1
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Anderson KW, Hudgens JW. Hydrophilic Interaction Liquid Chromatography at Subzero Temperature for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2672-2679. [PMID: 37930109 PMCID: PMC10704588 DOI: 10.1021/jasms.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Chromatographic separations at subzero temperature significantly improve the precision of back-exchange-corrected hydrogen-deuterium exchange mass spectrometry (HDX-MS) determinations. Our previously reported dual-enzyme HDX-MS analysis instrument used reversed phase liquid chromatography (RPLC) at -30 °C, but high backpressures limited flow rates and required materials and equipment rated for very high pressures. Here, we report the design and performance of a dual-enzyme HDX-MS analysis instrument comprising a RPLC trap column and a hydrophilic interaction liquid chromatography (HILIC) analytical column in a two-dimensional RPLC-HILIC configuration at subzero temperature. During operation at -30 °C, the HILIC column manifests greatly reduced backpressure, which enables faster analytical flow rates and the use of materials rated for lower maximum pressures. The average peptide eluted from a HILIC column during a 40 min gradient at -30 °C contained ≈13% more deuterium than peptides eluted from a tandem RPLC-RPLC apparatus using a conventional 8 min gradient at 0 °C. A subset of peptides eluted from the HILIC apparatus contained ≈24% more deuterium.
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Affiliation(s)
- Kyle W. Anderson
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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2
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Damont A, Legrand A, Cao C, Fenaille F, Tabet JC. Hydrogen/deuterium exchange mass spectrometry in the world of small molecules. MASS SPECTROMETRY REVIEWS 2023; 42:1300-1331. [PMID: 34859466 DOI: 10.1002/mas.21765] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 06/07/2023]
Abstract
The combined use of hydrogen/deuterium exchange (HDX) and mass spectrometry (MS), referred to as HDX-MS, is a powerful tool for exploring molecular edifices and has been used for over 60 years. Initially for structural and mechanistic investigation of low-molecular weight organic compounds, then to study protein structure and dynamics, then, the craze to study small molecules by HDX-MS accelerated and has not stopped yet. The purpose of this review is to present its different facets with particular emphasis on recent developments and applications. Reversible H/D exchanges of mobilizable protons as well as stable exchanges of non-labile hydrogen are considered whether they are taking place in solution or in the gas phase, or enzymatically in a biological media. Some fundamental principles are restated, especially for gas-phase processes, and an overview of recent applications, ranging from identification to quantification through the study of metabolic pathways, is given.
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Affiliation(s)
- Annelaure Damont
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Anaïs Legrand
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Chenqin Cao
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - François Fenaille
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Jean-Claude Tabet
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, France
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3
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Neumann J, Schmidtsdorff S, Schmidt AH, Parr MK. Ternary eluent compositions in supercritical fluid chromatography improved fingerprinting of therapeutic peptides. J Sep Sci 2023; 46:e2201007. [PMID: 36601991 DOI: 10.1002/jssc.202201007] [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: 12/11/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023]
Abstract
Currently, little information has been published on the application of ternary eluent compositions in supercritical fluid chromatography for separating peptides. This work investigates the benefits of adding acetonitrile to methanol as the modifier. Three cyclic antibiotic peptides (bacitracin, colistin, and daptomycin) ranging between 1000 and 2000 Da were chosen as model substances. The ternary mixture of carbon dioxide, methanol, and acetonitrile is optimized to increase the resolution of the peptide's fingerprint. In addition, varying compositions of methanol and acetonitrile were found to change the elution order of the analytes, which is a valuable tool during method development. An individual gradient method using two Torus 2-PIC columns (each 100 × 3.0 mm, 1.7 μm), carbon dioxide, and a modifier consisting of acetonitrile/methanol/water/methanesulfonic acid (60:40:2:0.1, v:v:v:v) was optimized for each of the peptides. Subsequently, a generic method development protocol applicable to polypeptides is proposed.
