1
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Jethva PN, Gross ML. Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1118749. [PMID: 37746528 PMCID: PMC10512744 DOI: 10.3389/frans.2023.1118749] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the antigen, making them a vital approach for epitope mapping. In this review, we describe in detail the principles of hydrogen deuterium exchange mass spectrometry in application to epitope mapping. We also show that a combination of MS-based approaches can assist or complement epitope mapping and push the limit of structural resolution to the residue level. We describe in detail the MS methods used in epitope mapping, provide our perspective about the approaches, and focus on elucidating the role that HDX-MS is playing now and in the future by organizing a discussion centered around several improvements in prototype instrument/applications used for epitope mapping. At the end, we provide a tabular summary of the current literature on HDX-MS-based epitope mapping.
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Affiliation(s)
- Prashant N. Jethva
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
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2
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Peterle D, DePice D, Wales TE, Engen JR. Increase the flow rate and improve hydrogen deuterium exchange mass spectrometry. J Chromatogr A 2023; 1689:463742. [PMID: 36586285 PMCID: PMC9872520 DOI: 10.1016/j.chroma.2022.463742] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Reversed-phase peptide separation in hydrogen deuterium exchange (HDX) mass spectrometry (MS) must be done with conditions where the back exchange is the slowest possible, the so-called quench conditions of low pH and low temperature. To retain maximum deuterium, separation must also be done as quickly as possible. The low temperature (0 °C) of quench conditions complicates the separation and leads primarily to a reduction in separation quality and an increase in chromatographic backpressure. To improve the separation in HDX MS, one could use a longer gradient, smaller particles, a different separation mechanism (for example, capillary electrophoresis), or multi-dimensional separations such as combining ion mobility separation with reversed-phase separation. Another way to improve separations under HDX MS quench conditions is to use a higher flow rate where separation efficiency at 0 °C is more ideal. Higher flow rates, however, require chromatographic systems (both pumps and fittings) with higher backpressure limits. We tested what improvements could be realized with a commercial UPLC/UHPLC system capable of ∼20,000 psi backpressure. We found that a maximum flow rate of 225 µL/min (using a 1 × 50 mm column packed with 1.8 µm particles) was possible and that higher flow rate clearly led to higher peak capacity. HDX MS analysis of both simple and particularly complex samples improved, permitting both shorter separation time, if desired, and providing more deuterium recovery.
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Affiliation(s)
- Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Mailstop 412 TF, 360 Huntington Avenue, Boston, MA 02115, United States
| | - David DePice
- Department of Chemistry and Chemical Biology, Northeastern University, Mailstop 412 TF, 360 Huntington Avenue, Boston, MA 02115, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Mailstop 412 TF, 360 Huntington Avenue, Boston, MA 02115, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Mailstop 412 TF, 360 Huntington Avenue, Boston, MA 02115, United States.
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3
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Aerts J, Andrén PE, Jansson ET. Zero-Degree Celsius Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry. Anal Chem 2022; 95:1149-1158. [PMID: 36546842 PMCID: PMC9850406 DOI: 10.1021/acs.analchem.2c03893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Currently, fast liquid chromatographic separations at low temperatures are exclusively used for the separation of peptides generated in hydrogen deuterium exchange (HDX) workflows. However, it has been suggested that capillary electrophoresis may be a better option for use with HDX. We performed in solution HDX on peptides and bovine hemoglobin (Hb) followed by quenching, pepsin digestion, and cold capillary electrophoretic separation coupled with mass spectrometry (MS) detection for benchmarking a laboratory-built HDX-MS platform. We found that capillaries with a neutral coating to eliminate electroosmotic flow and adsorptive processes provided fast separations with upper limit peak capacities surpassing 170. In contrast, uncoated capillaries achieved 30% higher deuterium retention for an angiotensin II peptide standard owing to faster separations but with only half the peak capacity of coated capillaries. Data obtained using two different separation conditions on peptic digests of Hb showed strong agreement of the relative deuterium uptake between methods. Processed data for denatured versus native Hb after deuterium labeling for the longest timepoint in this study (50,000 s) also showed agreement with subunit interaction sites determined by crystallographic methods. All proteomic data are available under DOI: 10.6019/PXD034245.
