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Hwang H, Park KH, Kwon JL, Park HO, Kim J. Analysis of Self-Assembled Micelle Inhibitory RNA (SAMiRNA) Drug Using Ion-Pairing Reversed-Phase Liquid Chromatography Combined with Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1301-1309. [PMID: 38657000 DOI: 10.1021/jasms.4c00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Small interfering RNA (siRNA) is known for its ability to silence the expression of specific genes, demonstrating its promising potential as a therapeutic approach. Self-assembled micelle inhibitory RNA (SAMiRNA) is an oligonucleotide duplex developed to overcome the in vivo delivery limitations of siRNA. SAMiRNA has hydrophilic and hydrophobic groups at both ends of a sense strand, forming a spherical nanostructure that enhances the in vivo delivery efficiency. Ion-pairing reversed-phase liquid chromatography (IP-RPLC) is the most commonly used method for the analysis of oligonucleotides. Since SAMiRNA is heavily chemically modified, the behavior of SAMiRNA in IP-RPLC combined with mass spectrometry (MS) is anticipated to differ from that of the conventional siRNA drug. The current investigation using IP-RPLC-MS revealed that a distinct duplex peak along with two minor separate strands of antisense and sense was observed at column temperatures below 35 °C in the IP-RPLC system with a 100 mM ammonium bicarbonate buffer system. At column temperatures higher than 35 °C, however, two fully denatured single strands were observed. The mass spectrum from the chromatographic peak of the SAMiRNA duplex contained signals from the duplex, the antisense, and the sense, probably due to duplex denaturation during the MS ionization process. The current comprehensive analysis results will make a substantial contribution to the future application of IP-RPLC-MS in the analysis of SAMiRNA.
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Affiliation(s)
- Hyojin Hwang
- Department of Chemistry, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kyu H Park
- Bioneer Corporation, Daejeon 34013, Republic of Korea
| | - Ju-Lee Kwon
- siRNAgen Therapeutics Inc., Daejeon 34302, Republic of Korea
| | - Han-Oh Park
- Bioneer Corporation, Daejeon 34013, Republic of Korea
- siRNAgen Therapeutics Inc., Daejeon 34302, Republic of Korea
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon 34134, Republic of Korea
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2
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Sun RX, Zuo MQ, Zhang JS, Dong MQ. Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37463304 DOI: 10.1021/jasms.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1- to 5-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.
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Affiliation(s)
- Rui-Xiang Sun
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Ji-Shuai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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Lauman R, Kim HJ, Pino LK, Scacchetti A, Xie Y, Robison F, Sidoli S, Bonasio R, Garcia BA. Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography. Anal Chem 2023; 95:5187-5195. [PMID: 36916610 PMCID: PMC10190205 DOI: 10.1021/acs.analchem.2c04114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in the fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before MS identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA MS increases both coverage and throughput, while EMLC LC-MS orthogonally separates RNA molecules of different lengths and charges. The combination of the two methods offers a broadly applicable platform to improve the length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.
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Affiliation(s)
- Richard Lauman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetic Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay K. Pino
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandro Scacchetti
- Epigenetic Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Faith Robison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Roberto Bonasio
- Epigenetic Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
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4
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Li F, Chen S, Studzińska S, Lämmerhofer M. Polybutylene terephthalate-based stationary phase for ion-pair-free reversed-phase liquid chromatography of small interfering RNA. Part 1: Direct coupling with mass spectrometry. J Chromatogr A 2023; 1694:463898. [PMID: 36921562 DOI: 10.1016/j.chroma.2023.463898] [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: 10/22/2022] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 03/18/2023]
Abstract
Nowadays, ion-pairing reversed-phase liquid chromatography (IP-RPLC) is the dominating generic method for the analysis of nucleic acid related compounds, such as antisense-oligonucleotides (ASO), small-interfering ribonucleic acid (siRNA) or other DNA or RNA type molecules and their conjugates. Despite of its effective performance, the usage of a high concentration of ion-pairing reagent in the eluent in IP-RPLC is unfavorable for the hyphenation with mass spectrometry (MS) which is required for a detailed structural characterization of the analytes and their structurally related impurities. In this work, we tested a polybutylene terephthalate (PBT)-bonded silica-based stationary phase for the separation of generically synthesized Patisiran as siRNA (antisense and sense single strands as well as their annealed double strand) giving some unexpected selectivity without any presence of ion-pairing reagents. Important chromatographic conditions affecting the separation have been investigated and evaluated. Furthermore, MS and tandem MS (MS/MS) characterization was possible without contamination of the MS system with ion-pair agent and related problems.
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Affiliation(s)
- Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Shenkai Chen
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Sylwia Studzińska
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany; Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 7 Gagarin Str., Toruń PL-87-100, Poland
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany.
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Lardeux H, Goyon A, Zhang K, Nguyen JM, Lauber MA, Guillarme D, D'Atri V. The impact of low adsorption surfaces for the analysis of DNA and RNA oligonucleotides. J Chromatogr A 2022; 1677:463324. [PMID: 35858489 DOI: 10.1016/j.chroma.2022.463324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/20/2022]
Abstract
As interest in oligonucleotide (ON) therapeutics is increasing, there is a need to develop suitable analytical methods able to properly analyze those molecules. However, an issue exists in the adsorption of ONs on different parts of the instrumentation during their analysis. The goal of the present paper was to comprehensively evaluate various types of bioinert materials used in ion-pairing reversed-phase (IP-RPLC) and hydrophilic interaction chromatography (HILIC) to mitigate this issue for 15- to 100-mer DNA and RNA oligonucleotides. The whole sample flow path was considered under both conditions, including chromatographic columns, ultra-high-performance liquid chromatography (UHPLC) system, and ultraviolet (UV) flow cell. It was found that a negligible amount of non-specific adsorption might be attributable to the chromatographic instrumentation. However, the flow cell of a detector should be carefully subjected to sample-based conditioning, as the material used in the UV flow cell was found to significantly impact the peak shapes of the largest ONs (60- to 100-mer). Most importantly, we found that the choice of column hardware had the most significant impact on the extent of non-specific adsorption. Depending on the material used for the column walls and frits, adsorption can be more or less pronounced. It was proved that any type of bioinert RPLC/HILIC column hardware offered some clear benefits in terms of adsorption in comparison to their stainless-steel counterparts. Finally, the evaluation of a large set of ONs was performed, including a DNA duplex and DNA or RNA ONs having different base composition, furanose sugar, and modifications occurring at the phosphate linkage or at the sugar moiety. This work represents an important advance in understanding the overall ON adsorption, and it helps to define the best combination of materials when analyzing a wide range of unmodified and modified 20-mer DNA and RNA ONs.
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Affiliation(s)
- Honorine Lardeux
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland
| | - Alexandre Goyon
- Small Molecule Pharmaceutical Sciences, Genentech Inc., DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Small Molecule Pharmaceutical Sciences, Genentech Inc., DNA Way, South San Francisco, CA 94080, USA
| | | | | | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland
| | - Valentina D'Atri
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland.
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6
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Li W, Zheng J, Chen M, Liu B, Liu Z, Gong L. Simultaneous determination of oxalate and citrate in urine and serum of calcium oxalate kidney stone rats by IP-RP LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1208:123395. [DOI: 10.1016/j.jchromb.2022.123395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/31/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
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7
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Morreel K, t’Kindt R, Debyser G, Jonckheere S, Sandra P. Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography–Mass Spectrometry-Based Oligonucleotide Profiling. LCGC EUROPE 2022. [DOI: 10.56530/lcgc.eu.jk3969w4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The production process of in vitro transcribed messenger RNA (IVT-mRNA)-based vaccines has matured in recent years, partly due to the fight against infectious diseases such as COVID-19. One key to success has been the use of modified, next to canonical, nucleotides and the efficient addition of a Cap-structure and poly A tail to the 5’ and 3’ end, respectively, of this massive biomolecule. These important features affect mRNA stability and impact translation efficiency, consequently boosting the optimization and implementation of liquid chromatography–mass spectrometry (LC–MS)-based oligonucleotide profiling methods for their characterization. This article will provide an overview of these LC–MS methods at a fundamental and application level. It will be shown how LC–MS is implemented in mRNA-based vaccine analysis to determine the capping efficiency and the poly A tail length, and how it allows, via RNA mapping, (i) to determine the mRNA sequence, (ii) to screen the fidelity of the manufactured modifications, and (iii) to identify and quantify unwanted modifications resulting from manufacturing or storage, and sequence variants resulting from mutation or transcription errors.