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Affiliation(s)
- Jonas Neumann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany.,Chromicent GmbH, Berlin, Germany
| | - Sebastian Schmidtsdorff
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany.,Chromicent GmbH, Berlin, Germany
| | | | - Maria K Parr
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
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4
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Anderson KW, Hudgens JW. Chromatography at -30 °C for Reduced Back-Exchange, Reduced Carryover, and Improved Dynamic Range for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1282-1292. [PMID: 35732031 PMCID: PMC9264389 DOI: 10.1021/jasms.2c00096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
For hydrogen-deuterium exchange mass spectrometry (HDX-MS) to have an increased role in quality control of biopharmaceuticals, H for D back-exchange occurring during protein analyses should be minimized to promote greater reproducibility. Standard HDX-MS analysis systems that digest proteins and separate peptides at pH 2.7 and 0 °C can lose >30% of the deuterium marker within 15 min of sample injection. This report describes the architecture and performance of a dual-enzyme, HDX-MS instrument that conducts liquid chromatography (LC) separations at subzero temperature, thereby reducing back-exchange and supporting longer LC separations with improved chromatographic resolution. LC separations of perdeuterated, fully reduced, iodoacetamide-treated BSA protein digest standard peptides were performed at 0, -10, -20, and -30 °C in ethylene glycol (EG)/H2O mixtures. Analyses conducted at -20 and -30 °C produced similar results. After subtracting for deuterium retained in arginine side chains, the average peptide eluted during a 40 min gradient contained ≈16% more deuterium than peptides eluted with a conventional 8 min gradient at 0 °C. A subset of peptides exhibited ≈26% more deuterium. Although chromatographic peaks shift with EG concentration and temperature, the apparatus elutes unbroadened LC peaks. Electrospray ion intensity does not decline with increasing EG fraction. To minimize bias from sample carryover, the fluidic circuits allow flush and backflush cleaning of all enzyme and LC columns. The system can perform LC separations and clean enzyme columns simultaneously. Temperature zones are controlled ±0.058 °C. The potential of increased sensitivity by mixing acetonitrile with the analytical column effluent was also examined.
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Affiliation(s)
- Kyle W. Anderson
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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5
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Beres M. Expanding the boundaries of SFC: Analysis of biomolecules. SEP SCI TECHNOL 2022. [DOI: 10.1016/b978-0-323-88487-7.00011-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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6
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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: 101] [Impact Index Per Article: 33.7] [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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7
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Hamuro Y. Tutorial: Chemistry of Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:133-151. [PMID: 33227208 DOI: 10.1021/jasms.0c00260] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chemistry related to hydrogen/deuterium exchange-mass spectrometry (HDX-MS) for the analysis of proteins is described. First, the HDX rates of various functional groups in proteins are explained by reviewing the observed rates described in the literature, followed by estimating rates of all types of heteroatom hydrogens in proteins using proton transfer theory and the pKa values. The estimated HDX rates match well with the respective observed rates for most functional groups, with the exception of indole and amide groups. The discrepancies between the observed and estimated HDX rates for these groups are explained by the reaction mechanisms. Second, the factors that affect the HDX rates of backbone amide hydrogen, including side chain, N- and C-terminals, pH, temperature, organic solvent, and isotopes, are discussed. These factors are important for the proper design of exchange reactions and downstream process as well as the analysis and interpretation of HDX-MS data.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
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8
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Gordillo R. Supercritical fluid chromatography hyphenated to mass spectrometry for metabolomics applications. J Sep Sci 2020; 44:448-463. [DOI: 10.1002/jssc.202000805] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ruth Gordillo
- Touchstone Diabetes Center University of Texas Southwestern Medical Center Dallas Texas USA
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9
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Molineau J, Hideux M, West C. Chromatographic analysis of biomolecules with pressurized carbon dioxide mobile phases - A review. J Pharm Biomed Anal 2020; 193:113736. [PMID: 33176241 DOI: 10.1016/j.jpba.2020.113736] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/24/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022]
Abstract
Biomolecules like proteins, peptides and nucleic acids widely emerge in pharmaceutical applications, either as synthetic active pharmaceutical ingredients, or from natural products as in traditional Chinese medicine. Liquid-phase chromatographic methods (LC) are widely employed for the analysis and/or purification of such molecules. On another hand, to answer the ever-increasing requests from scientists involved in biomolecules projects, other chromatographic methods emerge as useful complements to LC. In particular, there is a growing interest for chromatography with a mobile phase comprising pressurized carbon dioxide, which can be named either (i) supercritical (or subcritical) fluid chromatography (SFC) when CO2 is the major constituent of the mobile phase, or (ii) enhanced fluidity liquid chromatography (EFLC) when hydro-organic or purely organic solvents are the major constituents of the mobile phase. Despite the low polarity of CO2, supposedly inadequate to solubilize such biomolecules, SFC and EFLC were both employed in many occasions for this purpose. This paper specifically reviews the literature related to the SFC/EFLC analysis of free amino acids, peptides, proteins, nucleobases, nucleosides and nucleotides. The analytical conditions employed for specific molecular families are presented, with a focus on the nature of the stationary phase and the mobile phase composition. We also discuss the potential benefits of combining SFC/EFLC to LC in a single gradient elution, a method sometimes designated as unified chromatography (UC). Finally, detection issues are presented, and more particularly hyphenation to mass spectrometry.