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Affiliation(s)
- Jordan
T. Aerts
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden,Science
for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, Uppsala751 24, Sweden
| | - Erik T. Jansson
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden,
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4
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Madren S, Yi L. Microchip electrophoresis separation coupled to mass spectrometry (MCE-MS) for the rapid monitoring of multiple quality attributes of monoclonal antibodies. Electrophoresis 2022; 43:2453-2465. [PMID: 36027045 DOI: 10.1002/elps.202200129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 12/14/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) are highly heterogeneous as a result of posttranslational modifications (PTMs) during bioprocessing and storage. The modifications that impact mAb product quality are regarded as critical quality attributes and require monitoring. The conventional LC-mass spectrometer (MS) method used for product quality monitoring may require protein A purification prior to analysis. In this paper, we present a high-throughput microchip electrophoresis (<4 min) in-line with MS (MCE-MS) that enables baseline separation and characterization of Fc, Fd', and light chain (LC) domains of IdeS-treated mAb sample directly from bioreactor. The NISTmAb was used to optimize the MCE separation and to assess its capability of multiple attribute monitoring. The MCE-MS can uniquely separate and characterize deamidated species at domain level compared to LC-MS method. Two case studies were followed to demonstrate the method capability of monitoring product quality of mAb samples from stability studies or directly from bioreactors.
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Affiliation(s)
- Seth Madren
- Analytical Development Department, Biogen, Research Triangle Park, Durham, North Carolina, USA
| | - Linda Yi
- Analytical Development Department, Biogen, Research Triangle Park, Durham, North Carolina, USA
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5
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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6
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Svejdal RR, Sticker D, Sønderby C, Kutter JP, Rand KD. Thiol-ene microfluidic chip for fast on-chip sample clean-up, separation and ESI mass spectrometry of peptides and proteins. Anal Chim Acta 2020; 1140:168-177. [DOI: 10.1016/j.aca.2020.09.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/13/2023]
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7
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Ozohanics O, Ambrus A. Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes. Life (Basel) 2020; 10:E286. [PMID: 33203161 PMCID: PMC7696067 DOI: 10.3390/life10110286] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other structural biology approaches. HDX-MS is capable of providing information on individual proteins as well as large protein complexes. Owing to recent methodological advancements and improving availability of instrumentation, HDX-MS is becoming a routine technique for some applications. When dealing with samples of low to medium complexity and sizes of less than 150 kDa, conformation and ligand interaction analyses by HDX-MS are already almost routine applications. This is also well supported by the rapid evolution of the computational (software) background that facilitates the analysis of the obtained experimental data. HDX-MS can cope at times with analytes that are difficult to tackle by any other approach. Large complexes like viral capsids as well as disordered proteins can also be analyzed by this method. HDX-MS has recently become an established tool in the drug discovery process and biopharmaceutical development, as it is now also capable of dissecting post-translational modifications and membrane proteins. This mini review provides the reader with an introduction to the technique and a brief overview of the most common applications. Furthermore, the most challenging likely applications, the analyses of glycosylated and membrane proteins, are also highlighted.
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Affiliation(s)
- Oliver Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
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8
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Engen JR, Botzanowski T, Peterle D, Georgescauld F, Wales TE. Developments in Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2020; 93:567-582. [DOI: 10.1021/acs.analchem.0c04281] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas Botzanowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Florian Georgescauld
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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9
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Gomes FP, Yates JR. Recent trends of capillary electrophoresis-mass spectrometry in proteomics research. MASS SPECTROMETRY REVIEWS 2019; 38:445-460. [PMID: 31407381 PMCID: PMC6800771 DOI: 10.1002/mas.21599] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis-mass spectrometry (CE-MS) in the past few years. This review provides highlights of recent advances in CE-MS for proteomics research, including a short introduction to top-down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE-MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1-16, 2019.