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8
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Rentel C, Gaus H, Bradley K, Luu N, Kolkey K, Mai B, Madsen M, Pearce M, Bock B, Capaldi D. Assay, Purity, and Impurity Profile of Phosphorothioate Oligonucleotide Therapeutics by Ion Pair-High-Performance Liquid Chromatography-Mass Spectrometry. Nucleic Acid Ther 2022; 32:206-220. [PMID: 35238617 DOI: 10.1089/nat.2021.0056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The relatively large molecular size, diastereoisomeric nature, and complex impurity profiles of therapeutic phosphorothioate oligonucleotides create significant analytical challenges for the quality control laboratory. To overcome the lack of selectivity inherent to traditional chromatographic approaches, an ion pair liquid chromatography-mass spectrometry (LCMS) method combining ultraviolet and mass spectrometry quantification was developed and validated for >35 different oligonucleotide drug substances and products, including several commercialized drugs. The selection of chromatographic and spectrometric conditions, data acquisition and processing, critical aspects of sample and buffer preparation and instrument maintenance, and results from method validation experiments are discussed.
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Affiliation(s)
- Claus Rentel
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Hans Gaus
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Kym Bradley
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Nhuy Luu
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Kimmy Kolkey
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Bao Mai
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Mark Madsen
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Megan Pearce
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Brandon Bock
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Daniel Capaldi
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
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9
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Hu Q, Sun Y, Yuan P, Lei H, Zhong H, Wang Y, Tang H. Quantitative structure-retention relationship for reliable metabolite identification and quantification in metabolomics using ion-pair reversed-phase chromatography coupled with tandem mass spectrometry. Talanta 2022; 238:123059. [PMID: 34808567 DOI: 10.1016/j.talanta.2021.123059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Hydrophilic metabolites are essential for all biological systems with multiple functions and their quantitative analysis forms an important part of metabolomics. However, poor retention of these metabolites on reversed-phase (RP) chromatographic column hinders their effective analysis with RPLC-MS methods. Herein, we developed a method for detecting hydrophilic metabolites using the ion-pair reversed-phase liquid-chromatography coupled with mass spectrometry (IPRP-LC-MS/MS) in scheduled multiple-reaction-monitoring (sMRM) mode. We first developed a hexylamine-based IPRP-UHPLC-QTOFMS method and experimentally measured retention time (tR) for 183 hydrophilic metabolites. We found that tRs of these metabolites were dominated by their electrostatic potential depending upon the numbers and types of their ionizable groups. We then systematically investigated the quantitative structure-retention relationship (QSRR) and constructed QSRR models using the measured tR. Subsequently, we developed a retention time predictive model using the random-forest regression algorithm (r2 = 0.93, q2 = 0.70, MAE = 1.28 min) for predicting metabolite retention time, which was applied in IPRP-UHPLC-MS/MS method in sMRM mode for quantitative metabolomic analysis. Our method can simultaneously quantify more than 260 metabolites. Moreover, we found that this method was applicable for multiple major biological matrices including biofluids and tissues. This approach offers an efficient method for large-scale quantitative hydrophilic metabolomic profiling even when metabolite standards are unavailable.
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Affiliation(s)
- Qingyu Hu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuting Sun
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peihong Yuan
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hehua Lei
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Huiqin Zhong
- Waters Technologies (Shanghai) Limited, 1000 Jinhai Road, Shanghai, 201206, China
| | - Yulan Wang
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 639798, Singapore.
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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Donegan M, Nguyen JM, Gilar M. Effect of ion-pairing reagent hydrophobicity on liquid chromatography and mass spectrometry analysis of oligonucleotides. J Chromatogr A 2022; 1666:462860. [PMID: 35123169 DOI: 10.1016/j.chroma.2022.462860] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
We performed a systematic study of thirteen alkylamines used as ion-pairing reagents for ion-pair reversed-phase liquid chromatography (IP RP LC) separations of oligonucleotides on a C18 column. We proposed a method to classify the hydrophobicity of alkylamines by their retention in RP LC. The IP reagent hydrophobicity correlated with the retention and resolution of oligonucleotides in the corresponding IP mobile phases. The baseline resolution was achieved up to 30 mer for hydrophilic, or up to 50 mer for hydrophobic IP reagents. Hydrophobic alkylamines permitted useful oligonucleotide separations at relatively low buffer concentrations, such as 5-10 mM alkylamine-acetate IP systems. These buffers were compatible with mass spectrometry detection, however, replacement of acetic acid with hexafluoroisopropanol in the mobile phase improved the MS signal by 2-3 orders of magnitude. Experiments with native and chemically modified oligonucleotides highlighted the mixed-mode nature of IP RP LC. When using hydrophobic IP reagents, the ionic retention mechanism of oligonucleotides is enhanced while hydrophobic retention is diminished.
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Affiliation(s)
| | | | - Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA 01757, USA.
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11
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Evaluating the interplay among stationary phases/ion-pairing reagents/sequences for liquid chromatography mass spectrometry analysis of oligonucleotides. Anal Biochem 2021; 625:114194. [PMID: 33910045 DOI: 10.1016/j.ab.2021.114194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/05/2021] [Accepted: 03/27/2021] [Indexed: 11/22/2022]
Abstract
The correlation among stationary phases, ion-pairing reagents (IPR) and sequences for ion-pair reversed-phase liquid chromatography mass spectrometry (IP-RP LC-MS) analysis of oligonucleotide (ODN) remains unclear. The present study aimed to evaluate such correlation using particle-packed C18 columns in order to search for the optimal combination among them. Five C18 columns packed with core-shell silica, polymer, porous silica and hybrid particles, respectively, were evaluated for the analysis of synthetic and chemically modified ODNs with six different IPRs. Our results showed that silica-based porous particles, compared to other particles, retained ODN the strongest no matter which IPR was used. Meanwhile, among the six IPRs hexylamine (HA) produced the longest retention for all ODNs, regardless of the types of C18 particles. For the separation of ODNs, C18 columns performed similarly under identical LC conditions. However, the separation ability of C18 columns is highly dependent on the type of IPR and ODN sequences. Moreover, the type of particles has little impact on the signals of ODNs for the majority of synthetic sequences, but such impact could be dramatic for chemically modified sequences. On the other hand, both the type of IPR and ODN sequence have a significant effect on MS signals for synthetic and chemically modified ODNs.
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12
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Impurity profiling of siRNA by two-dimensional liquid chromatography-mass spectrometry with quinine carbamate anion-exchanger and ion-pair reversed-phase chromatography. J Chromatogr A 2021; 1643:462065. [PMID: 33780886 DOI: 10.1016/j.chroma.2021.462065] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/21/2022]
Abstract
A short RNA with the sequence of the antisense strand of Patisiran has been selected as test material for the investigation of its common impurities using three different two-dimensional liquid chromatography (2D-LC) platforms. On the one hand, a quinine (QN) carbamate-based weak anion-exchange (AX) stationary phase (QN-AX) and a classical C18 reversed phase (RP) stationary phase in ion-pair (IP) mode with tripropylammonium acetate, respectively, have been used in the first dimension (1D) to provide the selectivity for impurities formed during the synthesis of the RNA. In the next step, certain peaks of interest from 1D have been transferred by multiple-heart-cutting (MHC) into a 2D in which an ESI-MS-compatible non-ionpairing RP method has been used for desalting via a diverter valve to remove non-volatile phosphate buffer components and ion-pair agents, respectively. Thus, a sensitive electrospray-ionization quadrupole time of flight mass spectrometry (ESI-TOF-MS) analysis of resolved impurity peaks of the siRNA has become possible under MS-friendly conditions. With both 2D-LC setups, peak purity of the ON has been evaluated by selective comprehensive (high resolution) sampling of the main peak. In a third MHC 2D-LC approach, the QN-AX LC mode was online coupled with the IP-RPLC in the 2D using UV detection. It allows the separation of additional impurities which coeluted in the first dimension. The potential of these methods for comprehensive impurity profiling of ON therapeutics is illustrated and discussed.
