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Application of CE-MS for the analysis of histones and histone modifications. Methods 2020; 184:125-134. [PMID: 32014606 DOI: 10.1016/j.ymeth.2020.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/02/2019] [Accepted: 01/26/2020] [Indexed: 02/02/2023] Open
Abstract
The analysis, identification and quantification of histones and their post-translational modifications plays a central role in chromatin research and in studying epigenetic regulations during physiological processes. In the last decade analytical strategies based on mass spectrometry have been greatly improved for providing a global view of single modification abundances or to determine combinatorial patterns of modifications. Presented here is a newly developed strategy for histone protein analysis and a number of applications are illustrated with an emphasis on PTM characterization. Capillary electrophoresis is coupled to mass spectrometry (CE-MS) and has proven to be a very promising concept as it enables to study intact histones (top-down proteomics) as well as the analysis of enzymatically digested proteins (bottom-up proteomics). This technology combines highly efficient low-flow CE separations with ionization in a single device and offers an orthogonal separation principle to conventional LC-MS analysis, thus expanding the existing analytical repertoire in a perfect manner.
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52
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Zhang W, Guled F, Hankemeier T, Ramautar R. Profiling nucleotides in low numbers of mammalian cells by sheathless CE-MS in positive ion mode: Circumventing corona discharge. Electrophoresis 2020; 41:360-369. [PMID: 31907937 DOI: 10.1002/elps.201900417] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022]
Abstract
Negative ion mode nano-ESI-MS is often considered for the analysis of acidic compounds, including nucleotides. However, under high aqueous separation conditions, corona discharge is frequently observed at emitter tips, which may result in low ion abundances and reduced nano-ESI needle emitter lifetimes. In this work, we introduce a sheathless CE-MS method for the highly efficient and sensitive analysis of nucleotides employing ESI in positive ion mode, thereby fully circumventing corona discharge. By using a background electrolyte of 16 mM ammonium acetate (pH 9.7) a mixture of 12 nucleotides, composed of mono-, di-, and tri-phosphates, could be efficiently analyzed with plate numbers per meter above 220 000 and with LODs in the range from 0.06 to 1.3 nM, corresponding to 0.4 to 8.6 attomole, when using an injection volume of about 6.5 nL only. The utility of the method was demonstrated for the profiling of nucleotides in low numbers of mammalian cells using HepG2 cells as a model system. Endogenous nucleotides could be efficiently analyzed in extracts from 50 000 down to 500 HepG2 cells only. Moreover, apart from nucleotides, also some nicotinamide-adenine dinucleotides and amino acids could be analyzed under these conditions, thereby clearly illustrating the utility of this approach for metabolic profiling of low amounts of biological material.
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Affiliation(s)
- Wei Zhang
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Faisa Guled
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.,Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
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53
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Huang L, Wang Z, Cupp-Sutton KA, Smith K, Wu S. Spray-Capillary: An Electrospray-Assisted Device for Quantitative Ultralow-Volume Sample Handling. Anal Chem 2020; 92:640-646. [PMID: 31793760 PMCID: PMC7558432 DOI: 10.1021/acs.analchem.9b04131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The analysis of low-volume samples provides valuable insight into complex biological systems. However, the proteomic and metabolomic analysis of low-volume samples remains challenging due to the lack of simple, efficient, and reproducible microsampling techniques. We have developed an electrospray-assisted device for quantitative low-volume sample extraction, referred to here as "Spray-Capillary". Stable electrospray was achieved through a chemically etched tip from a long (e.g., 50 cm) capillary with a conductive sheath flow. This electrospray provided the driving force to quantitatively draw low-volume samples into the capillary. We evaluated the precision and accuracy of sample injection volumes using our spray-capillary as the electrospray voltage, capillary ID, and column length were varied. Our results demonstrate that spray-capillary allows for reproducible and quantitative microsampling with low injection flow rates (as low as 15 pL/s). Furthermore, spray-capillary can be directly coupled with capillary zone electrophoresis (CZE) for separation. Overall, spray-capillary is a simple microsampling device that holds great potential for high-throughput quantitative omics analysis of ultralow-volume samples.
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Affiliation(s)
- Lushuang Huang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kellye A. Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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54
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McCool EN, Lodge JM, Basharat AR, Liu X, Coon JJ, Sun L. Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2470-2479. [PMID: 31073891 PMCID: PMC6527361 DOI: 10.1007/s13361-019-02206-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 05/21/2023]
Abstract
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as an efficient approach for top-down proteomics recently for its high-capacity separation and highly sensitive detection of proteoforms. However, the commonly used collision-based dissociation methods often cannot provide extensive fragmentation of proteoforms for thorough characterization. Activated ion electron transfer dissociation (AI-ETD), that combines infrared photoactivation concurrent with ETD, has shown better performance for proteoform fragmentation than higher energy-collisional dissociation (HCD) and standard ETD. Here, we present the first application of CZE-AI-ETD on an Orbitrap Fusion Lumos mass spectrometer for large-scale top-down proteomics of Escherichia coli (E. coli) cells. CZE-AI-ETD outperformed CZE-ETD regarding proteoform and protein identifications (IDs). CZE-AI-ETD reached comparable proteoform and protein IDs with CZE-HCD. CZE-AI-ETD tended to generate better expectation values (E values) of proteoforms than CZE-HCD and CZE-ETD, indicating a higher quality of MS/MS spectra from AI-ETD respecting the number of sequence-informative fragment ions generated. CZE-AI-ETD showed great reproducibility regarding the proteoform and protein IDs with relative standard deviations less than 4% and 2% (n = 3). Coupling size exclusion chromatography (SEC) to CZE-AI-ETD identified 3028 proteoforms and 387 proteins from E. coli cells with 1% spectrum level and 5% proteoform-level false discovery rates. The data represents the largest top-down proteomics dataset using the AI-ETD method so far. Single-shot CZE-AI-ETD of one SEC fraction identified 957 proteoforms and 253 proteins. N-terminal truncations, signal peptide cleavage, N-terminal methionine removal, and various post-translational modifications including protein N-terminal acetylation, methylation, S-thiolation, disulfide bonds, and lysine succinylation were detected.
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Affiliation(s)
- Elijah N McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Jean M Lodge
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Avenue, Indianapolis, IN, 46202, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Avenue, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN, 46202, USA
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA.