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Affiliation(s)
- Jérémy Molineau
- University of Orleans, ICOA, CNRS UMR 7311, rue de Chartres, BP 6759, 45067 Orléans, France
| | - Maria Hideux
- Institut de Recherches Servier, 11 rue des Moulineaux, 92150 Suresnes, France
| | - Caroline West
- University of Orleans, ICOA, CNRS UMR 7311, rue de Chartres, BP 6759, 45067 Orléans, France.
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10
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Hudgens JW. Construction of a Dual Protease Column, Subzero (-30 °C) Chromatography System and Multi-channel Precision Temperature Controller for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2020; vol:jres.vol.125.025. [PMID: 35573859 PMCID: PMC9097885 DOI: 10.6028/jres.125.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/31/2020] [Indexed: 05/12/2023]
Abstract
This tutorial provides mechanical drawings, electrical schematics, parts lists, stereolithography (STL) files for producing three-dimensional (3D)-printed parts, initial graphics exchange specification (IGS) files for automated machining, and instructions necessary for construction of a dual protease column, subzero, liquid chromatography system for hydrogen-deuterium exchange mass spectrometry (HDX-MS). Electro-mechanical schematics for construction of two multi-zone temperature controllers that regulate to ±0.05 oC are also included in this tutorial.
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Affiliation(s)
- Jeffrey W. Hudgens
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurement Division, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
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11
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Characterization and analysis of non-ionic surfactants by supercritical fluid chromatography combined with ion mobility spectrometry-mass spectrometry. Anal Bioanal Chem 2019; 411:2759-2765. [DOI: 10.1007/s00216-019-01777-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/21/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
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12
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Kostyukevich Y, Acter T, Zherebker A, Ahmed A, Kim S, Nikolaev E. Hydrogen/deuterium exchange in mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:811-853. [PMID: 29603316 DOI: 10.1002/mas.21565] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 05/22/2023]
Abstract
The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
| | - Thamina Acter
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
| | - Arif Ahmed
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
- Green Nano Center, Kyungpook National University, Daegu, Republic of Korea
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
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13
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Cho Y, Choi MH, Kim B, Kim S. Supercritical fluid chromatography coupled with in-source atmospheric pressure ionization hydrogen/deuterium exchange mass spectrometry for compound speciation. J Chromatogr A 2016; 1444:123-8. [DOI: 10.1016/j.chroma.2016.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/27/2016] [Accepted: 03/06/2016] [Indexed: 01/06/2023]
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14
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Walters BT, Ricciuti A, Mayne L, Englander SW. Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2132-9. [PMID: 22965280 PMCID: PMC3515739 DOI: 10.1007/s13361-012-0476-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/07/2012] [Accepted: 08/13/2012] [Indexed: 05/11/2023]
Abstract
The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by 3-fold only reduced back exchange by ~2%, while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (<20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90% ± 5%.
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Affiliation(s)
- Benjamin T Walters
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 1006 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104, USA.
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15
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Venable JD, Okach L, Agarwalla S, Brock A. Subzero temperature chromatography for reduced back-exchange and improved dynamic range in amide hydrogen/deuterium exchange mass spectrometry. Anal Chem 2012; 84:9601-8. [PMID: 23025328 DOI: 10.1021/ac302488h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Amide hydrogen/deuterium exchange is a commonly used technique for studying the dynamics of proteins and their interactions with other proteins or ligands. When coupled with liquid chromatography and mass spectrometry, hydrogen/deuterium exchange provides several unique advantages over other structural characterization techniques including very high sensitivity, the ability to analyze proteins in complex environments, and a large mass range. A fundamental limitation of the technique arises from the loss of the deuterium label (back-exchange) during the course of the analysis. A method to limit loss of the label during the separation stage of the analysis using subzero temperature reversed-phase chromatography is presented. The approach is facilitated by the use of buffer modifiers that prevent freezing. We evaluated ethylene glycol, dimethyl formamide, formamide, and methanol for their freezing point suppression capabilities, effects on peptide retention, and their compatibilities with electrospray ionization. Ethylene glycol was used extensively because of its good electrospray ionization compatibility; however, formamide has potential to be a superior modifier if detrimental effects on ionization can be overcome. It is demonstrated using suitable buffer modifiers that separations can be performed at temperatures as low as -30 °C with negligible loss of the deuterium label, even during long chromatographic separations. The reduction in back-exchange is shown to increase the dynamic range of hydrogen/deuterium exchange mass spectrometry in terms of mixture complexity and the magnitude with which changes in deuteration level can be quantified.
