51
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Comi TJ, Do TD, Rubakhin SS, Sweedler JV. Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry. J Am Chem Soc 2017; 139:3920-3929. [PMID: 28135079 PMCID: PMC5364434 DOI: 10.1021/jacs.6b12822] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Indexed: 02/06/2023]
Abstract
The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.
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Affiliation(s)
- Troy J. Comi
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Thanh D. Do
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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52
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Zhang Z, Zhu G, Peuchen EH, Dovichi NJ. Preparation of linear polyacrylamide coating and strong cationic exchange hybrid monolith in a single capillary, and its application as an automated platform for bottom-up proteomics by capillary electrophoresis-mass spectrometry. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2084-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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53
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Krokhin OV, Anderson G, Spicer V, Sun L, Dovichi NJ. Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis. Anal Chem 2017; 89:2000-2008. [PMID: 28208305 DOI: 10.1021/acs.analchem.6b04544] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A multiparametric sequence-specific model for predicting peptide electrophoretic mobility has been developed using large-scale bottom-up proteomic CE-MS data (5% (∼0.8M) acetic acid as background electrolyte). Peptide charge (Z) and size (molecular mass, M) are the two major factors determining electrophoretic mobility, in complete agreement with previous studies. The extended size of the data set (>4000 peptides) permits access to many sequence-specific factors that impact peptide mobility. The presence of acidic residues Asp and Glu near the peptide N-terminus is by far the most prominent among them. The induction effect of the side chain of N-terminal Asp reduces the basicity of the N-terminal amino group and, as hence, its charge, by ∼0.27 units, lowering mobility. The correlation of the model (R2 ∼ 0.995) indicates that the peptide separation process in CZE is relatively simple and can be predicted to a much higher precision than current RP-HPLC models. Similar to RP-HPLC prediction studies, we anticipate future developments that introduce peptide migration standards, collect larger data sets for modeling through the alignment of multiple CZE-MS acquisitions, and study of the behavior of peptides carrying post-translational modifications. The increased size of data sets will also permit investigation of the fine-scale effects of peptide secondary structure on peptide mobility. We observed that peptides with higher helical propensity tend to have higher than predicted electrophoretic mobility; the incorporation of these features into CZE migration models will require significantly larger data sets.
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Affiliation(s)
| | | | | | - Liangliang Sun
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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54
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Chen D, Shen X, Sun L. Capillary zone electrophoresis–mass spectrometry with microliter-scale loading capacity, 140 min separation window and high peak capacity for bottom-up proteomics. Analyst 2017; 142:2118-2127. [DOI: 10.1039/c7an00509a] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CZE–MS can approach a microliter-scale loading capacity and a 140 min separation window for large-scale bottom-up proteomics.
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Affiliation(s)
- Daoyang Chen
- Department of Chemistry
- Michigan State University
- East Lansing
- USA 48824
| | - Xiaojing Shen
- Department of Chemistry
- Michigan State University
- East Lansing
- USA 48824
| | - Liangliang Sun
- Department of Chemistry
- Michigan State University
- East Lansing
- USA 48824
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55
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KAWAI T. Recent Studies on Online Sample Preconcentration Methods inCapillary Electrophoresis Coupled with Mass Spectrometry. CHROMATOGRAPHY 2017. [DOI: 10.15583/jpchrom.2017.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Takayuki KAWAI
- Quantitative Biology Center, RIKEN
- Japan Science and Technology Agency, PRESTO
- Graduate School of Frontier Biosciences, Osaka University
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56
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Zhu G, Sun L, Heidbrink-Thompson J, Kuntumalla S, Lin HY, Larkin CJ, McGivney JB, Dovichi NJ. Capillary zone electrophoresis tandem mass spectrometry detects low concentration host cell impurities in monoclonal antibodies. Electrophoresis 2016; 37:616-22. [PMID: 26530276 DOI: 10.1002/elps.201500301] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/02/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022]
Abstract
We have evaluated CZE-ESI-MS/MS for detection of trace amounts of host cell protein impurities in recombinant therapeutics. Compared to previously published procedures, we have optimized the buffer pH used in the formation of a pH junction to increase injection volume. We also prepared a 5-point calibration curve by spiking 12 standard proteins into a solution of a human mAb. A custom CZE-MS/MS system was used to analyze the tryptic digest of this mixture without depletion of the antibody. CZE generated a ∼70-min separation window (∼90-min total analysis duration) and ∼300-peak capacity. We also analyzed the sample using ultra-performance LC-MS/MS. CZE-MS/MS generated approximately five times higher base peak intensity and more peptide identifications for low-level spiked proteins. Both methods detected all proteins spiked at ∼100 ppm level with respect to the antibody.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Hung-yu Lin
- Department of Analytical Biotechnology, MedImmune, Gaithersburg, MD, USA
| | | | - James B McGivney
- Department of Analytical Biotechnology, MedImmune, Gaithersburg, MD, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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57
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Characterization of a Porous Nano-electrospray Capillary Emitter at Ultra-low Flow Rates. J Chromatogr Sci 2016; 55:47-51. [DOI: 10.1093/chromsci/bmw148] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 08/12/2016] [Indexed: 11/15/2022]
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58
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Yuan F, Zhang XH, Nie J, Chen HX, Zhou YL, Zhang XX. Ultrasensitive determination of 5-methylcytosine and 5-hydroxymethylcytosine in genomic DNA by sheathless interfaced capillary electrophoresis-mass spectrometry. Chem Commun (Camb) 2016; 52:2698-700. [PMID: 26753520 DOI: 10.1039/c5cc10155g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A newly developed sheathless interface for capillary electrophoresis-mass spectrometry, using a porous tip sprayer, was first applied for highly sensitive determination of cytosine modifications. The system performed well in identification and quantification of both 5-methylcytosine and 5-hydroxymethylcytosine using only 125 pg (∼20 cells) genomic DNA samples.
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Affiliation(s)
- Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Xiao-Hui Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Ji Nie
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Hong-Xu Chen
- Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, Beijing, P. R. China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
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59
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Parr MK, Montacir O, Montacir H. Physicochemical characterization of biopharmaceuticals. J Pharm Biomed Anal 2016; 130:366-389. [DOI: 10.1016/j.jpba.2016.05.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
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60
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Štěpánová S, Kašička V. Recent applications of capillary electromigration methods to separation and analysis of proteins. Anal Chim Acta 2016; 933:23-42. [DOI: 10.1016/j.aca.2016.06.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/10/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
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61
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Lombard-Banek C, Reddy S, Moody SA, Nemes P. Label-free Quantification of Proteins in Single Embryonic Cells with Neural Fate in the Cleavage-Stage Frog (Xenopus laevis) Embryo using Capillary Electrophoresis Electrospray Ionization High-Resolution Mass Spectrometry (CE-ESI-HRMS). Mol Cell Proteomics 2016; 15:2756-68. [PMID: 27317400 PMCID: PMC4974349 DOI: 10.1074/mcp.m115.057760] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/16/2016] [Indexed: 12/12/2022] Open
Abstract
Quantification of protein expression in single cells promises to advance a systems-level understanding of normal development. Using a bottom-up proteomic workflow and multiplexing quantification by tandem mass tags, we recently demonstrated relative quantification between single embryonic cells (blastomeres) in the frog (Xenopus laevis) embryo. In this study, we minimize derivatization steps to enhance analytical sensitivity and use label-free quantification (LFQ) for single Xenopus cells. The technology builds on a custom-designed capillary electrophoresis microflow-electrospray ionization high-resolution mass spectrometry platform and LFQ by MaxLFQ (MaxQuant). By judiciously tailoring performance to peptide separation, ionization, and data-dependent acquisition, we demonstrate an ∼75-amol (∼11 nm) lower limit of detection and quantification for proteins in complex cell digests. The platform enabled the identification of 438 nonredundant protein groups by measuring 16 ng of protein digest, or <0.2% of the total protein contained in a blastomere in the 16-cell embryo. LFQ intensity was validated as a quantitative proxy for protein abundance. Correlation analysis was performed to compare protein quantities between the embryo and n = 3 different single D11 blastomeres, which are fated to develop into the nervous system. A total of 335 nonredundant protein groups were quantified in union between the single D11 cells spanning a 4 log-order concentration range. LFQ and correlation analysis detected expected proteomic differences between the whole embryo and blastomeres, and also found translational differences between individual D11 cells. LFQ on single cells raises exciting possibilities to study gene expression in other cells and models to help better understand cell processes on a systems biology level.