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55
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Abonamah JV, Eckenrode BA, Moini M. On-site detection of fentanyl and its derivatives by field portable nano-liquid chromatography-electron lonization-mass spectrometry (nLC-EI-MS). Forensic Chem 2019. [DOI: 10.1016/j.forc.2019.100180] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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56
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Balcells C, Foguet C, Tarragó-Celada J, de Atauri P, Marin S, Cascante M. Tracing metabolic fluxes using mass spectrometry: Stable isotope-resolved metabolomics in health and disease. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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57
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Shen X, Yang Z, McCool EN, Lubeckyj RA, Chen D, Sun L. Capillary zone electrophoresis-mass spectrometry for top-down proteomics. Trends Analyt Chem 2019; 120:115644. [PMID: 31537953 PMCID: PMC6752746 DOI: 10.1016/j.trac.2019.115644] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry (MS)-based top-down proteomics characterizes complex proteomes at the intact proteoform level and provides an accurate picture of protein isoforms and protein post-translational modifications in the cell. The progress of top-down proteomics requires novel analytical tools with high peak capacity for proteoform separation and high sensitivity for proteoform detection. The requirements have made capillary zone electrophoresis (CZE)-MS an attractive approach for advancing large-scale top-down proteomics. CZE has achieved a peak capacity of 300 for separation of complex proteoform mixtures. CZE-MS has shown drastically better sensitivity than commonly used reversed-phase liquid chromatography (RPLC)-MS for proteoform detection. The advanced CZE-MS identified 6,000 proteoforms of nearly 1,000 proteoform families from a complex proteome sample, which represents one of the largest top-down proteomic datasets so far. In this review, we focus on the recent progress in CZE-MS-based top-down proteomics and provide our perspectives about its future directions.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Elijah N. McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Rachele A. Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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58
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Ferré S, González-Ruiz V, Guillarme D, Rudaz S. Analytical strategies for the determination of amino acids: Past, present and future trends. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1132:121819. [PMID: 31704619 DOI: 10.1016/j.jchromb.2019.121819] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/27/2022]
Abstract
This review describes the analytical methods that have been developed over the years to tackle the high polarity and non-chromophoric nature of amino acids (AAs). First, the historical methods are briefly presented, with a strong focus on the use of derivatization reagents to make AAs detectable with spectroscopic techniques (ultraviolet and fluorescence) and/or sufficiently retained in reversed phase liquid chromatography. Then, an overview of the current analytical strategies for achiral separation of AAs is provided, in which mass spectrometry (MS) becomes the most widely used detection mode in combination with innovative liquid chromatography or capillary electrophoresis conditions to detect AAs at very low concentration in complex matrixes. Finally, some future trends of AA analysis are provided in the last section of the review, including the use of supercritical fluid chromatography (SFC), multidimensional liquid chromatography and electrophoretic separations, hyphenation of ion exchange chromatography to mass spectrometry, and use of ion mobility spectrometry mass spectrometry (IM-MS). Various application examples will also be presented throughout the review to highlight the benefits and limitations of these different analytical approaches for AAs determination.
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Affiliation(s)
- Sabrina Ferré
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland.
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
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59
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Zhang W, Segers K, Mangelings D, Van Eeckhaut A, Hankemeier T, Vander Heyden Y, Ramautar R. Assessing the suitability of capillary electrophoresis-mass spectrometry for biomarker discovery in plasma-based metabolomics. Electrophoresis 2019; 40:2309-2320. [PMID: 31025710 PMCID: PMC6767474 DOI: 10.1002/elps.201900126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 01/20/2023]
Abstract
The actual utility of capillary electrophoresis-mass spectrometry (CE-MS) for biomarker discovery using metabolomics still needs to be assessed. Therefore, a simulated comparative metabolic profiling study for biomarker discovery by CE-MS was performed, using pooled human plasma samples with spiked biomarkers. Two studies have been carried out in this work. Focus of study I was on comparing two sets of plasma samples, in which one set (class I) was spiked with five isotope-labeled compounds, whereas another set (class II) was spiked with six different isotope-labeled compounds. In study II, focus was also on comparing two sets of plasma samples, however, the isotope-labeled compounds were spiked to both class I and class II samples but with concentrations which differ by a factor two between both classes (with one compound absent in each class). The aim was to determine whether CEMS-based metabolomics could reveal the spiked biomarkers as the main classifiers, applying two different data analysis software tools (MetaboAnalyst and Matlab). Unsupervised analysis of the recorded metabolic profiles revealed a clear distinction between class I and class II plasma samples in both studies. This classification was mainly attributed to the spiked isotope-labeled compounds, thereby emphasizing the utility of CE-MS for biomarker discovery.
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Affiliation(s)
- Wei Zhang
- Biomedical Microscale AnalyticsDivision of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug ResearchLeiden UniversityThe Netherlands
| | - Karen Segers
- Biomedical Microscale AnalyticsDivision of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug ResearchLeiden UniversityThe Netherlands
- Department of Analytical ChemistryApplied Chemometrics and Molecular ModellingVrije Universiteit BrusselBrusselBelgium
- Department of Pharmaceutical ChemistryDrug Analysis and Drug InformationCenter for NeurosciencesVrije Universiteit BrusselBrusselBelgium
| | - Debby Mangelings
- Department of Analytical ChemistryApplied Chemometrics and Molecular ModellingVrije Universiteit BrusselBrusselBelgium
| | - Ann Van Eeckhaut
- Department of Pharmaceutical ChemistryDrug Analysis and Drug InformationCenter for NeurosciencesVrije Universiteit BrusselBrusselBelgium
| | - Thomas Hankemeier
- Biomedical Microscale AnalyticsDivision of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug ResearchLeiden UniversityThe Netherlands
| | - Yvan Vander Heyden
- Department of Analytical ChemistryApplied Chemometrics and Molecular ModellingVrije Universiteit BrusselBrusselBelgium
| | - Rawi Ramautar
- Biomedical Microscale AnalyticsDivision of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug ResearchLeiden UniversityThe Netherlands
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60
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van Mever M, Hankemeier T, Ramautar R. CE-MS for anionic metabolic profiling: An overview of methodological developments. Electrophoresis 2019; 40:2349-2359. [PMID: 31106868 PMCID: PMC6771621 DOI: 10.1002/elps.201900115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/24/2022]
Abstract
The efficient profiling of highly polar and charged metabolites in biological samples remains a huge analytical challenge in metabolomics. Over the last decade, new analytical techniques have been developed for the selective and sensitive analysis of polar ionogenic compounds in various matrices. Still, the analysis of such compounds, notably for acidic ionogenic metabolites, remains a challenging endeavor, even more when the available sample size becomes an issue for the total analytical workflow. In this paper, we give an overview of the possibilities of capillary electrophoresis-mass spectrometry (CE-MS) for anionic metabolic profiling by focusing on main methodological developments. Attention is paid to the development of improved separation conditions and new interfacing designs in CE-MS for anionic metabolic profiling. A complete overview of all CE-MS-based methods developed for this purpose is provided in table format (Table 1) which includes information on sample type, separation conditions, mass analyzer and limits of detection (LODs). Selected applications are discussed to show the utility of CE-MS for anionic metabolic profiling, especially for small-volume biological samples. On the basis of the examination of the reported literature in this specific field, we conclude that there is still room for the design of a highly sensitive and reliable CE-MS method for anionic metabolic profiling. A rigorous validation and the availability of standard operating procedures would be highly favorable in order to make CE-MS an alternative, viable analytical technique for metabolomics.
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Affiliation(s)
- Marlien van Mever
- Biomedical Microscale AnalyticsLeiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Thomas Hankemeier
- Analytical BioSciences & MetabolomicsLeiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Rawi Ramautar
- Biomedical Microscale AnalyticsLeiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
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61
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Lubeckyj RA, Basharat AR, Shen X, Liu X, Sun L. Large-Scale Qualitative and Quantitative Top-Down Proteomics Using Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry with Nanograms of Proteome Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1435-1445. [PMID: 30972727 PMCID: PMC6675661 DOI: 10.1007/s13361-019-02167-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has attracted attention recently for top-down proteomics because it can achieve highly efficient separation and very sensitive detection of proteins. However, separation window and sample loading volume of CZE need to be boosted for a better proteome coverage using CZE-MS/MS. Here, we present an improved CZE-MS/MS system that achieved a 180-min separation window and a 2-μL sample loading volume for top-down characterization of protein mixtures. The system obtained highly efficient separation of proteins with nearly one million theoretical plates for myoglobin and enabled baseline separation of three different proteoforms of myoglobin. The CZE-MS/MS system identified 797 ± 21 proteoforms and 258 ± 7 proteins (n = 2) from an Escherichia coli (E. coli) proteome sample in a single run with only 250 ng of proteins injected. The system still identified 449 ± 40 proteoforms and 173 ± 6 proteins (n = 2) from the E. coli sample when only 25 ng of proteins were injected per run. Single-shot CZE-MS/MS analyses of zebrafish brain cerebellum (Cb) and optic tectum (Teo) regions identified 1730 ± 196 proteoforms (n = 3) and 2024 ± 255 proteoforms (n = 3), respectively, with only 500-ng proteins loaded per run. Label-free quantitative top-down proteomics of zebrafish brain Cb and Teo regions revealed significant differences between Cb and Teo regarding the proteoform abundance. Over 700 proteoforms from 131 proteins had significantly higher abundance in Cb compared to Teo, and these proteins were highly enriched in several biological processes, including muscle contraction, glycolytic process, and mesenchyme migration. Graphical Abstract.