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Affiliation(s)
- John D Venable
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
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16
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West C, Khater S, Lesellier E. Characterization and use of hydrophilic interaction liquid chromatography type stationary phases in supercritical fluid chromatography. J Chromatogr A 2012; 1250:182-95. [DOI: 10.1016/j.chroma.2012.05.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/28/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
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17
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Iacob RE, Engen JR. Hydrogen exchange mass spectrometry: are we out of the quicksand? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1003-10. [PMID: 22476891 PMCID: PMC3389995 DOI: 10.1007/s13361-012-0377-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 05/12/2023]
Abstract
Although the use of hydrogen exchange (HX) mass spectrometry (MS) to study proteins and protein conformation is now over 20 years old, the perception lingers that it still has "issues." Is this method, in fact, still in the quicksand with many remaining obstacles to overcome? We do not think so. This critical insight addresses the "issues" and explores several broad questions including, have the limitations of HX MS been surmounted and has HX MS achieved "indispensable" status in the pantheon of protein structural analysis tools.
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Affiliation(s)
| | - John R. Engen
- Address reprint requests to: John R. Engen, Ph.D., Northeastern University, 360 Huntington Ave., Boston, MA 02115-5000, USA, , Fax: 617-373-2855
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18
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Amon S, Trelle MB, Jensen ON, Jørgensen TJD. Spatially resolved protein hydrogen exchange measured by subzero-cooled chip-based nanoelectrospray ionization tandem mass spectrometry. Anal Chem 2012; 84:4467-73. [PMID: 22536891 DOI: 10.1021/ac300268r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mass spectrometry has become a valuable method for studying structural dynamics of proteins in solution by measuring their backbone amide hydrogen/deuterium exchange (HDX) kinetics. In a typical exchange experiment one or more proteins are incubated in deuterated buffer at physiological conditions. After a given period of deuteration, the exchange reaction is quenched by acidification (pH 2.5) and cooling (0 °C) and the deuterated protein (or a digest thereof) is analyzed by mass spectrometry. The unavoidable loss of deuterium (back-exchange) that occurs under quench conditions is undesired as it leads to loss of information. Here we describe the successful application of a chip-based nanoelectrospray ionization mass spectrometry top-down fragmentation approach based on cooling to subzero temperature (-15 °C) which reduces the back-exchange at quench conditions to very low levels. For example, only 4% and 6% deuterium loss for fully deuterated ubiquitin and β(2)-microglobulin were observed after 10 min of back-exchange. The practical value of our subzero-cooled setup for top-down fragmentation HDX analyses is demonstrated by electron-transfer dissociation of ubiquitin ions under carefully optimized mass spectrometric conditions where gas-phase hydrogen scrambling is negligible. Our results show that the known dynamic behavior of ubiquitin in solution is accurately reflected in the deuterium contents of the fragment ions.
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Affiliation(s)
- Sabine Amon
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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19
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Valeja SG, Emmett MR, Marshall AG. Polar aprotic modifiers for chromatographic separation and back-exchange reduction for protein hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:699-707. [PMID: 22298288 PMCID: PMC3835171 DOI: 10.1007/s13361-011-0329-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/08/2011] [Accepted: 12/24/2011] [Indexed: 05/20/2023]
Abstract
Hydrogen/deuterium exchange monitored by mass spectrometry is an important non-perturbing tool to study protein structure and protein–protein interactions. However, water in the reversed-phase liquid chromatography mobile phase leads to back-exchange of D for H during chromatographic separation of proteolytic peptides following H/D exchange, resulting in incorrect identification of fast-exchanging hydrogens as unexchanged hydrogens. Previously, fast high-performance liquid chromatography (HPLC) and supercritical fluid chromatography have been shown to decrease back-exchange. Here, we show that replacement of up to 40% of the water in the LC mobile phase by the modifiers, dimethylformamide (DMF) and N-methylpyrrolidone (NMP) (i.e., polar organic modifiers that lack rapid exchanging hydrogens), significantly reduces back-exchange. On-line LC micro-ESI FT-ICR MS resolves overlapped proteolytic peptide isotopic distributions, allowing for quantitative determination of the extent of back-exchange. The DMF modified solvent composition also improves chromatographic separation while reducing back-exchange relative to conventional solvent.