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Affiliation(s)
| | - Sushma Reddy
- From the ‡Department of Chemistry and ¶Thomas Jefferson High School for Science and Technology, Alexandria, Virginia
| | - Sally A Moody
- §Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC
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62
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Zhu G, Sun L, Dovichi NJ. Dynamic pH junction preconcentration in capillary electrophoresis- electrospray ionization-mass spectrometry for proteomics analysis. Analyst 2016; 141:5216-20. [PMID: 27460877 DOI: 10.1039/c6an01140c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Capillary zone electrophoresis (CZE)-electrospray ionization (ESI)-mass spectrometry (MS) is an interesting complimentary technique to reversed phase liquid chromatography (RPLC)-ESI-MS for proteomics research. However, the low sample loading capacity of CZE (typically a few nL) can limit its application for large-scale proteomics. A number of on-line sample preconcentration methods have been developed to increase sample loading volumes. This review considers the dynamic pH junction as a simple on-line sample preconcentration method; this method is well suited for amphiprotic analytes. In the pH junction, these analytes are suspended in a basic buffer, injected by pressure into the capillary, and separated in an acidic background electrolyte, with no changes in either CZE-MS operations or instrumentation. We have demonstrated that the dynamic pH junction method can improve the sample loading volume to sub-μL volumes without significant loss of separation capacity for bottom-up proteomic analysis. The dynamic pH junction based CZE-ESI-MS system has been applied for a number of complex biological samples, including the E. coli proteome, impurities in recombinant antibody therapeutics, and the characterization of the phosphoproteome from a human cell line.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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63
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Sun L, Dubiak KM, Peuchen EH, Zhang Z, Zhu G, Huber PW, Dovichi NJ. Single Cell Proteomics Using Frog (Xenopus laevis) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content. Anal Chem 2016; 88:6653-7. [PMID: 27314579 DOI: 10.1021/acs.analchem.6b01921] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Single cell analysis is required to understand cellular heterogeneity in biological systems. We propose that single cells (blastomeres) isolated from early stage invertebrate, amphibian, or fish embryos are ideal model systems for the development of technologies for single cell analysis. For these embryos, although cell cleavage is not exactly symmetric, the content per blastomere decreases roughly by half with each cell division, creating a geometric progression in cellular content. This progression forms a ladder of single-cell targets for the development of successively higher sensitivity instruments. In this manuscript, we performed bottom-up proteomics on single blastomeres isolated by microdissection from 2-, 4-, 8-, 16-, 32-, and 50-cell Xenopus laevis (African clawed frog) embryos. Over 1 400 protein groups were identified in single-run reversed-phase liquid chromatography-electrospray ionization-tandem mass spectrometry from single balstomeres isolated from a 16-cell embryo. When the mass of yolk-free proteins in single blastomeres decreased from ∼0.8 μg (16-cell embryo) to ∼0.2 μg (50-cell embryo), the number of protein group identifications declined from 1 466 to 644. Around 800 protein groups were quantified across four blastomeres isolated from a 16-cell embryo. By comparing the protein expression among different blastomeres, we observed that the blastomere-to-blastomere heterogeneity in 8-, 16-, 32-, and 50-cell embryos increases with development stage, presumably due to cellular differentiation. These results suggest that comprehensive quantitative proteomics on single blastomeres isolated from these early stage embryos can provide valuable insights into cellular differentiation and organ development.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Kyle M Dubiak
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Elizabeth H Peuchen
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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64
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Kammeijer GSM, Kohler I, Jansen BC, Hensbergen PJ, Mayboroda OA, Falck D, Wuhrer M. Dopant Enriched Nitrogen Gas Combined with Sheathless Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry for Improved Sensitivity and Repeatability in Glycopeptide Analysis. Anal Chem 2016; 88:5849-56. [PMID: 27119460 DOI: 10.1021/acs.analchem.6b00479] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the last years, numerous strategies have been proposed to enhance both ionization efficiency and spray stability in electrospray ionization (ESI), in particular for nanospray applications. In nano-liquid chromatography-mass spectrometry (nano-LC-ESI-MS), a better ESI performance has been observed when a coaxial gas flow is added around the ESI emitter. Moreover, enrichment of the gas with an organic dopant has led to an improved desolvation and ionization efficiency with an overall enhanced sensitivity. In this study, the use of a dopant enriched nitrogen (DEN)-gas combined with sheathless capillary electrophoresis (CE)-ESI-MS was evaluated for glycopeptide analysis. Using acetonitrile as a dopant, an increased sensitivity was observed compared to conventional sheathless CE-ESI-MS. Up to 25-fold higher sensitivities for model glycopeptides were obtained, allowing for limits of detection unachieved by state-of-the-art nano-LC-ESI-MS. The effect of DEN-gas on the repeatability and intermediate precision was also investigated. When compared to previously reported nano-LC-ESI-MS measurements, similar values were found for CE-ESI-MS with DEN-gas. The enhanced repeatability fosters the use of DEN-gas sheathless CE-ESI-MS in protein glycosylation analysis, where precision is essential. The use of DEN-gas opens new avenues for highly sensitive sheathless CE-ESI-MS approaches in glycoproteomics research, by significantly improving sensitivity and precision.
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Affiliation(s)
- Guinevere S M Kammeijer
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Isabelle Kohler
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Bas C Jansen
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Paul J Hensbergen
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Oleg A Mayboroda
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - David Falck
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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65
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Ibrahim M, Gahoual R, Enkler L, Becker HD, Chicher J, Hammann P, François YN, Kuhn L, Leize-Wagner E. Improvement of Mitochondria Extract from Saccharomyces cerevisiae Characterization in Shotgun Proteomics Using Sheathless Capillary Electrophoresis Coupled to Tandem Mass Spectrometry. J Chromatogr Sci 2016; 54:653-63. [PMID: 26860395 PMCID: PMC4885408 DOI: 10.1093/chromsci/bmw005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/11/2015] [Indexed: 12/16/2022]
Abstract
In this work, we describe the characterization of a quantity-limited sample (100 ng) of yeast mitochondria by shotgun bottom-up proteomics. Sample characterization was carried out by sheathless capillary electrophoresis, equipped with a high sensitivity porous tip and coupled to tandem mass spectrometry (CESI-MS-MS) and concomitantly with a state-of-art nano flow liquid chromatography coupled to a similar mass spectrometry (MS) system (nanoLC-MS-MS). With single injections, both nanoLC-MS-MS and CESI-MS-MS 60 min-long separation experiments allowed us to identify 271 proteins (976 unique peptides) and 300 proteins (1,765 unique peptides) respectively, demonstrating a significant specificity and complementarity in identification depending on the physicochemical separation employed. Such complementary, maximizing the number of analytes detected, presents a powerful tool to deepen a biological sample's proteomic characterization. A comprehensive study of the specificity provided by each separating technique was also performed using the different properties of the identified peptides: molecular weight, mass-to-charge ratio (m/z), isoelectric point (pI), sequence coverage or MS-MS spectral quality enabled to determine the contribution of each separation. For example, CESI-MS-MS enables to identify larger peptides and eases the detection of those having extreme pI without impairing spectral quality. The addition of peptides, and therefore proteins identified by both techniques allowed us to increase significantly the sequence coverages and then the confidence of characterization. In this study, we also demonstrated that the two yeast enolase isoenzymes were both characterized in the CESI-MS-MS data set. The observation of discriminant proteotypic peptides is facilitated when a high number of precursors with high-quality MS-MS spectra are generated.