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Affiliation(s)
- Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA.
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62
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63
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Kawai T, Ota N, Okada K, Imasato A, Owa Y, Morita M, Tada M, Tanaka Y. Ultrasensitive Single Cell Metabolomics by Capillary Electrophoresis-Mass Spectrometry with a Thin-Walled Tapered Emitter and Large-Volume Dual Sample Preconcentration. Anal Chem 2019; 91:10564-10572. [PMID: 31357863 DOI: 10.1021/acs.analchem.9b01578] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Single cell metabolome analysis is essential for studying microscale life phenomena such as neuronal networks and tumor microenvironments. Capillary electrophoresis-mass spectrometry (CE-MS) is one of the most sensitive technologies; however, its sensitivity is still not enough for single cell analysis on general human cells such as HeLa. To address these issues, we first developed an efficient ionization emitter, named as a "nanoCESI" emitter, that had a thin-walled (∼10 μm) and tapered (5-10 μm) end. The thin conductive wall enabled sheathless ionization and minimized the flow rate of ionizing sample, and the tapered end efficiently ionized analytes via an electrospray ionization mechanism, providing up to 3.5-fold increase in sensitivity compared with a conventional sheathless emitter. Fifty repetitive analyses on 20 amino acids were successfully achieved with a nanoCESI emitter. Relative standard deviations of 50 analyses were 1.5%, 4.4%, and 6.8% for migration time, peak height, and peak area, respectively, where a limit of detection (LOD) of 170 pM (850 zmol) was achieved. Second, a sample enrichment method, large-volume dual preconcentration by isotachophoresis and stacking (LDIS), was applied to a newly designed protocol of nanoCESI-MS. This approach achieved up to 380-fold enhanced sensitivity and LOD of 450 fM. Compared with normal sheathless CE-MS, coupling of nanoCESI and LDIS provided up to 800-fold increase of sensitivity in total. Finally, metabolome analyses of single HeLa cells were performed, where 20 amino acids were successfully quantified with triple-quadrupole MS and 40 metabolites were identified with quadrupole-time-of-flight MS, as a promising analytical platform for microscale bioanalysis for the next generation.
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Affiliation(s)
- Takayuki Kawai
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan.,Japan Science and Technology Agency , PRESTO, Kawaguchi , Saitama 332-0012 , Japan.,Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Nobutoshi Ota
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Kaori Okada
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Akiko Imasato
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Yuri Owa
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Makiko Morita
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Misa Tada
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Yo Tanaka
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan.,Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka 565-0871 , Japan
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64
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Zhang F, Hong J, Xu W, Qu F. Straight nano-electrospray ionization and its coupling of mobility capillary electrophoresis to mass spectrometry. Talanta 2019; 206:120183. [PMID: 31514879 DOI: 10.1016/j.talanta.2019.120183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Mobility capillary electrophoresis (MCE) was developed previously in our group, which has the capabilities of ion separation and biomolecule hydrodynamic radius analysis. The coupling of MCE with mass spectrometry (MS) would greatly improve complex sample identification capability as well as system detection sensitivity. In the present study, a simple and robust ionization source, named as straight nano-electrospray ionization (nanoESI) source was developed, which was applied to couple MCE with MS. A stainless-steel needle attached directly at the end of an MCE capillary was used as the nanoESI emitter, and the connection between this emitter to the liquid flow in the MCE separation channel was established through a liquid bridge. After optimization, this straight nanoESI source enhanced the ion signal intensity by ~10 times when compared with a commercial nanoESI source. The MCE-straight nanoESI-MS system was also characterized in terms of mixture separation and peptide hydrodynamic radius measurements. Compared to our previous work when a UV detector was used in a commercial Lumex CE system (model Capel 105 M, St. Petersburg, Russia), peptides with much lower concentrations could be analyzed (from ~1 mg/mL to ~20 μg/mL) in terms of radius measurement.
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Affiliation(s)
- Fei Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Feng Qu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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65
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Zhang Z, Hebert AS, Westphall MS, Coon JJ, Dovichi NJ. Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry Produces over 4400 Phosphopeptide Identifications from a 220 ng Sample. J Proteome Res 2019; 18:3166-3173. [PMID: 31180221 DOI: 10.1021/acs.jproteome.9b00244] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The dependence of capillary zone electrophoresis (CZE) separations on the charge state of the analyte is useful for the analysis of many post-translational modifications in proteins. In this work, we coupled CZE to an Orbitrap Fusion Lumos Tribrid platform with an advanced peak determination algorithm for phosphoproteomics analysis. A linear-polyacrylamide-coated capillary with very low electroosmotic flow was used for the separation. The optimal injection volume was between 100 and 150 nL of a solution of phosphopeptides in 30 mM ammonium bicarbonate (pH 8.2) buffer, which produces a dynamic pH junction sample injection. Larger injection volumes resulted in serious peak broadening and decreased numbers of phosphopeptide identifications. The optimized system identified 4405 phosphopeptides from 220 ng of enriched phosphopeptides from mouse brain, which represents the state-of-the-art result for single-shot CZE-ESI-MS/MS-based phosphoproteome analysis. We found that the migration time for phosphopeptides is much longer than that for non-phosphopeptides and increased along with the number of phosphorylation sites on the peptides, as expected for the additional negative charges associated with the phosphate groups. We also investigated the phosphorylation site motifs; a number of motifs appeared in the CZE-ESI-MS/MS data but not in LC-ESI-MS/MS data, which suggested the complementary performance of the techniques. The data are available via ProteomeXchange with identifier PXD012888.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Alexander S Hebert
- Genome Center of Wisconsin and Departments of Chemistry and Biomolecular Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Michael S Westphall
- Genome Center of Wisconsin and Departments of Chemistry and Biomolecular Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Joshua J Coon
- Genome Center of Wisconsin and Departments of Chemistry and Biomolecular Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
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66
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Yu Y, Zhu SH, Yuan F, Zhang XH, Lu YY, Zhou YL, Zhang XX. Ultrasensitive and simultaneous determination of RNA modified nucleotides by sheathless interfaced capillary electrophoresis-tandem mass spectrometry. Chem Commun (Camb) 2019; 55:7595-7598. [PMID: 31180413 DOI: 10.1039/c9cc03195b] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A label-free ultrasensitive determination of eight RNA modified nucleotides simultaneously was first established based on a sheathless capillary electrophoresis-tandem mass spectrometry system. This system performed well using only 500 pg-5 ng practical RNA samples, and a downward trend of most target nucleotides in HCT 116 cells was observed with the increase of nickel concentration.
