins from a HeLa cell proteome digest in approximately 100 min. This performance is nearly an order of magnitude better than earlier CZE studies and is within a factor of two to four of the state-of-the-art nano ultrahigh-pressure LC system.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 (USA)
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145
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Sun L, Hebert AS, Yan X, Zhao Y, Westphall MS, Rush MJP, Zhu G, Champion MM, Coon JJ, Dovichi NJ. Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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146
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Fleurbaaij F, Heemskerk AAM, Russcher A, Klychnikov OI, Deelder AM, Mayboroda OA, Kuijper EJ, van Leeuwen HC, Hensbergen PJ. Capillary-electrophoresis mass spectrometry for the detection of carbapenemases in (multi-)drug-resistant Gram-negative bacteria. Anal Chem 2014; 86:9154-61. [PMID: 25155175 DOI: 10.1021/ac502049p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In a time in which the spread of multidrug resistant microorganisms is ever increasing, there is a need for fast and unequivocal identification of suspect organisms to supplement existing techniques in the clinical laboratory, especially in single bacterial colonies. Mass-spectrometry coupled with efficient peptide separation techniques offer great potential for identification of resistant-related proteins in complex microbiological samples in an unbiased manner. Here, we developed a capillary electrophoresis-electrospray ionization-tandem mass spectrometry CE-ESI-MS/MS bottom-up proteomics workflow for sensitive and specific peptide analysis with the emphasis on the identification of β-lactamases (carbapenemases OXA-48 and KPC in particular) in bacterial species. For this purpose, tryptic peptides from whole cell lysates were analyzed by sheathless CE-ESI-MS/MS and proteins were identified after searching of the spectral data against bacterial protein databases. The CE-ESI-MS/MS workflow was first evaluated using a recombinant TEM-1 β-lactamase, resulting in 68% of the amino acid sequence being covered by 20 different unique peptides. Subsequently, a resistant and susceptible Escherichia coli lab strain were analyzed and based on the observed β-lactamase peptides, the two strains could easily be discriminated. Finally, the method was tested in an unbiased setup using a collection of in-house characterized OXA-48 (n = 17) and KPC (n = 10) clinical isolates. The developed CE-ESI-MS/MS method was able to identify the presence of OXA-48 and KPC in all of the carbapenemase positive samples, independent of species and degree of susceptibility. Four negative controls were tested and classified as negative by this method. Furthermore, a number of extended-spectrum beta-lactamases (ESBL) were identified in the same analyses, confirming the multiresistant character in 19 out of 27 clinical isolates. Importantly, the method performed equally well on protein lysates from single colonies. As such, it demonstrates CE-ESI-MS/MS as a potential next generation mass spectrometry platform within the clinical microbiology laboratory.
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Affiliation(s)
- Frank Fleurbaaij
- Department of Medical Microbiology, Section Experimental Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
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147
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Sun L, Zhu G, Mou S, Zhao Y, Champion MM, Dovichi NJ. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for quantitative parallel reaction monitoring of peptide abundance and single-shot proteomic analysis of a human cell line. J Chromatogr A 2014; 1359:303-8. [PMID: 25082526 DOI: 10.1016/j.chroma.2014.07.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/25/2014] [Accepted: 07/10/2014] [Indexed: 12/14/2022]
Abstract
We coupled capillary zone electrophoresis (CZE) with an ultrasensitive electrokinetically pumped nanospray ionization source for tandem mass spectrometry (MS/MS) analysis of complex proteomes. We first used the system for the parallel reaction monitoring (PRM) analysis of angiotensin II spiked in 0.45mg/mL of bovine serum albumin (BSA) digest. A calibration curve was generated between the loading amount of angiotensin II and intensity of angiotensin II fragment ions. CZE-PRM generated a linear calibration curve across over 4.5 orders of magnitude dynamic range corresponding to angiotensin II loading amount from 2amole to 150fmole. The relative standard deviations (RSDs) of migration time were <4% and the RSDs of fragment ion intensity were ∼20% or less except 150fmole angiotensin II loading amount data (∼36% RSD). We further applied the system for the first bottom up proteomic analysis of a human cell line using CZE-MS/MS. We generated 283 protein identifications from a 1h long, single-shot CZE MS/MS analysis of the MCF7 breast cancer cell line digest, corresponding to ∼80ng loading amount. The MCF7 digest was fractionated using a C18 solid phase extraction column; single-shot analysis of a single fraction resulted in 468 protein identifications, which is by far the largest number of protein identifications reported for a mammalian proteomic sample using CZE.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Si Mou
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yimeng Zhao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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148
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Kelly RT, Wang C, Rausch SJ, Lee CS, Tang K. Pneumatic microvalve-based hydrodynamic sample injection for high-throughput, quantitative zone electrophoresis in capillaries. Anal Chem 2014; 86:6723-9. [PMID: 24865952 PMCID: PMC4082392 DOI: 10.1021/ac501910p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A hybrid microchip/capillary electrophoresis (CE) system was developed to allow unbiased and lossless sample loading and high-throughput repeated injections. This new hybrid CE system consists of a poly(dimethylsiloxane) (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel, and a fused-silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channel and the fused-silica capillary separation column. Analytes are rapidly separated in the fused-silica capillary, and following separation, high-sensitivity MS detection is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high-throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates, and CE separation voltages.