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Affiliation(s)
- Marianne Ibrahim
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
| | - Rabah Gahoual
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
| | - Ludovic Enkler
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Hubert Dominique Becker
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Johana Chicher
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FRC 1589, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FRC 1589, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FRC 1589, Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, 67008 Strasbourg, France
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66
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Heemskerk AAM, Deelder AM, Mayboroda OA. CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications. MASS SPECTROMETRY REVIEWS 2016; 35:259-271. [PMID: 24852088 DOI: 10.1002/mas.21432] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
With the development of more sensitive hyphenation strategies for capillary electrophoresis-electrospray-mass spectrometry the technique has reemerged as technique with high separation power combined with high sensitivity in the analysis of peptides and protein digests. This review will discuss the newly developed hyphenation strategies for CE-ESI-MS and their application in bottom-up proteomics as well as the applications in the same time span, 2009 to present, using co-axial sheathliquid. Subsequently all separate aspects in the development of a CE-ESI-MS method for bottom-up proteomics shall be discussed, highlighting certain applications and discussing pros and cons of the various choices. The separation of peptides in a capillary electrophoresis system is discussed including the great potential for modeling of this migration of peptides due to the simple electrophoretic separation process. Furthermore, the technical aspects of method development are discussed, namely; background electrolyte choice, coating of the separation capillary and chosen loading method. Finally, conclusions and an outlook on future developments in the field of bottom-up proteomics by CE-ESI-MS will be provided.
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Affiliation(s)
- Anthonius A M Heemskerk
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
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67
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Gahoual R, Beck A, François YN, Leize-Wagner E. Independent highly sensitive characterization of asparagine deamidation and aspartic acid isomerization by sheathless CZE-ESI-MS/MS. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:150-158. [PMID: 26889931 DOI: 10.1002/jms.3735] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/02/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Amino acids residues are commonly submitted to various physicochemical modifications occurring at physiological pH and temperature. Post-translational modifications (PTMs) require comprehensive characterization because of their major influence on protein structure and involvement in numerous in vivo process or signaling. Mass spectrometry (MS) has gradually become an analytical tool of choice to characterize PTMs; however, some modifications are still challenging because of sample faint modification levels or difficulty to separate an intact peptide from modified counterparts before their transfer to the ionization source. Here, we report the implementation of capillary zone electrophoresis coupled to electrospray ionization tandem mass spectrometry (CZE-ESI-MS/MS) by the intermediate of a sheathless interfacing for independent and highly sensitive characterization of asparagine deamidation (deaN) and aspartic acid isomerization (isoD). CZE selectivity regarding deaN and isoD was studied extensively using different sets of synthetic peptides based on actual tryptic peptides. Results demonstrated CZE ability to separate the unmodified peptide from modified homologous exhibiting deaN, isoD or both independently with a resolution systematically superior to 1.29. Developed CZE-ESI-MS/MS method was applied for the characterization of monoclonal antibodies and complex protein mixture. Conserved CZE selectivity could be demonstrated even for complex samples, and foremost results obtained showed that CZE selectivity is similar regardless of the composition of the peptide. Separation of modified peptides prior to the MS analysis allowed to characterize and estimate modification levels of the sample independently for deaN and isoD even for peptides affected by both modifications and, as a consequence, enables to distinguish the formation of l-aspartic acid or d-aspartic acid generated from deaN. Separation based on peptide modification allowed, as supported by the ESI efficiency provided by CZE-ESI-MS/MS properties, and enabled to characterize and estimate studied PTMs with an unprecedented sensitivity and proved the relevance of implementing an electrophoretic driven separation for MS-based peptide analysis.
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Affiliation(s)
- Rabah Gahoual
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (UdS-CNRS), Université de Strasbourg, Strasbourg, France
- Division of BioAnalytical Chemistry, AIMMS Research Group BioMolecular Analysis, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre, Saint-Julien-en-Genevois, France
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (UdS-CNRS), Université de Strasbourg, Strasbourg, France
| | - Emmanuelle Leize-Wagner
- Division of BioAnalytical Chemistry, AIMMS Research Group BioMolecular Analysis, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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68
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Zhao Y, Sun L, Knierman MD, Dovichi NJ. Fast separation and analysis of reduced monoclonal antibodies with capillary zone electrophoresis coupled to mass spectrometry. Talanta 2016; 148:529-33. [DOI: 10.1016/j.talanta.2015.11.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 12/18/2022]
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69
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Zhu G, Sun L, Dovichi NJ. Thermally-initiated free radical polymerization for reproducible production of stable linear polyacrylamide coated capillaries, and their application to proteomic analysis using capillary zone electrophoresis-mass spectrometry. Talanta 2016; 146:839-43. [PMID: 26695337 PMCID: PMC4690009 DOI: 10.1016/j.talanta.2015.06.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 02/03/2023]
Abstract
Proteomic analysis using capillary zone electrophoresis (CZE) typically is performed with linear polyacrylamide (LPA) coated capillaries. These capillaries both minimize the adsorption of peptides and proteins to the inner wall of the capillary and decrease electroosmosis, which increases the separation capacity. LPA coating protocols were first reported by Hjerten in 1985. Conventional LPA production is based on the use of tetramethylethylenediamine (TEMED) to catalyze the free-radical polymerization that couples acrylamide to a capillary wall that has been pretreated with γ-methacryloxypropyltrimethoxysilane. The treated capillary is filled with a mixture of monomer, TEMED, and ammonium persulfate; free radical polymerization forms the LPA coating. Over many years, we have observed significant variation in the electroosmotic properties of commercial LPA coated capillaries both along the capillary length and between lots. We believe this variation is due to differences in the time between initiation of the reaction and the filling of the capillary. Here, we report a simple method for the generation of very stable and reproducible coatings. In this protocol, the monomer mixture and an ammonium persulfate initiator are introduced into the capillary without TEMED initiator. The mixture is stable and does not begin polymerization at room temperature. The filled capillary is then heated in a water bath to initiate polymerization in a well-controlled manner. A mixture of four standard proteins was used to evaluate the coating performance. Compared with commercialized LPA capillaries, our LPA capillaries generate much better separation performance and superior protein peak shape in CZE analysis. We also analyzed an intact antibody (MW 150K) by CZE-MS with the new LPA capillary in triplicate runs. The intact antibody generated a Gaussian-shaped electrophoresis peak with 1.2% relative standard deviation in migration time and 8.5% in base peak intensity. An automated CZE-MS system was used to generate 97 successive separations of a BSA tryptic digest over a 145-h period. Separation efficiency averaged over 100,000 theoretical plates across this period with no systematic variation. The LPA coating protocol had excellent batch-to-batch reproducibility with relative standard deviation in migration time<7%, and in separation window<1%.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556, USA
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70
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Benavente F, Medina-Casanellas S, Giménez E, Sanz-Nebot V. On-Line Solid-Phase Extraction Capillary Electrophoresis Mass Spectrometry for Preconcentration and Clean-Up of Peptides and Proteins. Methods Mol Biol 2016; 1466:67-84. [PMID: 27473482 DOI: 10.1007/978-1-4939-4014-1_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of the major drawbacks of capillary electrophoresis (CE) and other microscale separation techniques, for the analysis of low abundant peptides and proteins in complex samples, are the poor concentration limits of detection. Several strategies have been developed to improve CE sensitivity. Here, we describe an on-line solid-phase extraction capillary electrophoresis mass spectrometry method with a commercial C18 sorbent for clean-up and preconcentration of neuropeptides from highly diluted biological samples.