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Affiliation(s)
- Yue Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Si-Hao Zhu
- Molecular Imaging Lab, Department of Biomedical Engineering, Peking University, Beijing 100871, China
| | - 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
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yan-Ye Lu
- Molecular Imaging Lab, Department of Biomedical Engineering, Peking University, Beijing 100871, 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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67
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Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics 2019; 19:e1800361. [PMID: 31050378 PMCID: PMC6602557 DOI: 10.1002/pmic.201800361] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/07/2019] [Indexed: 12/29/2022]
Abstract
A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post-translational modifications. In top-down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top-down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.
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Affiliation(s)
- Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Robert J Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry and Molecular Biosciences and the Division of Hematology and Oncology, Northwestern University, Evanston, IL, 60208, USA
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, 84602
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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68
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Advances in capillary electrophoresis for the life sciences. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1118-1119:116-136. [PMID: 31035134 DOI: 10.1016/j.jchromb.2019.04.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/15/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022]
Abstract
Capillary electrophoresis (CE) played an important role in developments in the life sciences. The technique is nowadays used for the analysis of both large and small molecules in applications where it performs better than or is complementary to liquid chromatographic techniques. In this review, principles of different electromigration techniques, especially capillary isoelectric focusing (CIEF), capillary gel (CGE) and capillary zone electrophoresis (CZE), are described and recent developments in instrumentation, with an emphasis on mass spectrometry (MS) coupling and microchip CE, are discussed. The role of CE in the life sciences is shown with applications in which it had a high impact over the past few decades. In this context, current practice for the characterization of biopharmaceuticals (therapeutic proteins) is shown with CIEF, CGE and CZE using different detection techniques, including MS. Subsequently, the application of CGE and CZE, in combination with laser induced fluorescence detection and CZE-MS are demonstrated for the analysis of protein-released glycans in the characterization of biopharmaceuticals and glycan biomarker discovery in biological samples. Special attention is paid to developments in capillary coatings and derivatization strategies for glycans. Finally, routine CE analysis in clinical chemistry and latest developments in metabolomics approaches for the profiling of small molecules in biological samples are discussed. The large number of CE applications published for these topics in recent years clearly demonstrates the established role of CE in life sciences.
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69
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Nyssen L, Fillet M, Cavalier E, Servais A. Highly sensitive and selective separation of intact parathyroid hormone and variants by sheathless CE‐ESI‐MS/MS. Electrophoresis 2019; 40:1550-1557. [DOI: 10.1002/elps.201800507] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/28/2019] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Laurent Nyssen
- Department of Clinical ChemistryCenter for Interdisciplinary Research on Medicines (CIRM)University of Liège Liège Belgium
- Laboratory for the Analysis of Medicines (LAM)Center for Interdisciplinary Research on Medicines (CIRM)University of Liège Liège Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM)Center for Interdisciplinary Research on Medicines (CIRM)University of Liège Liège Belgium
| | - Etienne Cavalier
- Department of Clinical ChemistryCenter for Interdisciplinary Research on Medicines (CIRM)University of Liège Liège Belgium
| | - Anne‐Catherine Servais
- Laboratory for the Analysis of Medicines (LAM)Center for Interdisciplinary Research on Medicines (CIRM)University of Liège Liège Belgium
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70
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Krenkova J, Kleparnik K, Luksch J, Foret F. Microfabricated liquid junction hybrid capillary electrophoresis-mass spectrometry interface for fully automated operation. Electrophoresis 2019; 40:2263-2270. [PMID: 30794321 DOI: 10.1002/elps.201900049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 11/07/2022]
Abstract
One of the challenging instrumental aspects in coupling an automated CE instrument with ESI mass spectrometry (CE-MS) is finding the balance between the stability, reproducibility and sensitivity of the analysis and compatibility with the standard CE instrumentation. Here, we present a development of a new liquid junction based electrospray interface for automated CE-MS, with a focus on the technical design followed by computer modeling of transport conditions as well as characterization of basic performance of the interface. This hybrid arrangement designed as a microfabricated unit attachable to the automated CE instrument allows using of a wide range of separation capillaries with respect to their diameter, length or internal coating (e.g., for suppressed electroosmotic flow). Different compositions of the ESI liquid and background electrolyte solutions can be used if needed. The microfabricated part, prepared by laser machining from polyimide, includes a self-aligning liquid junction, a short transport channel, and a pointed sprayer for the electrospray ionization. This microfabricated part is positioned in a plastic connection block securing the separation capillary and flushing ports. Transport conditions were modelled using computer simulation and the real life performance of the interface was compared to that of a commercial sheath liquid interface. The basic performance of the interface was demonstrated by separations of peptides, proteins, and oligosaccharides.
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Affiliation(s)
- Jana Krenkova
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
| | - Karel Kleparnik
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Luksch
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
| | - Frantisek Foret
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic.,CEITEC Masaryk University, Brno, Czech Republic
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71
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Sánchez-López E, Kammeijer GSM, Crego AL, Marina ML, Ramautar R, Peters DJM, Mayboroda OA. Sheathless CE-MS based metabolic profiling of kidney tissue section samples from a mouse model of Polycystic Kidney Disease. Sci Rep 2019; 9:806. [PMID: 30692602 PMCID: PMC6349881 DOI: 10.1038/s41598-018-37512-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/30/2018] [Indexed: 12/26/2022] Open
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) using a sheathless porous tip interface emerged as an attractive tool in metabolomics thanks to its numerous advantages. One of the main advantages compared to the classical co-axial sheath liquid interface is the increased sensitivity, while maintaining the inherent properties of CE, such as a high separation efficiency and low sample consumption. Specially, the ability to perform nanoliter-based injections from only a few microliters of material in the sample vial makes sheathless CE-MS a well-suited and unique approach for highly sensitive metabolic profiling of limited sample amounts. Therefore, in this work, we demonstrate the utility of sheathless CE-MS for metabolic profiling of biomass-restricted samples, namely for 20 µm-thick tissue sections of kidney from a mouse model of polycystic kidney disease (PKD). The extraction method was designed in such a way to keep a minimum sample-volume in the injection vial, thereby still allowing multiple nanoliter injections for repeatability studies. The developed strategy enabled to differentiate between different stages of PKD and as well changes in a variety of different metabolites could be annotated over experimental groups. These metabolites include carnitine, glutamine, creatine, betaine and creatinine. Overall, this study shows the utility of sheathless CE-MS for biomass-limited metabolomics studies.
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Affiliation(s)
- Elena Sánchez-López
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Madrid, Spain
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Antonio L Crego
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Madrid, Spain
| | - María Luisa Marina
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Madrid, Spain
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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72
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Ramautar R. Sheathless Capillary Electrophoresis-Mass Spectrometry for the Profiling of Charged Metabolites in Biological Samples. Methods Mol Biol 2019; 1738:183-192. [PMID: 29654590 DOI: 10.1007/978-1-4939-7643-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Capillary electrophoresis (CE) is well suited for the profiling of highly polar and charged metabolites as compounds are separated on the basis of their charge-to-size ratio. The protocol presented here is based on using a recently developed sheathless interfacing design, i.e., a porous tip interface, for coupling CE to electrospray ionization mass spectrometry (MS). It is demonstrated that sheathless CE-MS employing a bare fused-silica capillary at low-pH separation conditions can be used for the profiling of both cationic and anionic metabolites by only switching the MS detection and electrophoretic separation voltage polarity. The proposed sheathless CE-MS protocol allows efficient and sensitive profiles to be obtained for a broad array of charged metabolites, including amino acids, organic acids, nucleotides, and sugar phosphates, in various biological samples, such as urine and extracts of the glioblastoma cell line.