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Affiliation(s)
- Ryan T Kelly
- Environmental Molecular Sciences Laboratory and §Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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149
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Zhu G, Sun L, Yan X, Dovichi NJ. Bottom-up proteomics of Escherichia coli using dynamic pH junction preconcentration and capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry. Anal Chem 2014; 86:6331-6. [PMID: 24852005 PMCID: PMC4082393 DOI: 10.1021/ac5004486] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We report the use of the dynamic
pH junction based capillary zone
electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS)
for bottom-up proteomics with an electrokinetically pumped sheath-flow
nanospray capillary electrophoresis-mass spectrometry (CE-MS) interface
and both LTQ-XL and LTQ-Orbitrap-Velos mass spectrometers. Conventional
injection of 20 nL of a 1 mg/mL BSA digest identified 37 peptides
and produced 66% sequence coverage. In contrast, pH junction injection
of 130 nL (or larger) of a 0.05 mg/mL BSA digest identified 40 peptides
and produced 70% coverage using a pH 6.5 sample buffer and the LTQ.
A 20 nL conventional injection of a 1 mg/mL Escherichia coli digest identified 508 peptides and 199 proteins with the LTQ. A
400 nL pH junction injection of a 0.1 mg/mL E. coli digest identified 527 peptides and 179 proteins with the LTQ. Triplicate
technical replicates of a 0.01 mg/mL sample with 400-nL injection
volume using a pH junction identified 288 ± 9 peptides and 121
± 5 proteins with the LTQ. There was outstanding concordance
in migration time between the pH junction and normal injection. The
pH junction produced narrower peaks and significant concentration
for all but the most acidic components in the sample. Compared with
the conventional stacking method, the pH junction method can generate
comparable performance for small injection volume (20 nL) and significantly
better concentration performance for a large injection volume (200
nL). We also applied the pH junction to three intact standard proteins
and observed a >10× increase in peak intensity compared to
conventional
injection.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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150
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Zhao Y, Sun L, Champion MM, Knierman MD, Dovichi NJ. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for top-down characterization of the Mycobacterium marinum secretome. Anal Chem 2014; 86:4873-8. [PMID: 24725189 PMCID: PMC4033641 DOI: 10.1021/ac500092q] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Capillary zone electrophoresis (CZE) with an electrokinetically pumped sheath-flow nanospray interface was coupled with a high-resolution Q-Exactive mass spectrometer for the analysis of culture filtrates from Mycobacterium marinum. We confidently identified 22 gene products from the wildtype M. marinum secretome in a single CZE-tandem mass spectrometry (MS/MS) run. A total of 58 proteoforms were observed with post-translational modifications including signal peptide removal, N-terminal methionine excision, and acetylation. The conductivities of aqueous acetic acid and formic acid solutions were measured from 0.1% to 100% concentration (v/v). Acetic acid (70%) provided lower conductivity than 0.25% formic acid and was evaluated as low ionic-strength and a CZE-MS compatible sample buffer with good protein solubility.
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Affiliation(s)
- Yimeng Zhao
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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