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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Sutton JM, El Zahar NM, Bartlett MG. Oligonucleotide Anion Adduct Formation Using Negative Ion Electrospray Ion-Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:497-508. [PMID: 33476148 DOI: 10.1021/jasms.0c00380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Improving the mobile phase of electrospray oligonucleotides has been a major focus in the field of oligonucleotides. These improved mobile phases should reduce the charge state envelope of oligonucleotides coupled with electrospray ionization, which is key to reducing spectral complexity and increasing sensitivity. Traditional mobile phase compositions with fluorinated alcohol and alkylamine, like hexafluoroisopropanol (HFIP) and triethylamine (TEA), have a large amount of cationic adduction and many charge states. Utilizing different fluorinated alcohol and alkylamine combinations, like nonafluoro-tert-butyl alcohol (NFTB) and octylamine (OA), can selectively reduce the charge states analyzed. Other classes of biomolecules have been analyzed with anionic salts to stabilize complexes, increase the molecular peak detection, and even provide unique structural information about these molecules; however, there have been no studies using anionic salts with oligonucleotides. Our experiments systematically study the stability and binding of ammonium anionic salt. We show that anions selectively bind low charge states of these oligonucleotides. Ion-mobility measurements are made to determine the collision cross section (CCS) of these oligonucleotides with anion adduction. We utilize both a nucleic acid exact hard sphere simulation (EHSS) calibration and a protein calibration. We are able to show that NFTB/OA is a good choice for the study of oligonucleotides with reduced charge states for the binding of anionic salts and the determination of CCS using ion mobility.
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Affiliation(s)
- J Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 West Green Street, Athens, Georgia 30602-2352, United States
| | - Noha M El Zahar
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 West Green Street, Athens, Georgia 30602-2352, United States
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abassia, Cairo 11566, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University, Ras-Sedr, South Sinai Governorate 46612, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 West Green Street, Athens, Georgia 30602-2352, United States
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15
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Strzelecka D, Smietanski M, Sikorski PJ, Warminski M, Kowalska J, Jemielity J. Phosphodiester modifications in mRNA poly(A) tail prevent deadenylation without compromising protein expression. RNA (NEW YORK, N.Y.) 2020; 26:1815-1837. [PMID: 32820035 PMCID: PMC7668260 DOI: 10.1261/rna.077099.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/13/2020] [Indexed: 06/07/2023]
Abstract
Chemical modifications enable preparation of mRNAs with augmented stability and translational activity. In this study, we explored how chemical modifications of 5',3'-phosphodiester bonds in the mRNA body and poly(A) tail influence the biological properties of eukaryotic mRNA. To obtain modified and unmodified in vitro transcribed mRNAs, we used ATP and ATP analogs modified at the α-phosphate (containing either O-to-S or O-to-BH3 substitutions) and three different RNA polymerases-SP6, T7, and poly(A) polymerase. To verify the efficiency of incorporation of ATP analogs in the presence of ATP, we developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantitative assessment of modification frequency based on exhaustive degradation of the transcripts to 5'-mononucleotides. The method also estimated the average poly(A) tail lengths, thereby providing a versatile tool for establishing a structure-biological property relationship for mRNA. We found that mRNAs containing phosphorothioate groups within the poly(A) tail were substantially less susceptible to degradation by 3'-deadenylase than unmodified mRNA and were efficiently expressed in cultured cells, which makes them useful research tools and potential candidates for future development of mRNA-based therapeutics.
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Affiliation(s)
- Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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16
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Abstract
The discovery and analysis of modifications on proteins and nucleic acids has provided functional information that has rapidly accelerated the field of epigenetics. While protein post-translational modifications (PTMs), especially on histones, have been highlighted as critical components of epigenetics, the post-transcriptional modification of RNA has been a subject of more recently emergent interest. Multiple RNA modifications have been known to be present in tRNA and rRNA since the 1960s, but the exploration of mRNA, small RNA, and inducible tRNA modifications remains nascent. Sequencing-based methods have been essential to the field by creating the first epitranscriptome maps of m6A, m5C, hm5C, pseudouridine, and inosine; however, these methods possess significant limitations. Here, we discuss the past, present, and future of the application of mass spectrometry (MS) to the study of RNA modifications.
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MESH Headings
- Animals
- Humans
- Mass Spectrometry
- Molecular Structure
- Nucleosides
- Nucleotides
- Protein Processing, Post-Translational
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Richard Lauman
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Li F, Su X, Bäurer S, Lämmerhofer M. Multiple heart-cutting mixed-mode chromatography-reversed-phase 2D-liquid chromatography method for separation and mass spectrometric characterization of synthetic oligonucleotides. J Chromatogr A 2020; 1625:461338. [PMID: 32709362 DOI: 10.1016/j.chroma.2020.461338] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/20/2023]
Abstract
Until today, ion-pair reversed-phase chromatography is still the dominating method for analytical characterization of synthetic oligonucleotides. Its hyphenation with mass spectrometry, however, has some drawbacks such as ion-suppression in electrospray ionization. To overcome this problem, we present in this work a multiple heart-cutting (MHC) two-dimensional liquid chromatography (2D-LC) method with ultra-violet (UV) and electrospray ionization (ESI) mass spectrometry (MS) detection. A reversed-phase/weak anion-exchange (RP/WAX) stationary phase in the first dimension (1D) provides the selectivity for separation of structurally closely related oligonucleotide sequences and deletions (shortmers), respectively, using a mixed pH/triethylammonium phosphate buffer gradient at constant organic modifier content. Heart cuts of the oligonucleotide peaks are transferred to the second dimension (2D) via a multiple heart-cutting valve which is equipped with two loop decks. The 2D RP column is used for desalting via a diverter valve. Active solvent modulation enables to refocus the oligonucleotide peak into a sharp zone by 2D RP entirely free of non-volatile buffer components and ion-pair agents. Oligonucleotides can thus be sensitively detected by ESI-QTOF-MS under MS-compatible conditions.
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Affiliation(s)
- Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaoli Su
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefanie Bäurer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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18
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Challenges in Analysis of Hydrophilic Metabolites Using Chromatography Coupled with Mass Spectrometry. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00126-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Vallejos-Almirall A, Folch-Cano C, Rosas A, Vergara C. Development of liquid chromatography tandem mass spectrometry method to quantify cyclobutane pyrimidine dimer photolyase activity by detection of 15mer oligonucleotide as reaction product. J Chromatogr A 2019; 1611:460577. [PMID: 31591040 DOI: 10.1016/j.chroma.2019.460577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/11/2019] [Accepted: 09/26/2019] [Indexed: 11/15/2022]
Abstract
Ultraviolet radiation from sunlight causes DNA damage in skin cells by formation of photoproducts, mainly cyclobutane pyrimidine dimers (CPD), which are reverted by exogenous CPD-photolyase, preventing photoaging and skin cancer. High performance liquid chromatography tandem mass spectrometry method for quantification of CPD-photolyase activity was developed to search new enzymes sources for dermatology or clinical studies. The method was based in the enzymatic conversion of a 15mer oligonucleotide, containing a center cyclobutane thymidine dimer, to the restored 15mer oligonucleotide. Three ion pair reagent were evaluated by response surface methodology to increase mass intensities. Additionally, chromatographic separation of oligonucleotides was performed. The selected mobile phase was 15 mM diisopropylethylamine/20 mM hexafluoroisopropanol in methanol. The method allowed total separation between the oligonucleotides studied (resolution of 2.3) by using the core shell technology, which reduce the diffusion time of the analyte into the column, increasing the efficiency and minimizing the analysis time at 7 min. The mass spectrometry detection allowed a high selectivity and sensitivity. This is the first time where MRM modality has been employed with this specific purpose. Oligonucleotides recovery from reaction mixture was ∼ 94% and the limit of quantification was 13.4 nM for 15mer. The method was evaluated with a recombinant CPD-photolyase from Synechococcus leopoliensis using purified and crude protein extract. CPD-photolyase could be measured in terms of activity for enzymatic kinetics studies, for evaluation of UV-R effects in (micro)organisms and to identify new enzymes.
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Affiliation(s)
- A Vallejos-Almirall
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - C Folch-Cano
- Departamento de Agroindustrias, Facultad de Ingeniería Agrícola, Universidad de Concepción, Chillán, Chile
| | - A Rosas
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile
| | - C Vergara
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile.