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Affiliation(s)
- Rawi Ramautar
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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73
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Chen D, Ludwig KR, Krokhin OV, Spicer V, Yang Z, Shen X, Hummon AB, Sun L. Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Large-Scale Phosphoproteomics with the Production of over 11,000 Phosphopeptides from the Colon Carcinoma HCT116 Cell Line. Anal Chem 2019; 91:2201-2208. [PMID: 30624053 DOI: 10.1021/acs.analchem.8b04770] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphoproteomics requires better separation of phosphopeptides to boost the coverage of the phosphoproteome. We argue that an alternative separation method that produces orthogonal phosphopeptide separation to the widely used LC needs to be considered. Capillary zone electrophoresis (CZE) is one important alternative because CZE and LC are orthogonal for phosphopeptide separation and because the migration time of peptides in CZE can be accurately predicted. In this work, we coupled strong cation exchange (SCX)-reversed-phase LC (RPLC) to CZE-MS/MS for large-scale phosphoproteomics of the colon carcinoma HCT116 cell line. The CZE-MS/MS-based platform identified 11,555 phosphopeptides. The phosphopeptide data set is at least 100% larger than that from previous CZE-MS/MS studies and will be a valuable resource for building a model for predicting the migration time of phosphopeptides in CZE. Phosphopeptides migrate significantly slower than corresponding unphosphopeptides under acidic conditions of CZE separations and in a normal polarity. According to our modeling data, phosphorylation decreases peptide's charge roughly by one charge unit, resulting in dramatic decrease in electrophoretic mobility. Preliminary investigations demonstrate that electrophoretic mobility of phosphopeptides containing one phosphoryl group can be predicted with the same accuracy as for nonmodified peptides ( R2 ≈ 0.99). The CZE-MS/MS and LC-MS/MS were complementary in large-scale phosphopeptide identifications and produced different phosphosite motifs from the HCT116 cell line. The data highlight the value of CZE-MS/MS for phosphoproteomics as a complementary separation approach for not only improving the phosphoproteome coverage but also providing more insight into the phosphosite motifs.
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Affiliation(s)
- Daoyang Chen
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Katelyn R Ludwig
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | | | | | - Zhichang Yang
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Xiaojing Shen
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center , The Ohio State University , 414 Biomedical Research Tower , Columbus , Ohio 43201 , United States
| | - Liangliang Sun
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , Michigan 48824 , United States
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74
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Wu H, Yi L, Wojcik R, Shi T, Tang K. A separation voltage polarity switching method for higher sample loading capacity and better separation resolution in transient capillary isotachophoresis separation. Analyst 2019; 144:454-462. [PMID: 30444223 DOI: 10.1039/c8an01779d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A separation voltage polarity switching transient capillary isotachophoresis (PS-tCITP) was developed to overcome a major sample loading volume limitation in transient capillary isotachophoresis (tCITP). The fundamental idea of PS-tCITP is to let sample ions move back and forth in a separation capillary during their initial isotachophoresis focusing stage by switching the polarity of the separation voltage, in order to both increase the sample loading volume and improve the separation efficiency as compared to the conventional tCITP method. The experimental evaluation of the novel PS-tCITP method by using two peptide standards at 2 μM concentration showed that the maximum sample loading volume could be increased from 45% of the total separation capillary volume in tCITP to 70% in PS-tCITP, which resulted in a more than 1.5 fold increase in the peptide peak intensity at a given length/volume of the separation capillary. Due to the consecutive focusing of sample volume from each polarity switching of the separation voltage, the separation time window at a given sample loading volume was also increased significantly in PS-tCITP as compared to tCITP. Experiment comparison between tCITP and PS-tCITP at 45% sample loading volume using the same setup showed that the migration time difference between the two peptide peaks increased from 0.3 min in tCITP to 0.363 min in PS-tCITP with similar peak widths and heights, resulting in roughly a 21% improvement in separation resolution. The performance advantages of PS-tCITP separation over tCITP separation were further verified by using a mixture of six peptide standards.
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Affiliation(s)
- Huanming Wu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
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75
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Zhang W, Hankemeier T, Ramautar R. Capillary Electrophoresis-Mass Spectrometry for Metabolic Profiling of Biomass-Limited Samples. Methods Mol Biol 2019; 1972:165-172. [PMID: 30847790 DOI: 10.1007/978-1-4939-9213-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) is a strong separation technique for the highly efficient and selective analysis of polar and charged metabolites in biological samples. The CE approach is especially suited for the analysis of limited sample amounts due to its nanoliter injections from only a few microliters of material in the sample injection vial. In this protocol, a CE-MS strategy is outlined for the profiling of cationic metabolites in biomass-limited samples using a small amount of human hepatocellular carcinoma (HepG2) cells as a model system. By employing a sheathless interfacing design for coupling CE to MS, it is shown that information-rich profiles for cationic metabolites can be obtained when working with a starting amount of 10,000 HepG2 cells and even lower. Overall, the proposed CE-MS-based analytical workflow may be considered a useful tool for biomass-limited metabolomics studies.
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Affiliation(s)
- Wei Zhang
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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76
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Zhang W, Guled F, Hankemeier T, Ramautar R. Utility of sheathless capillary electrophoresis-mass spectrometry for metabolic profiling of limited sample amounts. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1105:10-14. [DOI: 10.1016/j.jchromb.2018.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/17/2018] [Accepted: 12/04/2018] [Indexed: 12/01/2022]
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77
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Ouyang Y, Han X, Xia Q, Chen J, Velagapudi S, Xia K, Zhang Z, Linhardt RJ. Negative-Ion Mode Capillary Isoelectric Focusing Mass Spectrometry for Charge-Based Separation of Acidic Oligosaccharides. Anal Chem 2018; 91:846-853. [DOI: 10.1021/acs.analchem.8b03500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Yilan Ouyang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215021, China
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering, and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Xiaorui Han
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering, and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Qiangwei Xia
- CMP Scientific Corporation, 760 Parkside Avenue, STE 211, Brooklyn, New York 11226, United States
| | - Jianle Chen
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering, and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Sheila Velagapudi
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering, and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Ke Xia
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering, and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Zhenqing Zhang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215021, China
| | - Robert J. Linhardt
- Departments of Chemistry and Chemical Biology, Biology, Chemical and Biological Engineering, and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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78
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Stolz A, Jooß K, Höcker O, Römer J, Schlecht J, Neusüß C. Recent advances in capillary electrophoresis-mass spectrometry: Instrumentation, methodology and applications. Electrophoresis 2018; 40:79-112. [PMID: 30260009 DOI: 10.1002/elps.201800331] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022]
Abstract
Capillary electrophoresis (CE) offers fast and high-resolution separation of charged analytes from small injection volumes. Coupled to mass spectrometry (MS), it represents a powerful analytical technique providing (exact) mass information and enables molecular characterization based on fragmentation. Although hyphenation of CE and MS is not straightforward, much emphasis has been placed on enabling efficient ionization and user-friendly coupling. Though several interfaces are now commercially available, research on more efficient and robust interfacing with nano-electrospray ionization (ESI), matrix-assisted laser desorption/ionization (MALDI) and inductively coupled plasma mass spectrometry (ICP) continues with considerable results. At the same time, CE-MS has been used in many fields, predominantly for the analysis of proteins, peptides and metabolites. This review belongs to a series of regularly published articles, summarizing 248 articles covering the time between June 2016 and May 2018. Latest developments on hyphenation of CE with MS as well as instrumental developments such as two-dimensional separation systems with MS detection are mentioned. Furthermore, applications of various CE-modes including capillary zone electrophoresis (CZE), nonaqueous capillary electrophoresis (NACE), capillary gel electrophoresis (CGE) and capillary isoelectric focusing (CIEF) coupled to MS in biological, pharmaceutical and environmental research are summarized.