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Affiliation(s)
| | - John R. Yates
- Correspondent author: , Phone number: (858) 784-8862, Departments of Molecular Medicine and Neurobiology, 10550 North Torrey Pines Road, SR302B, The Scripps Research Institute, La Jolla, CA 92037
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10
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Shen Y, Zhao X, Wang G, Chen DDY. Differential Hydrogen/Deuterium Exchange during Proteoform Separation Enables Characterization of Conformational Differences between Coexisting Protein States. Anal Chem 2019; 91:3805-3809. [DOI: 10.1021/acs.analchem.9b00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yue Shen
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Xiuxiu Zhao
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - David D. Y. Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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11
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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12
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Gilliland WM, Ramsey JM. Development of a Microchip CE-HPMS Platform for Cell Growth Monitoring. Anal Chem 2018; 90:13000-13006. [DOI: 10.1021/acs.analchem.8b03708] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Trabjerg E, Nazari ZE, Rand KD. Conformational analysis of complex protein states by hydrogen/deuterium exchange mass spectrometry (HDX-MS): Challenges and emerging solutions. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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14
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Oganesyan I, Lento C, Wilson DJ. Contemporary hydrogen deuterium exchange mass spectrometry. Methods 2018; 144:27-42. [DOI: 10.1016/j.ymeth.2018.04.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/16/2018] [Accepted: 04/21/2018] [Indexed: 02/07/2023] Open
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15
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Hao Y, Bao Y, Huang X, Hu Y, Xiong B. On-line pre-treatment, separation, and nanoelectrospray mass spectrometric determinations for pesticide metabolites and peptides based on a modular microfluidic platform. RSC Adv 2018; 8:39811-39817. [PMID: 35558234 PMCID: PMC9091297 DOI: 10.1039/c8ra08276f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022] Open
Abstract
In order to address time-consuming sample pre-treatment and separation prior to mass spectrometry (MS) identifications, highly integrated chips were developed, but damage to any functional unit in these chips would result in complete replacement. Herein, we propose a modular microfluidic platform comprising pre-treatment, liquid chromatography (LC) separation and nanoelectrospray ionization (nESI) chips for on-line enrichment, separation and nESI MS detection of pesticide metabolites and peptides. The pre-treatment chip is applicable in enriching pyridalyl and its metabolites, and it achieves optimal desalination efficiency, 98.5%, for polymerase chain reaction products. Additionally, the LC separation chip was fully characterised, and it demonstrated satisfactory separation efficiency, quantification ability and pressure durability. Finally, the modular microfluidic platform was used to identify the peptides in trypsin-digested casein. Four additional peptides were identified, indicating an improvement in detection ability compared with using off-line zip tips coupled with MS investigations. Because the proposed modular platform can significantly reduce manual work, it would be a potential tool to achieve high throughput and automatic MS identifications with low sample consumptions. A microfluidic platform, composed of enrichment, separation and nanoelectrospray ionization modulations was developed to on-line-investigate pesticide metabolites and peptides.![]()
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Affiliation(s)
- Yinyin Hao
- School of Mathematics and Statistics
- Wuhan University
- Wuhan
- China
- Key Laboratory of Pesticides & Chemical Biology
| | - Yajing Bao
- Key Laboratory of Pesticides & Chemical Biology
- Ministry of Education
- Institute of Public Health and Molecular Medicine Analysis
- College of Chemistry
- Central China Normal University
| | - Xueying Huang
- Key Laboratory of Pesticides & Chemical Biology
- Ministry of Education
- Institute of Public Health and Molecular Medicine Analysis
- College of Chemistry
- Central China Normal University
| | - Yijun Hu
- School of Mathematics and Statistics
- Wuhan University
- Wuhan
- China
| | - Bo Xiong