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20
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Liu R, Liu Z, Gong L. Triethylamine improves MS signals stability of diluted oligonucleotides caused by sample containers. Anal Biochem 2019; 587:113446. [PMID: 31545947 DOI: 10.1016/j.ab.2019.113446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 10/26/2022]
Abstract
The effect of sample containers made of different materials on the MS-based analysis of oligonucleotides remains unknown. Here, we evaluated five types of sample containers on the MS signal stability of oligonucleotide, and they were normal glass insert, silanized glass insert with three different silanization techniques, and polypropylene sample vial. Also, we attempted to tackle signal stability issue by varying modifiers in dissolution solvent. Our results showed that sample containers made of different materials can significantly influence the MS signal stability of oligonucleotide at low concentration. Triethylamine (TEA) evidently improved both the signal stability and intensity of oligonucleotide.
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Affiliation(s)
- Rong Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
| | - Lingzhi Gong
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China.
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21
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Jansons M, Pugajeva I, Bartkevics V. Evaluation of selected buffers for simultaneous determination of ionic and acidic pesticides including glyphosate using anion exchange chromatography with mass spectrometric detection. J Sep Sci 2019; 42:3077-3085. [PMID: 31347252 DOI: 10.1002/jssc.201900308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 11/06/2022]
Abstract
Ion chromatography coupled with mass spectrometry is an established technique for determination of ionic analytes, however, sophisticated buffer removal equipment is required to eliminate inorganic compounds from the eluate before introduction into the ion source of mass spectrometer. A standard high-performance liquid chromatography coupled with tandem mass spectrometry setup using an ion exchange column (Metrosep® A Supp 5) is proposed as an alternative approach. For that reason, some buffers including non-volatile carboxylic acid based solutions have been evaluated for simultaneous trace determination of ionic and acidic pesticides including glyphosate in the same extract without a need for sophisticated buffer removal equipment. Two differently designed ionisation sources were compared qualitatively for the application of non-volatile buffers. The study revealed that the choice of buffers had a strong influence on matrix effects in case of spiked extract injections. Finally, pesticides with very different physicochemical properties (logP < 0, logP ≥ 0) and structures (containing carboxylate, phosphonate, azolide, azanide, phenolate, bromate, and chlorate moieties) were quantified in spiked beer and oat extracts with acceptable recoveries (80-110%) using tandem mass spectrometry detection with AB SCIEX QTRAP 5500 instrument after separation using edetate buffer.
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Affiliation(s)
- Martins Jansons
- University of Latvia, Faculty of Chemistry, Riga, Latvia.,Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
| | - Iveta Pugajeva
- Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
| | - Vadims Bartkevics
- University of Latvia, Faculty of Chemistry, Riga, Latvia.,Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
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22
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Kaczmarkiewicz A, Nuckowski Ł, Studzińska S. Analysis of the first and second generation of antisense oligonucleotides in serum samples with the use of ultra high performance liquid chromatography coupled with tandem mass spectrometry. Talanta 2019; 196:54-63. [DOI: 10.1016/j.talanta.2018.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/22/2022]
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23
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Liu R, Ruan Y, Liu Z, Gong L. The role of fluoroalcohols as counter anions for ion-pairing reversed-phase liquid chromatography/high-resolution electrospray ionization mass spectrometry analysis of oligonucleotides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:697-709. [PMID: 30668892 DOI: 10.1002/rcm.8386] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Hexafluoroisopropanol (HFIP) has been widely used as a counter anion in the mobile phase for ion-pairing reversed-phase liquid chromatography/mass spectrometry (IP-RP-LC/MS) analysis of oligonucleotides. However, researchers are still searching for improvements to counter anions for LC/MS analysis of oligonucleotides. This study aimed to find alternatives to HFIP for analyzing oligonucleotides. METHODS The study was performed using an Agilent 1290 ultra-high-performance liquid chromatography (UHPLC) system coupled to an Agilent 6540 mass spectrometer by using an oligonucleotide BEH C18 column (100 × 2.1 mm, 1.7 μm). Buffer systems containing ion-pairing reagents (triethylamine, tripropylamine, hexylamine, dimethylbutylamine, diisopropylethylamine, N,N-dimethylcyclohexylamine, and octylamine) and fluoroalcohols (HFIP and hexafluoro-2-methyl-2-propanol (HFTP)) were compared chromatographically and mass spectrometrically. RESULTS Results showed that HFTP has better desalting ability than HFIP, but both HFIP and HFTP have comparable effects on the separation of oligonucleotides sized from 10mer to 40mer for most of ion-pairing reagents, with the exception of triethylamine and N,N-dimethylcyclohexylamine, where HFIP performed better than HFTP. CONCLUSIONS The choice of fluoroalcohols in IP-RP-LC/MS analysis of oligonucleotides depends on the type of ion-pairing reagents used in the mobile phase. As a guideline, we would recommend to use either HA-HFIP or HA-HFTP for small oligonucleotides, but TPA-HFTP for large oligonucleotides for IP-RP-LC/MS analysis of synthetic oligonucleotides.
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Affiliation(s)
- Rong Liu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
| | - Yanjiao Ruan
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
| | - Zhongqiu Liu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
| | - Lingzhi Gong
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, PR China
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24
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Oligonucleotide analysis by hydrophilic interaction liquid chromatography-mass spectrometry in the absence of ion-pair reagents. J Chromatogr A 2019; 1595:39-48. [PMID: 30772056 DOI: 10.1016/j.chroma.2019.02.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/02/2019] [Accepted: 02/06/2019] [Indexed: 01/09/2023]
Abstract
Improving our understanding of nucleic acids, both in biological and synthetic applications, remains a bustling area of research for both academic and industrial laboratories. As nucleic acids research evolves, so must the analytical techniques used to characterize nucleic acids. One powerful analytical technique has been coupled liquid chromatography - tandem mass spectrometry (LC-MS/MS). To date, the most successful chromatographic mode has been ion-pairing reversed-phase liquid chromatography. Hydrophilic interaction liquid chromatography (HILIC), in the absence of ion-pair reagents, has been investigated here as an alternative chromatographic approach to the analysis of oligonucleotides. By combining a mobile phase system using commonly employed in liquid chromatography-mass spectrometry (LC-MS) - i.e., water, acetonitrile, and ammonium acetate - and a new, commercially available diol-based HILIC column, high chromatographic and mass spectrometric performance for a wide range of oligonucleotides is demonstrated. Particular applications of HILIC-MS for the analysis of deoxynucleic acid (DNA) oligomers, modified and unmodified oligoribonucleotides, and phosphorothioate DNA oligonucleotides are presented. Based on the LC-MS performance, this HILIC-based approach provides an attractive, sensitive and robust alternative to prior ion-pairing dependent methods with potential utility for both qualitative and quantitative analyses of oligonucleotides without compromising chromatographic or mass spectrometric performance.
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25
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Kaczmarkiewicz A, Nuckowski Ł, Studzińska S, Buszewski B. Analysis of Antisense Oligonucleotides and Their Metabolites with the Use of Ion Pair Reversed-Phase Liquid Chromatography Coupled with Mass Spectrometry. Crit Rev Anal Chem 2019; 49:256-270. [PMID: 30612436 DOI: 10.1080/10408347.2018.1517034] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Antisense oligonucleotides (ASOs) have been widely investigated as a potential drugs because of their ability to bind with the target DNA or RNA strands, which may lead to inhibition of translational processes. This review presents currently approved oligonucleotide (OGN) drugs and summarizes their modification types, mechanisms of action, and application of ion pair reversed phase liquid chromatography for the analysis. Special attention was paid to the stationary phases selection for the separation of OGNs and the impact of different compositions of mobile phases on retention and signal intensity in mass spectrometry (MS). Moreover, the application of ion pair liquid chromatography coupled with MS for the separation and determination of metabolites of ASOs was described. The type of matrix, time of analysis, lower limits of quantification and detection, as well as precision, accuracy, and linearity of developed methods have been included as part of this contribution.