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Affiliation(s)
| | - Kevin Jooß
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Oliver Höcker
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Instrumental Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Jennifer Römer
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Regensburg, Germany
| | - Johannes Schlecht
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University, Jena, Germany
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79
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80
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McCool EN, Lubeckyj R, Shen X, Kou Q, Liu X, Sun L. Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry. J Vis Exp 2018. [PMID: 30417888 DOI: 10.3791/58644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as a useful tool for top-down proteomics that aims to characterize proteoforms in complex proteomes. However, the application of CZE-MS/MS for large-scale top-down proteomics has been impeded by the low sample-loading capacity and narrow separation window of CZE. Here, a protocol is described using CZE-MS/MS with a microliter-scale sample-loading volume and a 90-min separation window for large-scale top-down proteomics. The CZE-MS/MS platform is based on a linear polyacrylamide (LPA)-coated separation capillary with extremely low electroosmotic flow, a dynamic pH-junction-based online sample concentration method with a high efficiency for protein stacking, an electro-kinetically pumped sheath flow CE-MS interface with extremely high sensitivity, and an ion trap mass spectrometer with high mass resolution and scan speed. The platform can be used for the high-resolution characterization of simple intact protein samples and the large-scale characterization of proteoforms in various complex proteomes. As an example, a highly efficient separation of a standard protein mixture and a highly sensitive detection of many impurities using the platform is demonstrated. As another example, this platform can produce over 500 proteoform and 190 protein identifications from an Escherichia coli proteome in a single CZE-MS/MS run.
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Affiliation(s)
| | | | | | - Qiang Kou
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine
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81
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Mikšík I. Coupling of CE-MS for protein and peptide analysis. J Sep Sci 2018; 42:385-397. [PMID: 30238606 DOI: 10.1002/jssc.201800817] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022]
Abstract
The review is focused on the latest developments in the analysis of proteins and peptides by capillary electrophoresis techniques coupled to mass spectrometry. First, the methodology and instrumentation are overviewed. In this section, recent progress in capillary electrophoresis with mass spectrometry interfaces and capillary electrophoresis with matrix-assisted laser desorption/ionization is mentioned, as well as separation tasks. The second part is devoted to applications-mainly bottom-up and top-down proteomics. It is obvious that capillary electrophoresis with mass spectrometry methods are well suited for peptide and protein analysis (proteomic research) and it is described how these techniques are complementary and not competitive with the often used liquid chromatography with mass spectrometry methods.
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Affiliation(s)
- Ivan Mikšík
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague 4, Czech Republic
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82
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Nowak PM, Woźniakiewicz M. On-line coupling between capillary electrophoresis and microscale thermophoresis (CE-MST); the proof-of-concept. Analyst 2018; 143:4854-4859. [PMID: 30225471 DOI: 10.1039/c8an01191e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that microscale thermophoresis can be easily coupled with capillary electrophoresis in an on-line flow system (CE-MST), offering new potential possibilities. It takes advantage of sample separation and miniaturization prior to thermo-optical/MST analysis. No instrument modification is required. The future perspective is discussed.
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Affiliation(s)
- Paweł M Nowak
- Department of Analytical Chemistry, Faculty of Chemistry, Jagiellonian University in Kraków, Gronostajowa St. 2, 30-387 Kraków, Poland.
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83
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Yang Z, Shen X, Chen D, Sun L. Microscale Reversed-Phase Liquid Chromatography/Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Deep and Highly Sensitive Bottom-Up Proteomics: Identification of 7500 Proteins with Five Micrograms of an MCF7 Proteome Digest. Anal Chem 2018; 90:10479-10486. [PMID: 30102516 PMCID: PMC6156779 DOI: 10.1021/acs.analchem.8b02466] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has been well recognized for bottom-up proteomics. It has approached 4000-8000 protein identifications (IDs) from a human cell line, mouse brains, or Xenopus embryos via coupling with liquid chromatography (LC) prefractionation. However, at least 500 μg of complex proteome digests were required for the LC/CZE-MS/MS studies. This requirement of a large amount of initial peptide material impedes the application of CZE-MS/MS for deep bottom-up proteomics of mass-limited samples. In this work, we coupled microscale reversed-phase LC (μRPLC)-based peptide prefractionation to dynamic pH-junction-based CZE-MS/MS for deep bottom-up proteomics of the MCF7 breast cancer cell proteome starting with only 5 μg of peptides. The dynamic pH-junction-based CZE enabled a 500 nL sample injection from as low as a 1.5 μL peptide sample, using up to 33% of the available peptide material for an analysis. Two kinds of μRPLC prefractionation were investigated, C18 ZipTip and nanoflow RPLC. C18 ZipTip/CZE-MS/MS identified 4453 proteins from 5 μg of the MCF7 proteome digest and showed good qualitative and quantitative reproducibility. Nanoflow RPLC/CZE-MS/MS produced over 7500 protein IDs and nearly 60 000 peptide IDs from the 5 μg of MCF7 proteome digest. The nanoflow RPLC/CZE-MS/MS platform reduced the required amount of complex proteome digests for LC/CZE-MS/MS-based deep bottom-up proteomics by 2 orders of magnitude. Our work provides the proteomics community with a powerful tool for deep and highly sensitive proteomics.