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Affiliation(s)
- Santosh G. Valeja
- Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, USA
| | - Mark R. Emmett
- Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, USA
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310-4005, USA
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, USA
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310-4005, USA
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20
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Percy AJ, Rey M, Burns KM, Schriemer DC. Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review. Anal Chim Acta 2012; 721:7-21. [PMID: 22405295 DOI: 10.1016/j.aca.2012.01.037] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 11/17/2022]
Abstract
Assessing the functional outcome of protein interactions in structural terms is a goal of structural biology, however most techniques have a limited capacity for making structure-function determinations with both high resolution and high throughput. Mass spectrometry can be applied as a reader of protein chemistries in order to fill this void, and enable methodologies whereby protein structure-function determinations may be made on a proteome-wide level. Protein hydrogen/deuterium exchange (H/DX) offers a chemical labeling strategy suitable for tracking changes in "dynamic topography" and thus represents a powerful means of monitoring protein structure-function relationships. This review presents the exchange method in the context of interaction analysis. Applications involving interface detection, quantitation of binding, and conformational responses to ligation are discussed, and commentary on recent analytical developments is provided.
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Affiliation(s)
- Andrew J Percy
- Department of Chemistry, University of Calgary, Alberta, Canada
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21
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Althaus E, Canzar S, Ehrler C, Emmett MR, Karrenbauer A, Marshall AG, Meyer-Bäse A, Tipton JD, Zhang HM. Computing H/D-exchange rates of single residues from data of proteolytic fragments. BMC Bioinformatics 2010; 11:424. [PMID: 20701784 PMCID: PMC2936929 DOI: 10.1186/1471-2105-11-424] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 08/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides generated from the protease digest of the protein is related to the solvent accessibility of amide protons within the original protein construct. RESULTS In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue resolution. CONCLUSIONS With our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments.
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Affiliation(s)
- Ernst Althaus
- Institut für Informatik, Fachbereich 08, Staudingerweg 9, 55099 Mainz, Germany.
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Bou-Assaf GM, Chamoun JE, Emmett MR, Fajer PG, Marshall AG. Advantages of isotopic depletion of proteins for hydrogen/deuterium exchange experiments monitored by mass spectrometry. Anal Chem 2010; 82:3293-9. [PMID: 20337424 DOI: 10.1021/ac100079z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution-phase hydrogen/deuterium exchange (HDX) monitored by mass spectrometry is an excellent tool to study protein-protein interactions and conformational changes in biological systems, especially when traditional methods such as X-ray crystallography or nuclear magnetic resonance are not feasible. Peak overlap among the dozens of proteolytic fragments (including those from autolysis of the protease) can be severe, due to high protein molecular weight(s) and the broad isotopic distributions due to multiple deuterations of many peptides. In addition, different subunits of a protein complex can yield isomeric proteolytic fragments. Here, we show that depletion of (13)C and/or (15)N for one or more protein subunits of a complex can greatly simplify the mass spectra, increase the signal-to-noise ratio of the depleted fragment ions, and remove ambiguity in assignment of the m/z values to the correct isomeric peptides. Specifically, it becomes possible to monitor the exchange progress for two isobaric fragments originating from two or more different subunits within the complex, without having to resort to tandem mass spectrometry techniques that can lead to deuterium scrambling in the gas phase. Finally, because the isotopic distribution for a small to medium-size peptide is essentially just the monoisotopic species ((12)C(c)(1)H(h)(14)N(n)(16)O(o)(32)S(s)), it is not necessary to deconvolve the natural abundance distribution for each partially deuterated peptide during HDX data reduction.