- Key Laboratory of Pesticides & Chemical Biology
- Ministry of Education
- Institute of Public Health and Molecular Medicine Analysis
- College of Chemistry
- Central China Normal University
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16
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Dada OO, Zhao Y, Jaya N, Salas-Solano O. High-Resolution Capillary Zone Electrophoresis with Mass Spectrometry Peptide Mapping of Therapeutic Proteins: Improved Separation with Mixed Aqueous–Aprotic Dipolar Solvents (N,N-Dimethylacetamide and N,N-Dimethylformamide) as the Background Electrolyte. Anal Chem 2017; 89:11227-11235. [DOI: 10.1021/acs.analchem.7b03405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Oluwatosin O. Dada
- Department of Analytical
Sciences, Seattle Genetics, Inc., 21823 30th Drive SE, Bothell, Washington 98021, United States
| | - Yimeng Zhao
- Department of Analytical
Sciences, Seattle Genetics, Inc., 21823 30th Drive SE, Bothell, Washington 98021, United States
| | - Nomalie Jaya
- Department of Analytical
Sciences, Seattle Genetics, Inc., 21823 30th Drive SE, Bothell, Washington 98021, United States
| | - Oscar Salas-Solano
- Department of Analytical
Sciences, Seattle Genetics, Inc., 21823 30th Drive SE, Bothell, Washington 98021, United States
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17
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Jiang Y, He MY, Zhang WJ, Luo P, Guo D, Fang X, Xu W. Recent advances of capillary electrophoresis-mass spectrometry instrumentation and methodology. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Abstract
Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor. This article proposes to view bottom-up HDX as two steps to guide choices of detergent buffers and chromatography settings: (I) protein HDX labeling in native buffers, and (II) peptide-centric analysis of HDX labels, which applies (a) bottom-up MS/MS to construct peptide matrix and (b) HDX MS to locate and quantify H/D labels. The detergent-low-TCEP digestion method demystified the challenge of HDX-grade GPCR digestion. GPCR HDX proteomics is a structural approach, thus its choice of experimental conditions should let structure lead and digestion follow, not the opposite.
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Affiliation(s)
- Xi Zhang
- Independent Researcher, Montreal, QC, H2Y 1H3, Canada
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19
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Sheff JG, Hepburn M, Yu Y, Lees-Miller SP, Schriemer DC. Nanospray HX-MS configuration for structural interrogation of large protein systems. Analyst 2017; 142:904-910. [DOI: 10.1039/c6an02707e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An in-source column chiller supports nanoHX-MS workflows for analyzing proteins from cellular extracts.
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Affiliation(s)
- Joey G. Sheff
- Department of Chemistry
- University of Calgary
- Calgary
- Canada
| | - Morgan Hepburn
- Department of Biochemistry and Molecular Biology
- University of Calgary
- Calgary
- Canada
| | - Yaping Yu
- Department of Biochemistry and Molecular Biology
- University of Calgary
- Calgary
- Canada
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology
- University of Calgary
- Calgary
- Canada
| | - David C. Schriemer
- Department of Chemistry
- University of Calgary
- Calgary
- Canada
- Department of Biochemistry and Molecular Biology
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20
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Štěpánová S, Kašička V. Analysis of proteins and peptides by electromigration methods in microchips. J Sep Sci 2016; 40:228-250. [PMID: 27704694 DOI: 10.1002/jssc.201600962] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 11/07/2022]
Abstract
This review presents the developments and applications of microchip electromigration methods in the separation and analysis of peptides and proteins in the period 2011-mid-2016. The developments in sample preparation and preconcentration, microchannel material, and surface treatment are described. Separations by various microchip electromigration methods (zone electrophoresis in free and sieving media, affinity electrophoresis, isotachophoresis, isoelectric focusing, electrokinetic chromatography, and electrochromatography) are demonstrated. Advances in detection methods are reported and novel applications in the areas of proteomics and peptidomics, quality control of peptide and protein pharmaceuticals, analysis of proteins and peptides in biomatrices, and determination of physicochemical parameters are shown.