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Affiliation(s)
- Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
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84
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Shen X, Kou Q, Guo R, Yang Z, Chen D, Liu X, Hong H, Sun L. Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry. Anal Chem 2018; 90:10095-10099. [PMID: 30085653 PMCID: PMC6156775 DOI: 10.1021/acs.analchem.8b02725] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Native proteomics aims to characterize complex proteomes under native conditions and ultimately produces a full picture of endogenous protein complexes in cells. It requires novel analytical platforms for high-resolution and liquid-phase separation of protein complexes prior to native mass spectrometry (MS) and MS/MS. In this work, size-exclusion chromatography (SEC)-capillary zone electrophoresis (CZE)-MS/MS was developed for native proteomics in discovery mode, resulting in the identification of 144 proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli proteome. The protein complexes include four protein homodimers, 16 protein-metal complexes, two protein-[2Fe-2S] complexes, and one protein-glutamine complex. Half of them have not been reported in the literature. This work represents the first example of online liquid-phase separation-MS/MS for the characterization of a complex proteome under the native condition, offering the proteomics community an efficient and simple platform for native proteomics.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Qiang Kou
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202 USA
| | - Ruiqiong Guo
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, Indianapolis, IN 46202 USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
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85
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Konášová R, Koval D, Dytrtová JJ, Kašička V. Comparison of two low flow interfaces for measurement of mobilities and stability constants by affinity capillary electrophoresis–mass spectrometry. J Chromatogr A 2018; 1568:197-204. [DOI: 10.1016/j.chroma.2018.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 12/19/2022]
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86
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Wang L, Bo T, Zhang Z, Wang G, Tong W, Da Yong Chen D. High Resolution Capillary Isoelectric Focusing Mass Spectrometry Analysis of Peptides, Proteins, And Monoclonal Antibodies with a Flow-through Microvial Interface. Anal Chem 2018; 90:9495-9503. [PMID: 29993237 DOI: 10.1021/acs.analchem.8b02175] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lingyu Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China 210023
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Tao Bo
- Thermo Fisher Scientific, 7th Floor, Building F, Tower West, Yonghe Plaza, No. 28 Andingmen Street East, Beijing, China 100007
| | - Zhengxiang Zhang
- Thermo Fisher Scientific, 7th Floor, Building F, Tower West, Yonghe Plaza, No. 28 Andingmen Street East, Beijing, China 100007
| | - Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China 210023
| | - Wenjun Tong
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China 210023
| | - David Da Yong Chen
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China 210023
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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87
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Sheathless coupling of microchip electrophoresis to ESI-MS utilising an integrated photo polymerised membrane for electric contacting. Anal Bioanal Chem 2018; 410:5741-5750. [PMID: 29974150 DOI: 10.1007/s00216-018-1226-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/12/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
Abstract
In this article, we present a novel approach for the sheathless coupling of microchip electrophoresis (MCE) with electrospray mass spectrometry (ESI-MS). The key element is an ion-conductive hydrogel membrane, placed between the separation channel and an adjacent microfluidic supporting channel, contacted via platinum electrodes. This solves the persistent challenge in hyphenation of mass spectrometry to chip electrophoresis, to ensure a reliable electrical connection at the end of the electrophoresis channel without sacrificing separation performance and sensitivity. Stable electric contacting is achieved via a Y-shaped supporting channel structure, separated from the main channel by a photo polymerised, ion permeable hydrogel membrane. Thus, the potential gradient required for performing electrophoretic separations can be generated while simultaneously preventing gas formation due to electrolysis. In contrast to conventional make-up or sheathflow approaches, sample dilution is also avoided. Rapid prototyping allowed the study of different chip-based approaches, i.e. sheathless, open sheathflow and electrode support channel designs, for coupling MCE to ESI-MS. The performance was evaluated with fluorescence microscopy and mass spectrometric detection. The obtained results revealed that the detection sensitivity obtained in such Y-channel chips with integrated hydrogel membranes was superior because sample dilution or loss was prevented. Furthermore, band broadening is reduced compared to similar open structures without a membrane.
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88
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Characterization of a nanoflow sheath liquid interface and comparison to a sheath liquid and a sheathless porous-tip interface for CE-ESI-MS in positive and negative ionization. Anal Bioanal Chem 2018; 410:5265-5275. [DOI: 10.1007/s00216-018-1179-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 01/22/2023]
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89
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Chen H, Shi P, Fan F, Tu M, Xu Z, Xu X, Du M. Complementation of UPLC-Q-TOF-MS and CESI-Q-TOF-MS on identification and determination of peptides from bovine lactoferrin. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1084:150-157. [DOI: 10.1016/j.jchromb.2018.03.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/05/2018] [Accepted: 03/10/2018] [Indexed: 12/27/2022]
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90
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Moini M. Applications of liquid-based separation in conjunction with mass spectrometry to the analysis of forensic evidence. Electrophoresis 2018. [PMID: 29529344 DOI: 10.1002/elps.201700501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the past few years, there has been a significant effort by the forensic science community to develop new scientific techniques for the analysis of forensic evidence. Forensic chemists have been spearheaded to develop information-rich confirmatory technologies and techniques and apply them to a broad array of forensic challenges. The purpose of these confirmatory techniques is to provide alternatives to presumptive techniques that rely on data such as color changes, pattern matching, or retention time alone, which are prone to more false positives. To this end, the application of separation techniques in conjunction with mass spectrometry has played an important role in the analysis of forensic evidence. Moreover, in the past few years the role of liquid separation techniques, such as liquid chromatography and capillary electrophoresis in conjunction with mass spectrometry, has gained significant tractions and have been applied to a wide range of chemicals, from small molecules such as drugs and explosives, to large molecules such as proteins. For example, proteomics and peptidomics have been used for identification of humans, organs, and bodily fluids. A wide range of HPLC techniques including reversed phase, hydrophilic interaction, mixed-mode, supercritical fluid, multidimensional chromatography, and nanoLC, as well as several modes of capillary electrophoresis mass spectrometry, including capillary zone electrophoresis, partial filling, full filling, and micellar electrokenetic chromatography have been applied to the analysis drugs, explosives, and questioned documents. In this article, we review recent (2015-2017) applications of liquid separation in conjunction with mass spectrometry to the analysis of forensic evidence.
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Affiliation(s)
- Mehdi Moini
- Department of Forensic Sciences, George Washington University, Washington, D.C., USA
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91
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Hirayama A, Abe H, Yamaguchi N, Tabata S, Tomita M, Soga T. Development of a sheathless CE-ESI-MS interface. Electrophoresis 2018; 39:1382-1389. [PMID: 29493797 DOI: 10.1002/elps.201800017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 12/20/2022]
Abstract
A sheath-flow interface is the most common ionization technique in CE-ESI-MS. However, this interface dilutes the analytes with the sheath liquid and decreases the sensitivity. In this study, we developed a sheathless CE-MS interface to improve sensitivity. The interface was fabricated by making a small crack approximately 2 cm from the end of a capillary column fixed on a plastic plate, and then covering the crack with a dialysis membrane to prevent metabolite loss during separation. A voltage for CE separation was applied between the capillary inlet and the buffer reservoir. Under optimum conditions, 52 cationic metabolite standards were separated and selectively detected using MS. With a pressure injection of 5 kPa for 15 s (ca. 1.4 nL), the detection limits for the tested compounds were between 0.06 and 1.7 μmol/L (S/N = 3). The method was applied to analysis of cationic metabolites extracted from a small number (12 000) of cancer cells, and the number of peaks detected was about 2.5 times higher than when using conventional sheath-flow CE-MS. Because the interface is easy to construct, it is cost-effective and can be adapted to any commercially available capillaries. This method is a powerful new tool for highly sensitive CE-MS-based metabolomic analysis.
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Affiliation(s)
- Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Hiroshi Abe
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Nozomi Yamaguchi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Sho Tabata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
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92
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Jarvas G, Szigeti M, Guttman A. Effect of the flow profile on separation efficiency in pressure-assisted reversed-polarity capillary zone electrophoresis of anions: Simulation and experimental evaluation. J Sep Sci 2018; 41:2473-2478. [DOI: 10.1002/jssc.201701372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Gabor Jarvas
- Horváth Csaba Memorial Institute of Bioanalytical Research; Research Centre for Molecular Medicine; Faculty of Medicine; University of Debrecen; Debrecen Hungary
- MTA-PE Translational Glycomics Group; University of Pannonia; Veszprem Hungary
| | - Marton Szigeti
- Horváth Csaba Memorial Institute of Bioanalytical Research; Research Centre for Molecular Medicine; Faculty of Medicine; University of Debrecen; Debrecen Hungary
- MTA-PE Translational Glycomics Group; University of Pannonia; Veszprem Hungary
| | - Andras Guttman
- Horváth Csaba Memorial Institute of Bioanalytical Research; Research Centre for Molecular Medicine; Faculty of Medicine; University of Debrecen; Debrecen Hungary
- SCIEX Separations; Brea CA USA
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93
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Moini M. Toward Confirmatory On-Site Real-Time Detection of Emerging Drugs Using Portable Ultrafast Capillary Electrophoresis Mass Spectrometry. Methods Mol Biol 2018; 1810:43-58. [PMID: 29974416 DOI: 10.1007/978-1-4939-8579-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Currently, law enforcement agencies rely upon presumptive tests such as color tests (or spot tests) for on-site, real-time identification of forensic evidence, such as controlled substances. These tests are simple and easy to use and require no instrumentation. However, they are unreliable and have a large false positive rate. On the other hand, confirmatory tests are done in analytical laboratories using sophisticated instrumentation by expert analysts, and have lower false positive rates. However, they are bulky and impractical for on-site real-time analysis. To provide more accurate identification of forensic evidence on-site, in real-time, it is important to develop portable confirmatory instrumentation using information-rich technologies. Moreover, because the analysis of controlled substances could be complicated by the existence of various isomers (including optical isomers) it is desirable that the portable instruments have the capability to separate structural and optical isomers of the controlled substances, because scheduling is some times dependent upon which isomer is present. To this end, we have developed a portable ultrafast capillary electrophoresis (UFCE) system for the separation of controlled substances and their structural and optical isomers. The UFCE instrument has an integrated porous tip for facile interfacing with electrospray ionization mass spectrometry. The technique has been successfully applied to the analysis of mixtures of several controlled substances such as amphetamines, cathinones, nor-mephedrone, and pregabalin and their optical isomers in about a minute.