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Affiliation(s)
- Fernando Benavente
- Department of Analytical Chemistry, University of Barcelona, Av. Diagonal 647, Barcelona, 08028, Spain.
| | - Silvia Medina-Casanellas
- Department of Analytical Chemistry, University of Barcelona, Av. Diagonal 647, Barcelona, 08028, Spain
| | - Estela Giménez
- Department of Analytical Chemistry, University of Barcelona, Av. Diagonal 647, Barcelona, 08028, Spain
| | - Victoria Sanz-Nebot
- Department of Analytical Chemistry, University of Barcelona, Av. Diagonal 647, Barcelona, 08028, Spain
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71
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Affiliation(s)
- Rachel K Harstad
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Alexander C Johnson
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Megan M Weisenberger
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Michael T Bowser
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
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72
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Sun L, Zhu G, Yan X, Zhang Z, Wojcik R, Champion MM, Dovichi NJ. Capillary zone electrophoresis for bottom-up analysis of complex proteomes. Proteomics 2015; 16:188-96. [PMID: 26508368 DOI: 10.1002/pmic.201500339] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/30/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Capillary zone electrophoresis (CZE) is emerging as a useful tool in proteomic analysis. Interest arises from dramatic improvements in performance that result from improvements in the background electrolyte used for the separation, the incorporation of advanced sample injection methods, the development of robust and sensitive electrospray interfaces, and the coupling with Orbitrap mass spectrometers with high resolution and sensitivity. The combination of these technologies produces performance that is rapidly approaching the performance of UPLC-based methods for microgram samples and exceeds the performance of UPLC-based methods for mid- to low nanogram samples. These systems now produce over 10 000 peptide IDs in a single 100-min analysis of the HeLa proteome.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Roza Wojcik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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73
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Zhang Z, Sun L, Zhu G, Cox OF, Huber PW, Dovichi NJ. Nearly 1000 Protein Identifications from 50 ng of Xenopus laevis Zygote Homogenate Using Online Sample Preparation on a Strong Cation Exchange Monolith Based Microreactor Coupled with Capillary Zone Electrophoresis. Anal Chem 2015; 88:877-82. [PMID: 26670623 DOI: 10.1021/acs.analchem.5b03496] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A sulfonate-silica hybrid strong cation exchange monolith microreactor was synthesized and coupled to a linear polyacrylamide coated capillary for online sample preparation and capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) bottom-up proteomic analysis. The protein sample was loaded onto the microreactor in an acidic buffer. After online reduction, alkylation, and digestion with trypsin, the digests were eluted with 200 mM ammonium bicarbonate at pH 8.2 for CZE-MS/MS analysis using 1 M acetic acid as the background electrolyte. This combination of basic elution and acidic background electrolytes results in both sample stacking and formation of a dynamic pH junction. 369 protein groups and 1274 peptides were identified from 50 ng of Xenopus laevis zygote homogenate, which is comparable with an offline sample preparation method, but the time required for sample preparation was decreased from over 24 h to less than 40 min. Dramatically improved performance was produced by coupling the reactor to a longer separation capillary (∼100 cm) and a Q Exactive HF mass spectrometer. 975 protein groups and 3749 peptides were identified from 50 ng of Xenopus protein using the online sample preparation method.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Olivia F Cox
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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75
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Barroso A, Giménez E, Benavente F, Barbosa J, Sanz-Nebot V. Improved tryptic digestion assisted with an acid-labile anionic surfactant for the separation and characterization of glycopeptide glycoforms of a proteolytic-resistant glycoprotein by capillary electrophoresis time-of-flight mass spectrometry. Electrophoresis 2015; 37:987-97. [DOI: 10.1002/elps.201500255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/21/2015] [Accepted: 08/07/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Albert Barroso
- Department of Analytical Chemistry; University of Barcelona; Barcelona Spain
| | - Estela Giménez
- Department of Analytical Chemistry; University of Barcelona; Barcelona Spain
| | - Fernando Benavente
- Department of Analytical Chemistry; University of Barcelona; Barcelona Spain
| | - José Barbosa
- Department of Analytical Chemistry; University of Barcelona; Barcelona Spain
| | - Victoria Sanz-Nebot
- Department of Analytical Chemistry; University of Barcelona; Barcelona Spain
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76
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Ludwig KR, Sun L, Zhu G, Dovichi NJ, Hummon AB. Over 2300 phosphorylated peptide identifications with single-shot capillary zone electrophoresis-tandem mass spectrometry in a 100 min separation. Anal Chem 2015; 87:9532-7. [PMID: 26399161 PMCID: PMC4605816 DOI: 10.1021/acs.analchem.5b02457] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ultraperformance liquid chromatography (UPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) is typically employed for phosphoproteome analysis. Alternatively, capillary zone electrophoresis (CZE)-ESI-MS/MS has great potential for phosphoproteome analysis due to the significantly different migration times of phosphorylated and unphosphorylated forms of peptides. In this work, we systematically compared UPLC-MS/MS and CZE-MS/MS for phosphorylated peptide identifications (IDs) using an enriched phosphoproteome from the MCF-10A cell line. When the sample loading amount of UPLC was 10 times higher than that of CZE (2 μg vs 200 ng), UPLC generated more phosphorylated peptide IDs than CZE (3313 vs 1783). However, when the same sample loading amounts were used for CZE and UPLC (2-200 ng), CZE-MS/MS consistently and significantly outperformed UPLC-MS/MS in terms of phosphorylated peptide and total peptide IDs. This superior performance is most likely due to the higher peptide intensity generated by CZE-MS/MS. More importantly, compared with UPLC data from a 2 μg sample, CZE-MS/MS can identify over 500 unique phosphorylated peptides from a 200 ng sample, suggesting that CZE and UPLC are complementary for phosphorylated peptide IDs. With further improved loading capacity via a dynamic pH junction method, 2313 phosphorylated peptides were identified with single-shot CZE-MS/MS in a 100 min analysis. This number of phosphorylated peptide IDs is over 1 order of magnitude higher than the number of phosphorylated peptide IDs previously reported by single-shot CZE-MS/MS.
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Affiliation(s)
- Katelyn R. Ludwig
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
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77
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Zhang Z, Sun L, Zhu G, Yan X, Dovichi NJ. Integrated strong cation-exchange hybrid monolith coupled with capillary zone electrophoresis and simultaneous dynamic pH junction for large-volume proteomic analysis by mass spectrometry. Talanta 2015; 138:117-122. [PMID: 25863379 PMCID: PMC4394190 DOI: 10.1016/j.talanta.2015.01.040] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 10/24/2022]
Abstract
A sulfonate-silica hybrid strong cation-exchange (SCX) monolith was synthesized at the proximal end of a capillary zone electrophoresis column and used for on-line solid-phase extraction (SPE) sample preconcentration. Sample was prepared in an acidic buffer and deposited onto the SCX-SPE monolith and eluted using a basic buffer. Electrophoresis was performed in an acidic buffer. This combination of buffers results in formation of a dynamic pH junction, which allows use of relatively large elution buffer volume while maintaining peak efficiency and resolution. All experiments were performed with a 50 µm ID capillary, a 1cm long SCX-SPE monolith, a 60cm long separation capillary, and a electrokinetically pumped nanospray interface. The volume of the capillary is 1.1 µL. By loading 21 µL of a 1×10(-7) M angiotensin II solution, an enrichment factor of 3000 compared to standard electrokinetic injection was achieved on this platform while retaining efficient electrophoretic performance (N=44,000 plates). The loading capacity of the sulfonate SCX hybrid monolith was determined to be ~15 pmol by frontal analysis with 10(-5) M angiotensin II. The system was also applied to the analysis of a 10(-4) mg/mL bovine serum albumin tryptic digest; the protein coverage was 12% and 11 peptides were identified. Finally, by loading 5.5 µL of a 10(-3) mg/mL E. coli digest, 109 proteins and 271 peptides were identified in a 20 min separation; the median separation efficiency generated by these peptides was 25,000 theoretical plates.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA.