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Affiliation(s)
- Anna Kaczmarkiewicz
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Łukasz Nuckowski
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Sylwia Studzińska
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Bogusław Buszewski
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
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26
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Gao J, Li L, Cui C, Ziaee MA, Gong Y, Sa R, Zhong H. Experimental and theoretical study for CO2 activation and chemical fixation with epoxides. RSC Adv 2019; 9:13122-13127. [PMID: 35520791 PMCID: PMC9063868 DOI: 10.1039/c8ra10475a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/24/2019] [Indexed: 11/21/2022] Open
Abstract
The synthesis of five-membered cyclic carbonates via catalytic cycloaddition reaction of CO2 with epoxides is considered to be an effective technology for alleviation of the energy crisis and global warming. Various commercial organic bases and ionic salts were used as catalysts, while the relationship of catalytic activity and compound structure has been seldom explored. Herein, a facilely obtained binary catalytic system based on triethylamine/NBu4Br was developed for CO2 activation and chemical fixation. The highly efficient catalytic system showed outstanding conversion and above 99% selectivity under metal-free mild reaction conditions (100 °C, 1 atm) in one hour. The detailed process of CO2 activation and chemical fixation was investigated at the molecular level by a series of experiments and theoretical calculation, which provided a mode for the design and synthesis of a highly efficient catalytic system for conversion of CO2 under mild conditions. NEt3/NBu4Br works as an excellent metal-free catalyst for CO2 cycloaddition with epoxides and the detailed process of CO2 activation by NEt3 is first studied by theoretical calculation.![]()
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Affiliation(s)
- Jinwei Gao
- College of Science
- North University of China
- Taiyuan
- P. R. China
- State Key Laboratory of Structural Chemistry
| | - Liuyi Li
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou
- China
| | - Caiyan Cui
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou
- China
| | - Muhammad Asad Ziaee
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou
- China
| | - Yaqiong Gong
- College of Science
- North University of China
- Taiyuan
- P. R. China
| | - Rongjian Sa
- Institute of Oceanography
- Ocean College
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control
- Minjiang University
- Fuzhou
| | - Hong Zhong
- College of Science
- North University of China
- Taiyuan
- P. R. China
- State Key Laboratory of Structural Chemistry
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27
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Analytical Methods for Mass Spectrometry-Based Metabolomics Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:635-647. [DOI: 10.1007/978-3-030-15950-4_38] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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28
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Sasaki T, Kudalkar SN, Bertoletti N, Anderson KS. DRONE: Direct Tracking of DNA Cytidine Deamination and Other DNA Modifying Activities. Anal Chem 2018; 90:11735-11740. [PMID: 30256094 PMCID: PMC6410358 DOI: 10.1021/acs.analchem.8b01405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Enzymes that catalyze DNA modifying activities including cytidine deamination and cytosine methylation play important biological roles and have been implicated pathologically in diseases such as cancer. Here, we report Direct Resolution of ONE dalton difference (DRONE), an ultra high performance liquid chromatography (UHPLC)-based analytical method to track a single dalton change in the cytosine-to-uracil conversion catalyzed by the human apolipoprotein B m-RNA editing catalytic polypeptide-like 3 (APOBEC3) cytidine deaminases, implicated in cancer and antiviral defense. Additionally, we demonstrate broad applicability by tracking other important DNA modifications and assessing epigenetic enzyme inhibition. We have extended our methodology to obtain data on two distinct deamination events in the same oligonucleotide substrate designed from a putative APOBEC substrate, diversifying the utility of the described method. DRONE provides an important foundation for in-depth analysis of DNA-modifying enzymes and versatile detection of novel DNA modifications of interest.
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Affiliation(s)
- Tomoaki Sasaki
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
| | - Shalley N. Kudalkar
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
| | - Nicole Bertoletti
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
| | - Karen S. Anderson
- Department of Pharmacology, Yale University, 333 Cedar St. SHM B-350 New Haven, CT 06520
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29
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Su X, Liang R, Stolee JA. A facile one-step fluorescence method for the quantitation of low-content single base deamination impurity in synthetic oligonucleotides. J Pharm Biomed Anal 2018; 155:50-55. [PMID: 29614399 DOI: 10.1016/j.jpba.2018.03.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/20/2018] [Accepted: 03/25/2018] [Indexed: 11/27/2022]
Abstract
Oligonucleotides are being researched and developed as potential drug candidates for the treatment of a broad spectrum of diseases. The characterization of antisense oligonucleotide (ASO) impurities caused by base mutations (e.g. deamination) which are closely related to the target ASO is a significant analytical challenge. Herein, we describe a novel one-step method, utilizing a strategy that combines fluorescence-ON detection with competitive hybridization, to achieve single base mutation quantitation in extensively modified synthetic ASOs. Given that this method is highly specific and sensitive (LoQ = 4 nM), we envision that it will find utility for screening other impurities as well as sequencing modified oligonucleotides.
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Affiliation(s)
- Xiaoye Su
- Analytical Development, Biogen Inc., Cambridge, MA 02142, United States.
| | - Ruiting Liang
- Analytical Development, Biogen Inc., Cambridge, MA 02142, United States.
| | - Jessica A Stolee
- Analytical Development, Biogen Inc., Cambridge, MA 02142, United States.
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Bui HH, Sanders PE, Bodenmiller D, Kuo MS, Donoho GP, Fischl AS. Direct analysis of PI(3,4,5)P 3 using liquid chromatography electrospray ionization tandem mass spectrometry. Anal Biochem 2018; 547:66-76. [PMID: 29470948 DOI: 10.1016/j.ab.2018.02.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/08/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022]
Abstract
Phosphatidylinositol (3,4,5) trisphosphate (PIP3) is a biologically active membrane phospholipid that is essential for the growth and survival of all eukaryotic cells. We describe a new method that directly measures PIP3 and describe the HPLC separation and measurement of the positional isomers of phosphatidylinositol bisphosphate, PI(3,5)P2, PI(3,4)P2 and PI(4,5)P2. Mass spectrometric analyses were performed online using ultra-high performance liquid chromatography (UHPLC)-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) in the negative multiple-reaction monitoring (MRM) modes. Rapid separation of PIP3 from PI, phosphatidylinositol phosphate (PIP) and PIP2 was accomplished by C18 reverse phase chromatography with the addition of the ion pairing reagents diisopropylethanolamine (DiiPEA) and ethylenediamine tetraacetic acid tetrasodium salt dihydrate (EDTA) to the samples and mobile phase with a total run time, including equilibration, of 12 min. Importantly, these chromatography conditions result in no carryover of PIP, PIP2, and PIP3 between samples. To validate the new method, U87MG cancer cells were serum starved and treated with PDGF to stimulate PIP3 biosynthesis in the presence or absence of the phosphatidylinositol 3-kinase (PI3K) inhibitor LY294002. Results generated with the LC/MS method were in excellent agreement with results generated using [33P] phosphate radiolabeled U87MG cells and anion exchange chromatography analysis, a well validated method for measuring PIP3. To demonstrate the usefulness of the new method, we generated reproducible IC50 data for several well-characterized PI3K small molecule inhibitors using a U87MG cell-based assay as well as showing PIP3 can be measured from additional cancer cell lines. Together, our results demonstrate this novel method is sensitive, reproducible and can be used to directly measure PIP3 without radiolabeling or complex lipid derivatization.
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Affiliation(s)
- Hai H Bui
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA.
| | - Phillip E Sanders
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Diane Bodenmiller
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Ming Shang Kuo
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Gregory P Donoho
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Anthony S Fischl
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
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Franzoni S, Vezzelli A, Turtoro A, Solazzo L, Greco A, Tassone P, Di Martino M, Breda M. Development and validation of a bioanalytical method for quantification of LNA-i-miR-221, a 13-mer oligonucleotide, in rat plasma using LC–MS/MS. J Pharm Biomed Anal 2018; 150:300-307. [DOI: 10.1016/j.jpba.2017.12.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 10/18/2022]
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Gong L. Analysis of oligonucleotides by ion-pairing hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:2125-2134. [PMID: 28972295 DOI: 10.1002/rcm.8004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry (HILIC-LC/ESI-MS) has been proved to be useful for the quality control of oligonucleotides. However, the lack of separation for some oligonucleotides using HILIC-LC/MS has proved problematic. This study aimed to improve the resolving ability of HILIC-LC/MS. METHODS The study was performed on a Waters UPLC® system coupled to a Waters LCT premier XE ESI-TOF mass spectrometer using a Zorbax® RRHD HILIC column (2.1 mm × 100 mm, 1.8 μm). Buffer systems contained triethylammonium acetate (TEAA) and acetonitrile. The effects of the concentration of TEAA and the type of organic modifiers on the separation of oligonucleotides were investigated. RESULTS The results showed that the optimum concentration of TEAA is 10 mM and acetonitrile is a better organic solvent than methanol. The addition of TEAA in the HILIC mobile phase improved the separation of N from N + A significantly compared to the HILIC method buffered with ammonium acetate. The IP-HILIC chromatography has demonstrated that the separation of oligonucleotides is sequence dependent. In addition, the IP-HILIC method produces a much simpler mass spectrum of an oligonucleotide with very efficient desalting. CONCLUSIONS The HILIC-LC/MS method with the addition of TEAA at a MS-compatible concentration has improved the separation of oligonucleotides. The IP-HILIC-LC/MS method also produces very simple mass spectra with high desalting efficiency.