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Affiliation(s)
- Mehdi Moini
- Department of Forensic Sciences, George Washington University, Washington, DC, USA.
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94
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Isomeric Separation and Characterisation of Glycoconjugates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:77-99. [DOI: 10.1007/978-981-13-2158-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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95
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Fang P, Pan JZ, Fang Q. A robust and extendable sheath flow interface with minimal dead volume for coupling CE with ESI-MS. Talanta 2017; 180:376-382. [PMID: 29332826 DOI: 10.1016/j.talanta.2017.12.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/06/2017] [Accepted: 12/14/2017] [Indexed: 10/18/2022]
Abstract
In this paper, we describe a robust sheath flow-based CE-MS interface with minimal interface dead volume based on an extended pattern. A 20µm i.d. × 90µm o.d. fused-silica capillary with a chemically-etched thin-wall tip (30µm o.d.) was used as the separation capillary as well as electrospray emitter, and a 200µm i.d. × 375µm o.d. capillary with a tapered tip (40µm o.d.) was used as the sheath flow capillary. An extendable sheath-flow interface mode was adopted by decreasing the thickness of separation capillary tip and extending the separation capillary tip out from the sheath flow capillary tip, and allowing the sheath flow to be transferred to the separation capillary tip along its outer surface, forming a surface sheath flow to mix with sample flow at the separation capillary tip. Such a strategy could significantly reduce the interface dead volume and thus improve the CE separation efficiency and detection sensitivity, as well as evidently enhance the working reliability of the CE-MS interface. We investigated various factors affecting the interface performance, including capillary extending distance, emitter diameters, sheath flow capillary shape, and sheath flow rate. Under the optimized conditions, a minimal interface dead volume of ca. 4pL was obtained which is the smallest one compared with previously-reported sheath flow-based CE-MS interfaces. The feasibility and applicability of the present CE-MS interface were demonstrated in the separation of a peptide mixture with high separation efficiency of 2.07-3.38µm plate heights and good repeatabilities (< 6.1% RSD, n = 5). We except such a simple and robust interface could provide a possible solution for the development of commercial CE-MS interfaces differing from the currently-used ones, and has the potentials to be applied in routine analytical laboratories for various studies such as proteomics, metabolomics, or single cell analysis.
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Affiliation(s)
- Pan Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
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96
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Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR. Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2614-2634. [PMID: 28875426 PMCID: PMC5709234 DOI: 10.1007/s13361-017-1781-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/04/2023]
Abstract
Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). Graphical Abstract ᅟ.
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Affiliation(s)
- Arseniy M Belov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - David M Horn
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA.
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97
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González-Ruiz V, Codesido S, Rudaz S, Schappler J. Evolution in the design of a low sheath-flow interface for CE-MS and application to biological samples. Electrophoresis 2017; 39:853-861. [DOI: 10.1002/elps.201700328] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Víctor González-Ruiz
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva Switzerland
| | | | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva Switzerland
| | - Julie Schappler
- School of Pharmaceutical Sciences, University of Geneva; University of Lausanne; Geneva Switzerland
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98
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Yi L, Piehowski PD, Shi T, Smith RD, Qian WJ. Advances in microscale separations towards nanoproteomics applications. J Chromatogr A 2017; 1523:40-48. [PMID: 28765000 PMCID: PMC6042839 DOI: 10.1016/j.chroma.2017.07.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023]
Abstract
Microscale separation (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. In recent decades significant advances have been achieved in MS-based proteomics. However, the current proteomics platforms still face an analytical challenge in overall sensitivity towards nanoproteomics applications for starting materials of less than 1μg total proteins (e.g., cellular heterogeneity in tissue pathologies). Herein, we review recent advances in microscale separation techniques and integrated sample processing strategies that improve the overall sensitivity and proteome coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.
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Affiliation(s)
- Lian Yi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
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99
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Lubeckyj RA, McCool EN, Shen X, Kou Q, Liu X, Sun L. Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms. Anal Chem 2017; 89:12059-12067. [PMID: 29064224 DOI: 10.1021/acs.analchem.7b02532] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as an invaluable platform for top-down proteomics. However, the scale of top-down proteomics using CZE-MS/MS is still limited due to the low loading capacity and narrow separation window of CZE. In this work, for the first time we systematically evaluated the dynamic pH junction method for focusing of intact proteins during CZE-MS. The optimized dynamic pH junction-based CZE-MS/MS approached a 1 μL loading capacity, 90 min separation window, and high peak capacity (∼280) for characterization of an Escherichia coli proteome. The results represent the largest loading capacity and the highest peak capacity of CZE for top-down characterization of complex proteomes. Single-shot CZE-MS/MS identified about 2800 proteoform-spectrum matches, nearly 600 proteoforms, and 200 proteins from the Escherichia coli proteome with spectrum-level false discovery rate (FDR) less than 1%. The number of identified proteoforms in this work is over three times higher than that in previous single-shot CZE-MS/MS studies. Truncations, N-terminal methionine excision, signal peptide removal, and some post-translational modifications including oxidation and acetylation were detected.
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Affiliation(s)
- Rachele A Lubeckyj
- Department of Chemistry, Michigan State University , 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Elijah N McCool
- Department of Chemistry, Michigan State University , 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University , 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qiang Kou
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , 719 Indiana Avenue, Indianapolis, Indiana 46202, United States
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , 719 Indiana Avenue, Indianapolis, Indiana 46202, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine , 410 W. 10th Street, Indianapolis, Indiana 46202, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University , 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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100
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Faserl K, Sarg B, Sola L, Lindner HH. Enhancing Proteomic Throughput in Capillary Electrophoresis-Mass Spectrometry by Sequential Sample Injection. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700310] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/06/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Klaus Faserl
- Division of Clinical Biochemistry, Biocenter; Innsbruck Medical University; Innsbruck Austria
| | - Bettina Sarg
- Division of Clinical Biochemistry, Biocenter; Innsbruck Medical University; Innsbruck Austria
| | - Laura Sola
- Institute of Chemistry of Molecular Recognition; National Research Council of Italy; Milano Italy
| | - Herbert H. Lindner
- Division of Clinical Biochemistry, Biocenter; Innsbruck Medical University; Innsbruck Austria
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