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Affiliation(s)
- George M Bou-Assaf
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
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23
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Fitzgerald MC, West GM. Painting proteins with covalent labels: what's in the picture? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1193-1206. [PMID: 19269190 DOI: 10.1016/j.jasms.2009.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/06/2009] [Accepted: 02/09/2009] [Indexed: 05/27/2023]
Abstract
Knowledge about the structural and biophysical properties of proteins when they are free in solution and/or in complexes with other molecules is essential for understanding the biological processes that proteins regulate. Such knowledge is also important to drug discovery efforts, particularly those focused on the development of therapeutic agents with protein targets. In the last decade a variety of different covalent labeling techniques have been used in combination with mass spectrometry to probe the solution-phase structures and biophysical properties of proteins and protein-ligand complexes. Highlighted here are five different mass spectrometry-based covalent labeling strategies including: continuous hydrogen/deuterium (H/D) exchange labeling, hydroxyl radical-mediated footprinting, SUPREX (stability of unpurified proteins from rates of H/D exchange), PLIMSTEX (protein-ligand interaction by mass spectrometry, titration, and H/D exchange), and SPROX (stability of proteins from rates of oxidation). The basic experimental protocols used in each of the above-cited methods are summarized along with the kind of biophysical information they generate. Also discussed are the relative strengths and weaknesses of the different methods for probing the wide range of conformational states that proteins and protein-ligand complexes can adopt when they are in solution.
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Affiliation(s)
- Michael C Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708-0346, USA.
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24
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Farrell WP, Aurigemma CM, Masters-Moore DF. Advances in High Throughput Supercritical Fluid Chromatography. J LIQ CHROMATOGR R T 2009. [DOI: 10.1080/10826070902956394] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- William P. Farrell
- a Pfizer Global Research and Development, La Jolla Laboratories , San Diego, California, USA
| | - Christine M. Aurigemma
- a Pfizer Global Research and Development, La Jolla Laboratories , San Diego, California, USA
| | - David F. Masters-Moore
- a Pfizer Global Research and Development, La Jolla Laboratories , San Diego, California, USA
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25
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Zhang HM, Bou-Assaf GM, Emmett MR, Marshall AG. Fast reversed-phase liquid chromatography to reduce back exchange and increase throughput in H/D exchange monitored by FT-ICR mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:520-4. [PMID: 19095461 PMCID: PMC2673454 DOI: 10.1016/j.jasms.2008.11.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 11/15/2008] [Accepted: 11/17/2008] [Indexed: 05/12/2023]
Abstract
In solution-phase hydrogen/deuterium exchange (HDX), it is essential to minimize the back-exchange level of H for D after the exchange has been quenched, to accurately assign protein conformation and protein-protein or protein-ligand interactions. Reversed-phase HPLC is conducted at low pH and low temperature to desalt and separate proteolytic fragments. However, back exchange averages roughly 30% because of the long exposure to H(2)O in the mobile phase. In this report, we first show that there is no significant backbone amide hydrogen back exchange during quench and digestion; backbone exchange occurs primarily during subsequent liquid chromatography separation. We then show that a rapid reversed-phase separation reduces back exchange for HDX by at least 25%, resulting from the dramatically reduced retention time of the peptide fragments on the column. The influence of retention time on back exchange was also evaluated. The rapid separation coupled with high-resolution FT-ICR MS at 14.5 T provides high amino acid sequence coverage, high sample throughput, and high reproducibility and reliability.
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Affiliation(s)
- Hui-Min Zhang
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL 32310-4005
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306
| | - George M. Bou-Assaf
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL 32310-4005
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
| | - Mark R. Emmett
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL 32310-4005
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
| | - Alan G. Marshall
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL 32310-4005
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
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26
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Affiliation(s)
- Larry T. Taylor
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061-0212
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27
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Suchanova B, Tuma R. Folding and assembly of large macromolecular complexes monitored by hydrogen-deuterium exchange and mass spectrometry. Microb Cell Fact 2008; 7:12. [PMID: 18394161 PMCID: PMC2365927 DOI: 10.1186/1475-2859-7-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 04/04/2008] [Indexed: 11/26/2022] Open
Abstract
Recent advances in protein mass spectrometry (MS) have enabled determinations of hydrogen deuterium exchange (HDX) in large macromolecular complexes. HDX-MS became a valuable tool to follow protein folding, assembly and aggregation. The methodology has a wide range of applications in biotechnology ranging from quality control for over-expressed proteins and their complexes to screening of potential ligands and inhibitors. This review provides an introduction to protein folding and assembly followed by the principles of HDX and MS detection, and concludes with selected examples of applications that might be of interest to the biotechnology community.
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28
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:689-700. [PMID: 17474104 DOI: 10.1002/jms.1074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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