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Affiliation(s)
- Lingzhi Gong
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Studzińska S. Review on investigations of antisense oligonucleotides with the use of mass spectrometry. Talanta 2017; 176:329-343. [PMID: 28917758 DOI: 10.1016/j.talanta.2017.08.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022]
Abstract
Antisense oligonucleotides have been investigated as potential drugs for years. They inhibit target gene or protein expression. The present review summarizes their modifications, modes of action, and applications of liquid chromatography coupled with mass spectrometry for qualitative and quantitative analysis of these compounds. The most recent reports on a given topic were given prominence, while some early studies were reviewed in order to provide a theoretical background. The present review covers the issues of using ion-exchange chromatography, ion-pair reversed-phase high performance liquid chromatography and hydrophilic interaction chromatography for the separation of antisense oligonucleotides. The application of mass spectrometry was described with regard to the ionization type used for the determination of these potential therapeutics. Moreover, the current approaches and applications of mass spectrometry for quantitative analysis of antisense oligonucleotides and their metabolites as well as their impurities during in vitro and in vivo studies were discussed. Finally, certain conclusions and perspectives on the determination of therapeutic oligonucleotides in various samples were briefly described.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland.
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Basiri B, Murph MM, Bartlett MG. Assessing the Interplay between the Physicochemical Parameters of Ion-Pairing Reagents and the Analyte Sequence on the Electrospray Desorption Process for Oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1647-1656. [PMID: 28405940 PMCID: PMC5569388 DOI: 10.1007/s13361-017-1671-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/10/2017] [Accepted: 03/20/2017] [Indexed: 05/25/2023]
Abstract
Alkylamines are widely used as ion-pairing agents during LC-MS of oligonucleotides. In addition to a better chromatographic separation, they also assist with the desorption of oligonucleotide ions into the gas phase, cause charge state reduction, and decrease cation adduction. However, the choice of such ion-pairing agents has considerable influence on the MS signal intensity of oligonucleotides as they can also cause significant ion suppression. Interestingly, optimal ion-pairing agents should be selected on a case by case basis as their choice is strongly influenced by the sequence of the oligonucleotide under investigation. Despite imposing major practical difficulties to analytical method development, such a highly variable system that responds very strongly to the nuances of the electrospray composition provides an excellent opportunity for a fundamental study of the electrospray ionization process. Our investigations using this system quantitatively revealed the major factors that influenced the ESI ionization efficiency of oligonucleotides. Parameters such as boiling point, proton affinity, partition coefficient, water solubility, and Henry's law constants for the ion-pairing reagents and the hydrophobic thymine content of the oligonucleotides were found to be the most significant contributors. Identification of these parameters also allowed for the development of a statistical predictive algorithm that can assist with the choice of an optimum IP agent for each particular oligonucleotide sequence. We believe that research in the field of oligonucleotide bioanalysis will significantly benefit from this algorithm (included in Supplementary Material) as it advocates for the use of lesser-known but more suitable ion-pair alternatives to TEA for many oligonucleotide sequences. Graphical Abstract ᅟ.
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Affiliation(s)
- Babak Basiri
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA
| | - Mandi M Murph
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA.
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Husser C, Brink A, Zell M, Müller MB, Koller E, Schadt S. Identification of GalNAc-Conjugated Antisense Oligonucleotide Metabolites Using an Untargeted and Generic Approach Based on High Resolution Mass Spectrometry. Anal Chem 2017; 89:6821-6826. [PMID: 28520401 DOI: 10.1021/acs.analchem.7b01244] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antisense oligonucleotides linked by phosphorothioates are an important class of therapeutics under investigation in various pharmaceutical companies. Antisense oligonucleotides may be coupled to high-affinity ligands (triantennary N-acetyl galactosamine = GalNAc) for hepatocyte-specific asialoglycoprotein receptors (ASGPR) to enhance uptake to hepatocytes and to increase potency. Since disposition and biotransformation of GalNAc-conjugated oligonucleotides is different from unconjugated oligonucleotides, appropriate analytical methods are required to identify main cleavage sites and degradation products of GalNAc conjugated and unconjugated oligonucleotides in target cells. A highly sensitive method was developed to identify metabolites of oligonucleotides using capillary flow liquid chromatography with column switching coupled to a high resolution Orbitrap Fusion mass spectrometer. Detection of GalNAc-conjugated oligonucleotides and their metabolites was achieved by combining full scan MS with two parallel MS2 experiments, one data-dependent scan and an untargeted MS2 experiment (all ion fragmentation) applying high collision energy. In the all ion fragmentation scan, a diagnostic fragment originating from the phosphorothioate backbone (O2PS-: m/z 94.936) was formed efficiently upon collisional activation. Based on this fragment an accurate determination of metabolites of oligonucleotides was achieved, independent of their sequence or conjugation in an untargeted but highly selective manner. The method was effectively applied to investigate uptake and metabolism of GalNAc-conjugated oligonucleotides in incubations of primary rat hepatocytes; the elucidation of expected and unexpected degradation products was achieved in subnanomolar range.
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Affiliation(s)
- Christophe Husser
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Andreas Brink
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Manfred Zell
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Martina B Müller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Erich Koller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Simone Schadt
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
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Mateos-Vivas M, Domínguez-Álvarez J, Rodríguez-Gonzalo E, Carabias-Martínez R. Capillary electrophoresis coupled to mass spectrometry employing hexafluoro-2-propanol for the determination of nucleosides and nucleotide mono-, di- and tri-phosphates in baby foods. Food Chem 2017; 233:38-44. [PMID: 28530588 DOI: 10.1016/j.foodchem.2017.04.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 03/31/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022]
Abstract
The present work describes a method for the simultaneous determination of unmodified nucleosides and nucleotide mono-, di- and tri-phosphates by capillary electrophoresis coupled to mass spectrometry (CE-MS). The use of hexafluoro-2-propanol (HFIP) in the separation medium, and as an additive to the sheath liquid of the electrospray interface (ESI), generated a highly efficient and sensitive method. Instrumental limits of detection in the range of 14-53ngmL-1 for nucleosides and 7-23, 20-49 and 64-124ngmL-1 for nucleotide mono-, di-, and tri-phosphates, respectively, were found. Sample treatment involved diluting an aliquot of baby food with ultra-high quality water and applying centrifugation-assisted ultrafiltration (CUF). The proposed method was validated and used to analyse a variety of baby food samples (16 in total) such as fish, meat, fruits, and baby dairy desserts that may endogenously contain these analytes.
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Affiliation(s)
- María Mateos-Vivas
- Department of Analytical Chemistry, Nutrition and Food Science, University of Salamanca, 37008 Salamanca, Spain.
| | - Javier Domínguez-Álvarez
- Department of Analytical Chemistry, Nutrition and Food Science, University of Salamanca, 37008 Salamanca, Spain.
| | | | - Rita Carabias-Martínez
- Department of Analytical Chemistry, Nutrition and Food Science, University of Salamanca, 37008 Salamanca, Spain.