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78
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Faserl K, Kremser L, Müller M, Teis D, Lindner HH. Quantitative proteomics using ultralow flow capillary electrophoresis-mass spectrometry. Anal Chem 2015; 87:4633-40. [PMID: 25839223 PMCID: PMC4423236 DOI: 10.1021/acs.analchem.5b00312] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
In this work, we evaluate the incorporation
of an ultralow flow
interface for coupling capillary electrophoresis (CE) and mass spectrometry
(MS), in combination with reversed-phase high-pressure liquid chromatography
(HPLC) fractionation as an alternate workflow for quantitative proteomics.
Proteins, extracted from a SILAC (stable isotope labeling by amino
acids in cell culture) labeled and an unlabeled yeast strain were
mixed and digested enzymatically in solution. The resulting peptides
were fractionated using RP-HPLC and analyzed by CE–MS yielding
a total of 28 538 quantified peptides that correspond to 3 272
quantified proteins. CE–MS analysis was performed using a neutral
capillary coating, providing the highest separation efficiency at
ultralow flow conditions (<10 nL/min). Moreover, we were able to
demonstrate that CE–MS is a powerful method for the identification
of low-abundance modified peptides within the same sample. Without
any further enrichment strategies, we succeeded in quantifying 1 371
phosphopeptides present in the CE–MS data set and found 49
phosphopeptides to be differentially regulated in the two yeast strains.
Including acetylation, phosphorylation, deamidation, and oxidized
forms, a total of 8 106 modified peptides could be identified
in addition to 33 854 unique peptide sequences found. The work
presented here shows the first quantitative proteomics approach that
combines SILAC labeling with CE–MS analysis.
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Affiliation(s)
- Klaus Faserl
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Leopold Kremser
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Martin Müller
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - David Teis
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Herbert H Lindner
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
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79
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Zhang Z, Yan X, Sun L, Zhu G, Dovichi NJ. Detachable strong cation exchange monolith, integrated with capillary zone electrophoresis and coupled with pH gradient elution, produces improved sensitivity and numbers of peptide identifications during bottom-up analysis of complex proteomes. Anal Chem 2015; 87:4572-7. [PMID: 25822566 DOI: 10.1021/acs.analchem.5b00789] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A detachable sulfonate-silica hybrid strong cation-exchange monolith was synthesized in a fused silica capillary, and used for solid phase extraction with online pH gradient elution during capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) proteomic analysis. Tryptic digests were prepared in 50 mM formic acid and loaded onto the strong cation-exchange monolith. Fractions were eluted using a series of buffers with lower concentration but higher pH values than the 50 mM formic acid background electrolyte. This combination of elution and background electrolytes results in both sample stacking and formation of a dynamic pH junction and allows use of relatively large elution buffer volumes while maintaining reasonable peak efficiency and resolution. A series of five pH bumps were applied to elute E. coli tryptic peptides from the monolith, followed by analysis using CZE coupled to an LTQ-Orbitrap Velos mass spectrometer; 799 protein groups and 3381 peptides were identified from 50 ng of the digest in a 2.5 h analysis, which approaches the identification rate for this organism that was obtained with an Orbitrap Fusion. We attribute the improved numbers of peptide and protein identifications to the efficient fractionation by the online pH gradient elution, which decreased the complexity of the sample in each elution step and improved the signal intensity of low abundance peptides. We also performed a comparative analysis using a nanoACQUITY UltraPerformance LCH system. Similar numbers of protein and peptide identifications were produced by the two methods. Protein identifications showed significant overlap between the two methods, whereas peptide identifications were complementary.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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80
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Sun L, Zhu G, Zhang Z, Mou S, Dovichi NJ. Third-generation electrokinetically pumped sheath-flow nanospray interface with improved stability and sensitivity for automated capillary zone electrophoresis-mass spectrometry analysis of complex proteome digests. J Proteome Res 2015; 14:2312-21. [PMID: 25786131 DOI: 10.1021/acs.jproteome.5b00100] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have reported a set of electrokinetically pumped sheath flow nanoelectrospray interfaces to couple capillary zone electrophoresis with mass spectrometry. A separation capillary is threaded through a cross into a glass emitter. A side arm provides fluidic contact with a sheath buffer reservoir that is connected to a power supply. The potential applied to the sheath buffer drives electro-osmosis in the emitter to pump the sheath fluid at nanoliter per minute rates. Our first-generation interface placed a flat-tipped capillary in the emitter. Sensitivity was inversely related to orifice size and to the distance from the capillary tip to the emitter orifice. A second-generation interface used a capillary with an etched tip that allowed the capillary exit to approach within a few hundred micrometers of the emitter orifice, resulting in a significant increase in sensitivity. In both the first- and second-generation interfaces, the emitter diameter was typically 8 μm; these narrow orifices were susceptible to plugging and tended to have limited lifetime. We now report a third-generation interface that employs a larger diameter emitter orifice with very short distance between the capillary tip and the emitter orifice. This modified interface is much more robust and produces much longer lifetime than our previous designs with no loss in sensitivity. We evaluated the third-generation interface for a 5000 min (127 runs, 3.5 days) repetitive analysis of bovine serum albumin digest using an uncoated capillary. We observed a 10% relative standard deviation in peak area, an average of 160,000 theoretical plates, and very low carry-over (much less than 1%). We employed a linear-polyacrylamide (LPA)-coated capillary for single-shot, bottom-up proteomic analysis of 300 ng of Xenopus laevis fertilized egg proteome digest and identified 1249 protein groups and 4038 peptides in a 110 min separation using an LTQ-Orbitrap Velos mass spectrometer; peak capacity was ∼330. The proteome data set using this third-generation interface-based CZE-MS/MS is similar in size to that generated using a commercial ultraperformance liquid chromatographic analysis of the same sample with the same mass spectrometer and similar analysis time.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Si Mou
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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81
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Pontillo C, Filip S, Borràs DM, Mullen W, Vlahou A, Mischak H. CE-MS-based proteomics in biomarker discovery and clinical application. Proteomics Clin Appl 2015; 9:322-34. [DOI: 10.1002/prca.201400115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/10/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Claudia Pontillo
- Department of R&D; Mosaiques Diagnostics GmbH; Hanover Germany
- Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Szymon Filip
- Charité-Universitätsmedizin Berlin; Berlin Germany
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
| | - Daniel M. Borràs
- Department of R&D; ServiceXS; Leiden The Netherlands
- Institut National de la Santé et de la Recherche Médicale (INSERM); Institute of Cardiovascular and Metabolic Disease; Toulouse France
- Université Toulouse III Paul-Sabatier; Toulouse France
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
| | - Antonia Vlahou
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
- School of Biomedical and Healthcare Sciences; Plymouth University; Plymouth UK
| | - Harald Mischak
- Department of R&D; Mosaiques Diagnostics GmbH; Hanover Germany
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
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82
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Parker SJ, Raedschelders K, Van Eyk JE. Emerging proteomic technologies for elucidating context-dependent cellular signaling events: A big challenge of tiny proportions. Proteomics 2015; 15:1486-502. [PMID: 25545106 DOI: 10.1002/pmic.201400448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/31/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Aberrant cell signaling events either drive or compensate for nearly all pathologies. A thorough description and quantification of maladaptive signaling flux in disease is a critical step in drug development, and complex proteomic approaches can provide valuable mechanistic insights. Traditional proteomics-based signaling analyses rely heavily on in vitro cellular monoculture. The characterization of these simplified systems generates a rich understanding of the basic components and complex interactions of many signaling networks, but they cannot capture the full complexity of the microenvironments in which pathologies are ultimately made manifest. Unfortunately, techniques that can directly interrogate signaling in situ often yield mass-limited starting materials that are incompatible with traditional proteomics workflows. This review provides an overview of established and emerging techniques that are applicable to context-dependent proteomics. Analytical approaches are illustrated through recent proteomics-based studies in which selective sample acquisition strategies preserve context-dependent information, and where the challenge of minimal starting material is met by optimized sensitivity and coverage. This review is organized into three major technological themes: (i) LC methods in line with MS; (ii) antibody-based approaches; (iii) MS imaging with a discussion of data integration and systems modeling. Finally, we conclude with future perspectives and implications of context-dependent proteomics.