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Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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21
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A simple sheathless CE-MS interface with a sub-micrometer electrical contact fracture for sensitive analysis of peptide and protein samples. Anal Chim Acta 2016; 936:157-67. [PMID: 27566351 DOI: 10.1016/j.aca.2016.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
Online coupling of capillary electrophoresis (CE) to electrospray ionization mass spectrometry (MS) has shown considerable potential, however, technical challenges have limited its use. In this study, we have developed a simple and sensitive sheathless CE-MS interface based on the novel concept of forming a sub-micrometer fracture directly in the capillary. The simple interface design allowed the generation of a stable ESI spray capable of ionization at low nanoliter flow-rates (45-90 nL/min) for high sensitivity MS analysis of challenging samples like those containing proteins and peptides. By analysis of a model peptide (leucine enkephalin), a limit of detection (LOD) of 0.045 pmol/μL (corresponding to 67 attomol in a sample volume of ∼15 nL) was obtained. The merit of the CE-MS approach was demonstrated by analysis of bovine serum albumin (BSA) tryptic peptides. A well-resolved separation profile was achieved and comparable sequence coverage was obtained by the CE-MS method (73%) compared to a representative UPLC-MS method (77%). The CE-MS interface was subsequently used to analyse a more complex sample of pharmaceutically relevant human proteins including insulin, tissue factor and α-synuclein. Efficient separation and protein ESI mass spectra of adequate quality could be achieved using only a small amount of sample (30 fmol). In addition, analysis of ubiquitin samples under both native and denatured conditions, indicate that the CE-MS setup can facilitate native MS applications to probe the conformational properties of proteins. Thus, the described CE-MS setup should be useful for a wide range of high-sensitivity applications in protein research.
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22
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Cong H, Xu X, Yu B, Liu H, Yuan H. Fabrication of anti-protein-fouling poly(ethylene glycol) microfluidic chip electrophoresis by sandwich photolithography. BIOMICROFLUIDICS 2016; 10:044106. [PMID: 27493702 PMCID: PMC4958108 DOI: 10.1063/1.4959239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
Microfluidic chip electrophoresis (MCE) is a powerful separation tool for biomacromolecule analysis. However, adsorption of biomacromolecules, particularly proteins onto microfluidic channels severely degrades the separation performance of MCE. In this paper, an anti-protein-fouling MCE was fabricated using a novel sandwich photolithography of poly(ethylene glycol) (PEG) prepolymers. Photopatterned microchannel with a minimum resolution of 10 μm was achieved. After equipped with a conventional online electrochemical detector, the device enabled baseline separation of bovine serum albumin, lysozyme (Lys), and cytochrome c (Cyt-c) in 53 s under a voltage of 200 V. Compared with a traditional polydimethylsiloxane MCE made by soft lithography, the PEG MCE made by the sandwich photolithography not only eliminated the need of a master mold and the additional modification process of the microchannel but also showed excellent anti-protein-fouling properties for protein separation.
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Affiliation(s)
| | - Xiaodan Xu
- College of Materials Science and Engineering, Qingdao University , Qingdao 266071, China
| | | | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Hua Yuan
- College of Materials Science and Engineering, Qingdao University , Qingdao 266071, China
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23
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Redman EA, Ramos-Payan M, Mellors JS, Ramsey JM. Analysis of Hemoglobin Glycation Using Microfluidic CE-MS: A Rapid, Mass Spectrometry Compatible Method for Assessing Diabetes Management. Anal Chem 2016; 88:5324-30. [PMID: 27100069 DOI: 10.1021/acs.analchem.6b00622] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Diabetes has become a significant health problem worldwide with the rate of diagnosis increasing rapidly in recent years. Measurement of glycated blood proteins, particularly glycated hemoglobin (HbA1c), is an important diagnostic tool used to detect and manage the condition in patients. Described here is a method using microfluidic capillary electrophoresis with mass spectrometry detection (CE-MS) to assess hemoglobin glycation in whole blood lysate. Using denaturing conditions, the hemoglobin (Hb) tetramer dissociates into the alpha and beta subunits (α- and β-Hb), which are then separated via CE directly coupled to MS detection. Nearly baseline resolution is achieved between α-Hb, β-Hb, and glycated β-Hb. A second glycated β-Hb isomer that is partially resolved from β-Hb is detected in extracted ion electropherograms for glycated β-Hb. Glycation on α-Hb is also detected in the α-Hb mass spectrum. Additional modifications to the β-Hb are detected, including acetylation and a +57 Da species that could be the addition of a glyoxal moiety. Patient blood samples were analyzed using the microfluidic CE-MS method and a clinically used immunoassay to measure HbA1c. The percentage of glycated α-Hb and β-Hb was calculated from the microfluidic CE-MS data using peak areas generated from extracted ion electropherograms. The values for glycated β-Hb were found to correlate well with the HbA1c levels derived in the clinic, giving a slope of 1.20 and an R(2) value of 0.99 on a correlation plot. Glycation of human serum albumin (HSA) can also be measured using this technique. It was observed that patients with elevated glycated Hb levels also had higher levels of HSA glycation. Interestingly, the sample with the highest HbA1c levels did not have the highest levels of glycated HSA. Because the lifetime of HSA is shorter than Hb, this could indicate a recent lapse in glycemic control for that patient. The ability to assess both Hb and HSA glycation has the potential to provide a more complete picture of a patient's glycemic control in the months leading up to blood collection. The results presented here demonstrate that the microfluidic CE-MS method is capable of rapidly assessing Hb and HSA glycation from low volumes of whole blood with minimal sample preparation and has the potential to provide more information in a single analysis step than current technologies.