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Tailored liquid chromatography–mass spectrometry analysis improves the coverage of the intracellular metabolome of HepaRG cells. J Chromatogr A 2017; 1487:168-178. [DOI: 10.1016/j.chroma.2017.01.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 01/15/2017] [Accepted: 01/22/2017] [Indexed: 12/12/2022]
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Studzińska S, Rola R, Buszewski B. The impact of ion-pairing reagents on the selectivity and sensitivity in the analysis of modified oligonucleotides in serum samples by liquid chromatography coupled with tandem mass spectrometry. J Pharm Biomed Anal 2017; 138:146-152. [PMID: 28208106 DOI: 10.1016/j.jpba.2017.02.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/04/2017] [Accepted: 02/06/2017] [Indexed: 11/28/2022]
Abstract
Present study highlights the usage of various ion-pairing agents and their impact on the process of separation and ionization of oligonucleotides in the fortified human serum samples. What is more, retention studies involved different stationary phases, including: octadecyl, phenyl, pentafluorophenyl groups and ligands with embedded polar groups. It was proved that retention of oligonucleotides strongly depends on the alkyl chain branching in the structure of ion pairing reagent. Furthermore ion-pairing agents build of straight alkyl chain are more easily adsorbed on the stationary phase modified with octadecyl groups, while branching of alkyl chain caused more effective adsorption of studied compounds at phenyl groups compared to octadecyl ones. The lowest limit of quantification values were obtained for 5mMN,N-dimethylbutylamine, while the highest values are characteristic for hexylamine. Moreover it was shown that a 2-fold increase of ion-pairing agent concentration results in higher LOQ. The greatest sensitivity was obtained for 2.5mMN,N-dimethylbutylamine/150mM hexafluoroisopropanol. On the other hand Hypersil GOLD aQ column was the most appropriate in terms of time and separation effectiveness. The developed method was successfully used for the determination of studied oligonucleotides and their metabolites in human serum samples. The compounds were separated in just 3.5min with high sensitivity (0.09-0.16ng).
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland.
| | - Rafał Rola
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland
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Recent Advances in the Characterization and Analysis of Therapeutic Oligonucleotides by Analytical Separation Methods Coupling with Mass Spectrometry. ADVANCES IN CHROMATOGRAPHY 2016. [DOI: 10.1201/9781315370385-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Mikulášek K, Jaroň KS, Kulhánek P, Bittová M, Havliš J. Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography-A structure-retention study assisted by soft-modelling and molecular dynamics. J Chromatogr A 2016; 1469:88-95. [PMID: 27692640 DOI: 10.1016/j.chroma.2016.09.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/22/2016] [Accepted: 09/24/2016] [Indexed: 10/21/2022]
Abstract
We studied sequence-dependent retention properties of synthetic 5'-terminal phosphate absent trinucleotides containing adenine, guanine and thymine through reversed-phase liquid chromatography (RPLC) and QSRR modelling. We investigated the influence of separation conditions, namely mobile phase composition (ion interaction agent content, pH and organic constituent content), on sequence-dependent separation by means of ion-interaction RPLC (II-RPLC) using two types of models: experimental design-artificial neural networks (ED-ANN), and linear regression based on molecular dynamics data. The aim was to determine those properties of the above-mentioned analytes responsible for the retention dependence of the sequence. Our results show that there is a deterministic relation between sequence and II-RPLC retention properties of the studied trinucleotides. Further, we can conclude that the higher the content of ion-interaction agent in the mobile phase, the more prominent these properties are. We also show that if we approximate the polar component of solvation energy in QSRR by the electrostatic work in transferring molecules from vacuum to water, and the non-polar component by the solvent accessible surface area, these parameters best describe the retention properties of trinucleotides. There are some exceptions to this finding, namely sequences 5'-NAN-3', 5'-ANN-3', 5'-TGN-3', 5'-NTA-3'and 5'-NGA-3' (N stands for generic nucleotide). Their role is still unknown, but since linear regression including these specific constellations showed a higher observable variance coverage than the model with only the basic descriptors, we may assume that solvent-analyte interactions are responsible for the exceptional behaviour of 5'-NAN-3' & 5'-ANN-3' trinucleotides and some intramolecular interactions of neighbouring nucleobases for 5'-TGN-3', 5'-NTA-3'and 5'-NGA-3' trinucleotides.
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Affiliation(s)
- Kamil Mikulášek
- Masaryk University, Faculty of Science, Department of Chemistry, Kamenice 5, 62500 Brno, Czech Republic; Masaryk University, CEITEC - Central European Institute of Technology, Kamenice 5, 62500 Brno, Czech Republic
| | - Kamil S Jaroň
- Academy of Sciences of the Czech Republic, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic
| | - Petr Kulhánek
- Masaryk University, CEITEC - Central European Institute of Technology, Kamenice 5, 62500 Brno, Czech Republic; Masaryk University, Faculty of Science, National Centre of Biomolecular Research, Kamenice 5, 62500 Brno, Czech Republic
| | - Miroslava Bittová
- Masaryk University, Faculty of Science, Department of Chemistry, Kamenice 5, 62500 Brno, Czech Republic
| | - Jan Havliš
- Masaryk University, CEITEC - Central European Institute of Technology, Kamenice 5, 62500 Brno, Czech Republic; Masaryk University, Faculty of Science, National Centre of Biomolecular Research, Kamenice 5, 62500 Brno, Czech Republic.
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Guo L, Worth AJ, Mesaros C, Snyder NW, Glickson JD, Blair IA. Diisopropylethylamine/hexafluoroisopropanol-mediated ion-pairing ultra-high-performance liquid chromatography/mass spectrometry for phosphate and carboxylate metabolite analysis: utility for studying cellular metabolism. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1835-45. [PMID: 27476658 PMCID: PMC4970762 DOI: 10.1002/rcm.7667] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 05/21/2023]
Abstract
RATIONALE Mass spectrometric (MS) analysis of low molecular weight polar metabolites can be challenging because of poor chromatographic resolution of isomers and insufficient ionization efficiency. These metabolites include intermediates in key metabolic pathways, such as glycolysis, the pentose phosphate pathway, and the Krebs cycle. Therefore, sensitive, specific, and comprehensive quantitative analysis of these metabolites in biological fluids or cell culture models can provide insight into multiple disease states where perturbed metabolism plays a role. METHODS An ion-pairing reversed-phase ultra-high-performance liquid chromatography (IP-RP-UHPLC)/MS approach to separate and analyze biochemically relevant phosphate- and carboxylic acid-containing metabolites was developed. Diisopropylethylamine (DIPEA) was used as an IP reagent in combination with reversed-phase liquid chromatography (RP-LC) and a triple quadrupole mass spectrometer using selected reaction monitoring (SRM) and negative electrospray ionization (NESI). An additional reagent, hexafluoroisopropanol (HFIP), which has been previously used to improve sensitivity of nucleotide analysis by UHPLC/MS, was used to enhance sensitivity. RESULTS HFIP versus acetic acid, when added with the IP base, increased the sensitivity of IP-RP-UHPLC/NESI-MS up to 10-fold for certain analytes including fructose-1,6-bisphosphate, phosphoenolpyruvate, and 6-phosphogluconate. It also improved the retention of the metabolites on a C18 reversed-phase column, and allowed the chromatographic separation of important isomeric metabolites. This methodology was amenable to quantification of key metabolites in cell culture experiments. The applicability of the method was demonstrated by monitoring the metabolic adaptations resulting from rapamycin treatment of DB-1 human melanoma cells. CONCLUSIONS A rapid, sensitive, and specific IP-RP-UHPLC/NESI-MS method was used to quantify metabolites from several biochemical pathways. IP with DIPEA and HFIP increased the sensitivity and improved chromatographic separation when used with reversed-phase UHPLC.