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Affiliation(s)
- Sarah J Parker
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA; Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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83
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Breadmore MC, Tubaon RM, Shallan AI, Phung SC, Abdul Keyon AS, Gstoettenmayr D, Prapatpong P, Alhusban AA, Ranjbar L, See HH, Dawod M, Quirino JP. Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2012-2014). Electrophoresis 2015; 36:36-61. [DOI: 10.1002/elps.201400420] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 09/25/2014] [Accepted: 09/25/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Michael C. Breadmore
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Ria Marni Tubaon
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Aliaa I. Shallan
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Sui Ching Phung
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Aemi S. Abdul Keyon
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
- Faculty of Science; Department of Chemistry, Universiti Teknologi Malaysia; Johor Malaysia
| | - Daniel Gstoettenmayr
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Pornpan Prapatpong
- Faculty of Pharmacy; Department of Pharmaceutical Chemistry, Mahidol University; Rajathevee Bangkok Thailand
| | - Ala A. Alhusban
- Faculty of Health Sciences, School of Pharmacy; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Leila Ranjbar
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Hong Heng See
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
- Ibnu Sina Institute for Fundamental Science Studies; Universiti Teknologi Malaysia; Johor Malaysia
| | - Mohamed Dawod
- Department of Chemistry; University of Michigan; Ann Arbor MI USA
- Faculty of Pharmacy; Department of Analytical Chemistry, Al-Azhar University; Cairo Egypt
| | - Joselito P. Quirino
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
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84
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Han X, Wang Y, Aslanian A, Fonslow B, Graczyk B, Davis TN, Yates JR. In-line separation by capillary electrophoresis prior to analysis by top-down mass spectrometry enables sensitive characterization of protein complexes. J Proteome Res 2014; 13:6078-86. [PMID: 25382489 PMCID: PMC4262260 DOI: 10.1021/pr500971h] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Intact
protein analysis via top-down mass spectrometry (MS) provides
a bird’s eye view over the protein complexes and complex protein
mixtures with the unique capability of characterizing protein variants,
splice isoforms, and combinatorial post-translational modifications
(PTMs). Here we applied capillary electrophoresis (CE) through a sheathless
CE–electrospray ionization interface coupled to an LTQ Velos
Orbitrap Elite mass spectrometer to analyze the Dam1 complex from Saccharomyces cerevisiae. We achieved a 100-fold
increase in sensitivity compared to a reversed-phase liquid chromatography
coupled MS analysis of recombinant Dam1 complex with a total loading
of 2.5 ng (12 amol). N-terminal processing forms of individual subunits
of the Dam1 complex were observed as well as their phosphorylation
stoichiometry upon Mps1p kinase treatment.
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Affiliation(s)
- Xuemei Han
- Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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85
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Klepárník K. Recent advances in combination of capillary electrophoresis with mass spectrometry: Methodology and theory. Electrophoresis 2014; 36:159-78. [DOI: 10.1002/elps.201400392] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/11/2014] [Accepted: 09/11/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry; Academy of Sciences of the Czech Republic; Brno Czech Republic
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86
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Han X, Wang Y, Aslanian A, Bern M, Lavallée-Adam M, Yates JR. Sheathless capillary electrophoresis-tandem mass spectrometry for top-down characterization of Pyrococcus furiosus proteins on a proteome scale. Anal Chem 2014; 86:11006-12. [PMID: 25346219 PMCID: PMC4238646 DOI: 10.1021/ac503439n] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
Intact protein analysis via top-down
mass spectrometry (MS) provides
the unique capability of fully characterizing protein isoforms and
combinatorial post-translational modifications (PTMs) compared to
the bottom-up MS approach. Front-end protein separation poses a challenge
for analyzing complex mixtures of intact proteins on a proteomic scale.
Here we applied capillary electrophoresis (CE) through a sheathless
capillary electrophoresis-electrospray ionization (CESI) interface
coupled to an Orbitrap Elite mass spectrometer to profile the proteome
from Pyrococcus furiosus. CESI-top-down MS analysis
of Pyrococcus furiosus cell lysate identified 134
proteins and 291 proteoforms with a total sample consumption of 270
ng in 120 min of total analysis time. Truncations and various PTMs
were detected, including acetylation, disulfide bonds, oxidation,
glycosylation, and hypusine. This is the largest scale analysis of
intact proteins by CE-top-down MS to date.
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Affiliation(s)
- Xuemei Han
- Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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87
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Barroso A, Giménez E, Benavente F, Barbosa J, Sanz-Nebot V. Modelling the electrophoretic migration behaviour of peptides and glycopeptides from glycoprotein digests in capillary electrophoresis-mass spectrometry. Anal Chim Acta 2014; 854:169-77. [PMID: 25479881 DOI: 10.1016/j.aca.2014.10.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/08/2014] [Accepted: 10/26/2014] [Indexed: 10/24/2022]
Abstract
In this study, the classical semiempirical relationships between the electrophoretic mobility and the charge-to-mass ratio (me vs. q/M(α)) were used to model the migration behaviour of peptides and glycopeptides originated from the digestion of recombinant human erythropoietin (rhEPO), a biologically and therapeutically relevant glycoprotein. The Stoke's law (α=1/3), the classical polymer model (α=1/2) and the Offord's surface law (α=2/3) were evaluated to predict migration of peptides and glycopeptides, with and without sialic acids (SiA), in rhEPO digested with trypsin and trypsin-neuraminidase. The Stoke's law resulted in better correlations for the set of peptides used to evaluate the models, while glycopeptides fitted better with the classical polymer model. Once predicted migration times with both models, it was easy to simulate their separation electropherogram. Results were later validated predicting migration and simulating separation of a different set of rhEPO glycopeptides and also human transferrin (Tf) peptides and glycopeptides. The excellent agreement between the experimental and the simulated electropherograms with rhEPO and Tf digests confirmed the potential applicability of this simple strategy to predict, in general, the peptide-glycopeptide electrophoretic map of any digested glycoprotein.