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Cong H, Xu X, Yu B, Liu H, Yuan H. Fabrication of universal serial bus flash disk type microfluidic chip electrophoresis and application for protein analysis under ultra low voltage. BIOMICROFLUIDICS 2016; 10:024107. [PMID: 27042249 PMCID: PMC4798985 DOI: 10.1063/1.4943915] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
A simple and effective universal serial bus (USB) flash disk type microfluidic chip electrophoresis (MCE) was developed by using poly(dimethylsiloxane) based soft lithography and dry film based printed circuit board etching techniques in this paper. The MCE had a microchannel diameter of 375 μm and an effective length of 25 mm. Equipped with a conventional online electrochemical detector, the device enabled effectively separation of bovine serum albumin, lysozyme, and cytochrome c in 80 s under the ultra low voltage from a computer USB interface. Compared with traditional capillary electrophoresis, the USB flash disk type MCE is not only portable and inexpensive but also fast with high separation efficiency.
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Affiliation(s)
| | - Xiaodan Xu
- College of Materials Science and Engineering, Qingdao University , Qingdao 266071, China
| | | | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Hua Yuan
- College of Materials Science and Engineering, Qingdao University , Qingdao 266071, China
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25
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Maaty WS, Weis DD. Label-Free, In-Solution Screening of Peptide Libraries for Binding to Protein Targets Using Hydrogen Exchange Mass Spectrometry. J Am Chem Soc 2016; 138:1335-43. [PMID: 26741284 DOI: 10.1021/jacs.5b11742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There is considerable interest in the discovery of peptide ligands that bind to protein targets. Discovery of such ligands is usually approached by screening large peptide libraries. However, the individual peptides must be tethered to a tag that preserves their individual identities (e.g., phage display or one-bead one-compound). To overcome this limitation, we have developed a method for screening libraries of label-free peptides for binding to a protein target in solution as a single batch. The screening is based on decreased amide hydrogen exchange by peptides that bind to the target. Hydrogen exchange is measured by mass spectrometry. We demonstrate the approach using a peptide library derived from the Escherichia coli proteome that contained 6664 identifiable features. The library was spiked separately with a peptide spanning the calmodulin binding domain of endothelial nitric oxide synthase (eNOS, 494-513) and a peptide spanning the N-terminal 20 residues of bovine ribonuclease A (S peptide). Human calmodulin and bovine ribonuclease S (RNase S) were screened against the library. Using a novel data analysis workflow, we identified the eNOS peptide as the only calmodulin binding peptide and S peptide as the only ribonuclease S binding peptide in the library.
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Affiliation(s)
- Walid S Maaty
- Department of Nucleic Acid and Protein Structure, Agricultural Genetic Engineering Research Institute, Agricultural Research Center , Giza 12619, Egypt
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26
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Patabadige DEW, Jia S, Sibbitts J, Sadeghi J, Sellens K, Culbertson CT. Micro Total Analysis Systems: Fundamental Advances and Applications. Anal Chem 2015; 88:320-38. [DOI: 10.1021/acs.analchem.5b04310] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Damith E. W. Patabadige
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| | - Shu Jia
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| | - Jay Sibbitts
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| | - Jalal Sadeghi
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
- Laser & Plasma Research Institute, Shahid Beheshti University, Evin, Tehran, 1983963113, Iran
| | - Kathleen Sellens
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| | - Christopher T. Culbertson
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
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