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Affiliation(s)
- Lili Guo
- Penn SRP and Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew J. Worth
- Penn SRP and Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
| | - Clementina Mesaros
- Penn SRP and Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Jerry D. Glickson
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ian A. Blair
- Penn SRP and Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
- Corresponding author: Ian A. Blair, PhD, Center for Cancer Pharmacology, University of Pennsylvania, 854 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6160. Phone: 215-573-9885; Fax: 215-573-9889;
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Birdsall RE, Gilar M, Shion H, Yu YQ, Chen W. Reduction of metal adducts in oligonucleotide mass spectra in ion-pair reversed-phase chromatography/mass spectrometry analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1667-1679. [PMID: 28328039 PMCID: PMC5094505 DOI: 10.1002/rcm.7596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/28/2016] [Accepted: 05/01/2016] [Indexed: 05/09/2023]
Abstract
RATIONALE Electrospray ionization mass spectrometry (ESI-MS)-based techniques commonly used in oligonucleotide analyses are known to be sensitive to alkali metal adduct formation. Adducts directly impact the sensitivity of MS-based analyses as the available charge is distributed across the parent peak and adduct(s). The current study systematically evaluated common liquid chromatography (LC) components in LC/ESI-MS configurations used in oligonucleotide analysis to identify metal adduct contributions from LC instrumentation. METHODS A UPLC liquid chromatography system was configured with a single quadrupole MS detector (ACQUITY QDa, Waters Corp.) to monitor adduct formation in oligonucleotide separations. An ion-pairing mobile phase comprised of 15 mM triethylamine and 400 mM hexafluoro-2-propanol was used in conjunction with an oligonucleotide separation column (Waters OST BEH C18, 2.1 mm × 50 mm) for all separations. A 10-min method was used to provide statistical figures of merit and evaluate adduct formation over time. RESULTS Trace alkali metal salts in the mobile phase and reagents were determined to be the main source of metal salt adducts in LC/ESI-MS-based configurations. Non-specific adsorption sites located throughout the fluidic path contribute to adduct formation in oligonucleotide analyses. Ion-pairing mobile phases prepared at neutral or slightly basic pH result in up to a 57% loss of spectral abundance to adduct formation in the current study. CONCLUSIONS Implementation of a short low pH reconditioning step was observed to effectively displace trace metal salts non-specifically adsorbed to surfaces in the fluidic path and was able to maintain an average MS spectral abundance ≥94% with a high degree of repeatability (relative standard deviation (R.S.D.) 0.8%) over an extended time study. The proposed method offers the ability to rapidly regenerate adsorption sites with minimal impact on productivity while retaining assay sensitivity afforded by MS detection with reduced adduct formation. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.
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Affiliation(s)
| | - Martin Gilar
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
| | - Henry Shion
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
| | - Ying Qing Yu
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
| | - Weibin Chen
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
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Abstract
A common feature of ribonucleic acids (RNAs) is that they can undergo a variety of chemical modifications. As nearly all of these chemical modifications result in an increase in the mass of the canonical nucleoside, mass spectrometry has long been a powerful approach for identifying and characterizing modified RNAs. Over the past several years, significant advances have been made in method development and software for interpreting tandem mass spectra resulting in approaches that can yield qualitative and quantitative information on RNA modifications, often at the level of sequence specificity. We discuss these advances along with instrumentation developments that have increased our ability to extract such information from relatively complex biological samples. With the increasing interest in how these modifications impact the epitranscriptome, mass spectrometry will continue to play an important role in bioanalytical investigations revolving around RNA.
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Affiliation(s)
- Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172. and University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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Gong L. Comparing ion-pairing reagents and counter anions for ion-pair reversed-phase liquid chromatography/electrospray ionization mass spectrometry analysis of synthetic oligonucleotides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2402-2410. [PMID: 26563710 DOI: 10.1002/rcm.7409] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/18/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Ion-pair reversed-phase liquid chromatography/electrospray ionization mass spectrometry (IP-RP-LC/ESI-MS) has been widely used for the quality control of oligonucleotides. However, researchers are still looking to improve mobile phase systems for IP-RP-LC/ESI-MS analysis of oligonucleotides. This study compared the performance of six ion-pairing reagents with three different counter anions for IP-RP-LC/ESI-MS analysis of oligonucleotides. METHODS The study was performed using a Waters ultra-performance liquid chromatography (UPLC®) system coupled to a Waters LCT Premier XE mass spectrometer by using a UPLC® OST column (2.1 mm × 100 mm, 1.7 µm). Buffer systems containing acetate, bicarbonate, and hexafluoroisopropanolate salts of six ion-pairing reagents (triethylamine, tripropylamine, hexylamine, N,N-dimethylbutylamine, dibutylamine, N,N-diisopropylethylamine), respectively, were optimized for IP-RP-LC/ESI-MS analysis of oligonucleotides, and then the optimized conditions were applied for the separation of oligonucleotides. RESULTS Counter anions definitely play a role in IP-RP-LC/ESI-MS analysis of oligonucleotides. Buffer containing 30 mM diisopropylethylamine and 200 mM hexafluoroisopropanol provided the highest separation of unmodified heterogeneous oligonucleotides, but tripropylammonium hexafluoroisopropanolate achieved the most enhanced separation of sequence isomers. However, triethylammonium acetate and bicarbonate had equally the highest separation for positional isomers. CONCLUSIONS IP-RP-LC/ESI-MS separation of oligonucleotides is mainly sequence dependent, but it is also dependent on both the type of ion-pairing reagent and counter anion present in the mobile phase.
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Affiliation(s)
- Lingzhi Gong
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Hydrophilic interaction chromatography coupled to tandem mass spectrometry in the presence of hydrophilic ion-pairing reagents for the separation of nucleosides and nucleotide mono-, di- and triphosphates. J Chromatogr A 2015; 1414:129-37. [PMID: 26341591 DOI: 10.1016/j.chroma.2015.08.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022]
Abstract
A fast and efficient method for the simultaneous separation of highly polar compounds, in this case nucleosides and nucleotide mono-, di- and triphosphates, using hydrophilic interaction chromatography coupled with tandem mass spectrometry (HILIC-MS/MS) is proposed. This new separation method revealed the possibilities of the formation of hydrophilic ion-pairing compounds. Three stationary phases (HILIC XBridge-Amide, HILIC-CoreShell and ZIC-HILIC) were assayed for the separation of 20 target analytes, and a detailed study of the composition of the mobile phase was made using different salts at different concentrations in a organic-rich mobile phase. We report that in order to prevent the adsorption of nucleotides on the LC-MS setup and to enhance their retention on the HILIC stationary phase, a mobile phase containing hexafluoro-2-propanol and different cations should be used. Four cations were evaluated: ammonium, diethylammonium, triethylammonium and tetrabutylammonium. The results revealed the formation of an ionic-association compound between the phosphorylated analytes and the cationic ion-pairing reagents, whose retention increased with the polarity of the cationic ion-pairing reagent. HILIC XBridge-Amide was found to be the most suitable column for the separation of these analytes, and the optimized mobile phase consisted of an ACN/UHQ water mixture (3min of isocratic elution using 82:18%, v/v and then a fast gradient from 18% to 22% of water) with 100mM hexafluoro-2-propanol and 50mM diethylamine (w(w)pH 9-w(s)pH 10). In a total analysis time of 8min, good results were achieved in terms of resolution. Under these optimum conditions, a further comprehensive study of the retention mechanism was carried out.
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Studzińska S, Pietrzak L, Buszewski B. The Effects of Stationary Phases on Retention and Selectivity of Oligonucleotides in IP-RP-HPLC. Chromatographia 2014; 77:1589-1596. [PMID: 25477554 PMCID: PMC4244551 DOI: 10.1007/s10337-014-2766-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/19/2014] [Accepted: 09/01/2014] [Indexed: 11/23/2022]
Abstract
There is a growing demand for the separation and identification of short nucleic acid fragments, such as oligonucleotides. There were two main goals of the present investigation, namely, evaluation of the impact of stationary phase type and the influence of various ion-pair reagents on the retention behavior of oligonucleotides in ion-pair liquid chromatography. Three types of ion-pair reagents were studied: triethylammonium acetate, dimethylbuthylammonium acetate and mixtures of 1,1,1,3,3,3-hexafluoro-2-propanol and triethylamine. Two novel types of packing materials, namely, cholesterol and alkylamide were used for this purpose for the first time. The results indicate that the mechanism of oligonucleotides retention is determined by the hydrophobicity of ion-pair reagents and polar ligands localized on the surface of stationary phases. Oligonucleotides were most effectively separated with the use of alkylamide and cholesterol packings. These two stationary phases reduce the time of analysis in comparison with the octadecyl packing material. Moreover, separation was achieved under non-denaturating conditions.
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Affiliation(s)
- Sylwia Studzińska
- Chair of the Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St, PL-87 100 Torun, Poland
| | - Lidia Pietrzak
- Chair of the Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St, PL-87 100 Torun, Poland
| | - Bogusław Buszewski
- Chair of the Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St, PL-87 100 Torun, Poland
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Heydari R, Elyasi NS. Ion-pair cloud-point extraction: A new method for the determination of water-soluble vitamins in plasma and urine. J Sep Sci 2014; 37:2724-31. [DOI: 10.1002/jssc.201400642] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 06/28/2014] [Accepted: 06/28/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Rouhollah Heydari
- Razi Herbal Medicines Research Center; Lorestan University of Medical Sciences; Khorramabad Iran
| | - Najmeh S. Elyasi
- Department of Chemistry, Khouzestan Science & Research Branch; Islamic Azad University; Ahvaz Iran
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