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Affiliation(s)
- Albert Barroso
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - José Barbosa
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
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88
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Sun L, Hebert AS, Yan X, Zhao Y, Westphall MS, Rush MJP, Zhu G, Champion MM, Coon JJ, Dovichi NJ. Over 10,000 peptide identifications from the HeLa proteome by using single-shot capillary zone electrophoresis combined with tandem mass spectrometry. Angew Chem Int Ed Engl 2014; 53:13931-3. [PMID: 25346227 DOI: 10.1002/anie.201409075] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 09/26/2014] [Indexed: 01/14/2023]
Abstract
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has recently attracted attention as a tool for shotgun proteomics. However, its performance for this analysis has so far fallen far below that of reversed-phase liquid chromatography (RPLC)-MS/MS. The use of a CZE method with a wide separation window (up to 90 min) and high peak capacity (ca. 300) is reported. This method was coupled to an Orbitrap Fusion mass spectrometer through an electrokinetically pumped sheath-flow interface for the analysis of complex proteome digests. Single-shot CZE-MS/MS lead to the identification of over 10 000 peptides and 2100 proteins from a HeLa cell proteome digest in approximately 100 min. This performance is nearly an order of magnitude better than earlier CZE studies and is within a factor of two to four of the state-of-the-art nano ultrahigh-pressure LC system.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 (USA)
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89
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Sun L, Hebert AS, Yan X, Zhao Y, Westphall MS, Rush MJP, Zhu G, Champion MM, Coon JJ, Dovichi NJ. Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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90
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Liu JX, Zhang YW, Yuan F, Chen HX, Zhang XX. Differential detection of Rhizoma coptidis by capillary electrophoresis electrospray ionization mass spectrometry with a nanospray interface. Electrophoresis 2014; 35:3258-63. [PMID: 25143257 DOI: 10.1002/elps.201400334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 08/06/2014] [Accepted: 08/12/2014] [Indexed: 01/07/2023]
Abstract
A lab prototype CE-nanospray-MS platform with a high sensitivity porous sprayer was successfully applied in differential identification of Rhizoma coptidis in this paper. To obtain a stable and reliable nanospray, detailed optimizations about emitter geometry, buffer composition, emitter position, and spray voltage, as well as emitter cleanliness were discussed. Results showed that the reproducibility and sensitivity for separations of alkaloid standards were satisfactory using CE-nanospray-MS, which were also compared to ultra-HPLC (UHPLC)-MS. Their signal responds were at the same order of magnitude (intensities: 0.8 - 1.5 × 10(8) vs. 3.8 - 6.2 × 10(8) ), even though a 2 nL injection for CE was 2500-fold lower than UHPLC (5 μL injection). The absolute LOD results of CE-MS showed a remarkable superiority (18-24 fg), equal to 1000-fold lower than that of UHPLC-MS. Principal component analysis (PCA) of adulterated R. coptidis showed that this protocol had the ability to profile and qualify complex herb medicines, which also created a great potential for evaluation and qualification of rare and valuable Chinese medicines in future.
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Affiliation(s)
- Jing-Xin Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry, Peking University, Beijing, P. R. China
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91
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Gahoual R, Busnel JM, Beck A, François YN, Leize-Wagner E. Full Antibody Primary Structure and Microvariant Characterization in a Single Injection Using Transient Isotachophoresis and Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry. Anal Chem 2014; 86:9074-81. [DOI: 10.1021/ac502378e] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Rabah Gahoual
- Laboratoire
de Spectrométrie de Masse des Interactions et des Systèmes
(LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, Strasbourg, France
| | | | - Alain Beck
- Centre d’immunologie
Pierre Fabre, Saint-Julien-en-Genevois, France
| | - Yannis-Nicolas François
- Laboratoire
de Spectrométrie de Masse des Interactions et des Systèmes
(LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, Strasbourg, France
| | - Emmanuelle Leize-Wagner
- Laboratoire
de Spectrométrie de Masse des Interactions et des Systèmes
(LSMIS), UDS-CNRS UMR 7140, Université de Strasbourg, Strasbourg, France
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92
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Sun L, Zhu G, Mou S, Zhao Y, Champion MM, Dovichi NJ. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for quantitative parallel reaction monitoring of peptide abundance and single-shot proteomic analysis of a human cell line. J Chromatogr A 2014; 1359:303-8. [PMID: 25082526 DOI: 10.1016/j.chroma.2014.07.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/25/2014] [Accepted: 07/10/2014] [Indexed: 12/14/2022]
Abstract
We coupled capillary zone electrophoresis (CZE) with an ultrasensitive electrokinetically pumped nanospray ionization source for tandem mass spectrometry (MS/MS) analysis of complex proteomes. We first used the system for the parallel reaction monitoring (PRM) analysis of angiotensin II spiked in 0.45mg/mL of bovine serum albumin (BSA) digest. A calibration curve was generated between the loading amount of angiotensin II and intensity of angiotensin II fragment ions. CZE-PRM generated a linear calibration curve across over 4.5 orders of magnitude dynamic range corresponding to angiotensin II loading amount from 2amole to 150fmole. The relative standard deviations (RSDs) of migration time were <4% and the RSDs of fragment ion intensity were ∼20% or less except 150fmole angiotensin II loading amount data (∼36% RSD). We further applied the system for the first bottom up proteomic analysis of a human cell line using CZE-MS/MS. We generated 283 protein identifications from a 1h long, single-shot CZE MS/MS analysis of the MCF7 breast cancer cell line digest, corresponding to ∼80ng loading amount. The MCF7 digest was fractionated using a C18 solid phase extraction column; single-shot analysis of a single fraction resulted in 468 protein identifications, which is by far the largest number of protein identifications reported for a mammalian proteomic sample using CZE.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Si Mou
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yimeng Zhao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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93
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Zhu G, Sun L, Yan X, Dovichi NJ. Bottom-up proteomics of Escherichia coli using dynamic pH junction preconcentration and capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry. Anal Chem 2014; 86:6331-6. [PMID: 24852005 PMCID: PMC4082393 DOI: 10.1021/ac5004486] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We report the use of the dynamic
pH junction based capillary zone
electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS)
for bottom-up proteomics with an electrokinetically pumped sheath-flow
nanospray capillary electrophoresis-mass spectrometry (CE-MS) interface
and both LTQ-XL and LTQ-Orbitrap-Velos mass spectrometers. Conventional
injection of 20 nL of a 1 mg/mL BSA digest identified 37 peptides
and produced 66% sequence coverage. In contrast, pH junction injection
of 130 nL (or larger) of a 0.05 mg/mL BSA digest identified 40 peptides
and produced 70% coverage using a pH 6.5 sample buffer and the LTQ.
A 20 nL conventional injection of a 1 mg/mL Escherichia coli digest identified 508 peptides and 199 proteins with the LTQ. A
400 nL pH junction injection of a 0.1 mg/mL E. coli digest identified 527 peptides and 179 proteins with the LTQ. Triplicate
technical replicates of a 0.01 mg/mL sample with 400-nL injection
volume using a pH junction identified 288 ± 9 peptides and 121
± 5 proteins with the LTQ. There was outstanding concordance
in migration time between the pH junction and normal injection. The
pH junction produced narrower peaks and significant concentration
for all but the most acidic components in the sample. Compared with
the conventional stacking method, the pH junction method can generate
comparable performance for small injection volume (20 nL) and significantly
better concentration performance for a large injection volume (200
nL). We also applied the pH junction to three intact standard proteins
and observed a >10× increase in peak intensity compared to
conventional
injection.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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94
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Zhu G, Sun L, Linkous T, Kernaghan D, McGivney JB, Dovichi NJ. Absolute quantitation of host cell proteins in recombinant human monoclonal antibodies with an automated CZE-ESI-MS/MS system. Electrophoresis 2014; 35:1448-52. [DOI: 10.1002/elps.201300545] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN USA
| | - Travis Linkous
- Department of Analytical Biotechnology; MedImmune; Gaithersburg MD USA
| | - Dawn Kernaghan
- Department of Analytical Biotechnology; MedImmune; Gaithersburg MD USA
| | - James B. McGivney
- Department of Analytical Biotechnology; MedImmune; Gaithersburg MD USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN USA
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95
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Robledo VR, Smyth WF. Review of the CE-MS platform as a powerful alternative to conventional couplings in bio-omics and target-based applications. Electrophoresis 2014; 35:2292-308. [DOI: 10.1002/elps.201300561] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Virginia Rodríguez Robledo
- Faculty of Pharmacy; Department of Analytical Chemistry and Food Technology; University of Castilla-La Mancha (UCLM); Albacete Spain
| | - William Franklin Smyth
- School of Pharmacy and Pharmaceutical Sciences; University of Ulster; Coleraine Northern Ireland UK
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96
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Kitagawa F, Otsuka K. Recent applications of on-line sample preconcentration techniques in capillary electrophoresis. J Chromatogr A 2014; 1335:43-60. [DOI: 10.1016/j.chroma.2013.10.066] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/18/2013] [Accepted: 10/21/2013] [Indexed: 12/21/2022]
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97
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Sun L, Zhu G, Yan X, Champion MM, Dovichi NJ. Capillary zone electrophoresis for analysis of complex proteomes using an electrokinetically pumped sheath flow nanospray interface. Proteomics 2014; 14:622-8. [PMID: 24277677 PMCID: PMC3947435 DOI: 10.1002/pmic.201300295] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/18/2013] [Accepted: 09/02/2013] [Indexed: 12/14/2022]
Abstract
The vast majority of proteomic studies employ RP-HPLC coupled with MS/MS for analysis of the tryptic digest of a cellular lysate. This technology is quite mature, and typically provides identification of hundreds to thousands of peptides, which is used to infer the identity of hundreds to thousands of proteins. These studies usually require milligrams to micrograms of starting material. CZE provides an interesting alternative separation method based on a different separation mechanism than HPLC. CE received some attention for protein analysis beginning 25 years ago. Those efforts stalled because of the limited performance of the electrospray interfaces and the limited speed and sensitivity of mass spectrometers of that era. This review considers a new electrospray interface design coupled with Orbitrap Velos and linear Q-trap mass spectrometers. CZE coupled with this interface and these detectors provides single shot detection of >1250 peptides from an Escherichia coli digest in less than 1 h, identification of nearly 5000 peptides from analysis of seven fractions produced by SPE of the E. coli digest in a 6 h total analysis time, low attomole detection limits for peptides generated from standard proteins, and high zeptomole detection limits for selected ion monitoring of peptides. Incorporation of an integrated on-line immobilized trypsin microreactor allows digestion and analysis of picogram amounts of a complex eukaryotic proteome.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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98
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Zhu G, Sun L, Yan X, Dovichi NJ. Stable, reproducible, and automated capillary zone electrophoresis-tandem mass spectrometry system with an electrokinetically pumped sheath-flow nanospray interface. Anal Chim Acta 2014; 810:94-8. [PMID: 24439510 PMCID: PMC3918410 DOI: 10.1016/j.aca.2013.11.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/24/2013] [Accepted: 11/29/2013] [Indexed: 01/31/2023]
Abstract
A PrinCE autosampler was coupled to a Q-Exactive mass spectrometer by an electrokinetically pumped sheath-flow nanospray interface to perform automated capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS). 20ng aliquots of an Escherichia coli digest were injected to evaluate the system. Eight sequential injections over an 8-h period identified 1115±70 (relative standard deviation, RSD=6%) peptides and 270±8 (RSD=3%) proteins per run. The average RSDs of migration time, peak intensity, and peak area were 3%, 24% and 19%, respectively, for 340 peptides with high intensity. This is the first report of an automated CZE-ESI-MS/MS system using the electrokinetically pumped sheath-flow nanospray interface. The results demonstrate that this system is capable of reproducibly identifying over 1000 peptides from an E. coli tryptic digest in a 1-h analysis time.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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99
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Zhou F, Lu Y, Ficarro SB, Adelmant G, Jiang W, Luckey CJ, Marto JA. Genome-scale proteome quantification by DEEP SEQ mass spectrometry. Nat Commun 2014; 4:2171. [PMID: 23863870 PMCID: PMC3770533 DOI: 10.1038/ncomms3171] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/19/2013] [Indexed: 12/15/2022] Open
Abstract
Advances in chemistry and massively parallel detection underlie DNA sequencing platforms that are poised for application in personalized medicine. In stark contrast, systematic generation of protein-level data lags well-behind genomics in virtually every aspect: depth of coverage, throughput, ease of sample preparation, and experimental time. Here, to bridge this gap, we develop an approach based on simple detergent lysis and single-enzyme digest, extreme, orthogonal separation of peptides, and true nanoflow LC-MS/MS that provides high peak capacity and ionization efficiency. This automated, deep efficient peptide sequencing and quantification (DEEP SEQ) mass spectrometry platform provides genome-scale proteome coverage equivalent to RNA-seq ribosomal profiling and accurate quantification for multiplexed isotope labels. In a model of the embryonic to epiblast transition in murine stem cells, we unambiguously quantify 11,352 gene products that span 70% of Swiss-Prot and capture protein regulation across the full detectable range of high-throughput gene expression and protein translation.
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Affiliation(s)
- Feng Zhou
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, USA
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Medina-Casanellas S, Domínguez-Vega E, Benavente F, Sanz-Nebot V, Somsen GW, de Jong GJ. Low-picomolar analysis of peptides by on-line coupling of fritless solid-phase extraction to sheathless capillary electrophoresis-mass spectrometry. J Chromatogr A 2013; 1328:1-6. [PMID: 24438833 DOI: 10.1016/j.chroma.2013.12.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/09/2013] [Accepted: 12/24/2013] [Indexed: 01/01/2023]
Abstract
A novel fritless solid-phase extraction (SPE) microcartridge was designed for combination with sheathless capillary electrophoresis-mass spectrometry (sheathless CE-MS) employing a prototype porous-tip capillary for nanoelectrospray ionization (nanoESI). The inlet of the separation capillary (30μm inner diameter (id), 150μm outer diameter (od)) was inserted in a 4mm long SPE microcartridge (150μm id, 365μm od) packed with a C18 sorbent of 55-105μm particle size. Performance of the SPE-CE-MS system was evaluated using diluted solutions of the three opioid peptides dynorphin A (1-7) (DynA), endomorphin 1 (End1) and met-enkephalin (Met). Sample volumes of 1.5μL were loaded on the SPE microcartridge and the retained peptides were eluted with 22nL of an acidic methanol/water (60:40, v/v) solution. Using a pressure of 50mbar during separation to speed up the analysis, good peptide resolution was obtained with acceptable plate numbers (between 53,000 and 92,000). Intraday relative standard deviations (% RSD) for peptide migration times and peak areas were below 4% and 9%, respectively. The SPE-CE-MS method showed good linearity in the 0.05-5ngmL(-1) range and limits of detection (LODs) were 10pgmL(-1). However, loading a larger volume of sample (8μL), LODs could be decreased down to 2pgmL(-1) (2.2-3.5pM). This represents an improvement of up to 5000-fold with respect to the LODs achieved by sheathless CE-MS without on-line preconcentration demonstrating the potential of on-line SPE for further enhancing sensitivity.
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Affiliation(s)
- Silvia Medina-Casanellas
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain; Biomolecular Analysis, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Elena Domínguez-Vega
- Biomolecular Analysis, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Fernando Benavente
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
| | - Victoria Sanz-Nebot
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Govert W Somsen
- Biomolecular Analysis, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands; AIMMS Division of BioAnalytical Chemistry, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Gerhardus J de Jong
- Biomolecular Analysis, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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