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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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2
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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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3
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McPherson RL, Ong SE, Leung AKL. Ion-Pairing with Triethylammonium Acetate Improves Solid-Phase Extraction of ADP-Ribosylated Peptides. J Proteome Res 2020; 19:984-990. [PMID: 31859514 DOI: 10.1021/acs.jproteome.9b00696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ADP-ribosylation refers to the post-translational modification of protein substrates with monomers or polymers of the small molecule ADP-ribose. ADP-ribosylation is enzymatically regulated and plays roles in cellular processes including DNA repair, nucleic acid metabolism, cell death, cellular stress responses, and antiviral immunity. Recent advances in the field of ADP-ribosylation have led to the development of proteomics approaches to enrich and identify endogenous ADP-ribosylated peptides by liquid chromatography tandem mass spectrometry (LC-MS/MS). A number of these methods rely on reverse-phase solid-phase extraction as a critical step in preparing cellular peptides for further enrichment steps in proteomics workflows. The anionic ion-pairing reagent trifluoroacetic acid (TFA) is typically used during reverse-phase solid-phase extraction to promote retention of tryptic peptides. Here we report that TFA and other carboxylate ion-pairing reagents are inefficient for reverse-phase solid-phase extraction of ADP-ribosylated peptides. Substitution of TFA with cationic ion-pairing reagents, such as triethylammonium acetate (TEAA), improves recovery of ADP-ribosylated peptides. We further demonstrate that substitution of TFA with TEAA in a proteomics workflow specific for identifying ADP-ribosylated peptides increases identification rates of ADP-ribosylated peptides by LC-MS/MS.
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Affiliation(s)
- Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Shao-En Ong
- Department of Pharmacology , University of Washington , Seattle , Washington 98195 , United States
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Molecular Biology and Genetics, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Oncology, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
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4
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Friese OV, Sperry JB, He Y, Joseph L, Carroll JA, Rouse JC. Characterization of Apolipoprotein C3 (Apo C3) LNA/DNA Impurities and Degradation Products by LC-MS/MS. AAPS JOURNAL 2017; 19:1735-1744. [PMID: 28488174 DOI: 10.1208/s12248-017-0088-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/07/2017] [Indexed: 01/22/2023]
Abstract
Apolipoprotein C3 (Apo C3) LNA/DNA gapmer was evaluated under various stress and formulation conditions for the purpose of its development as a potential biotherapeutic for low density lipoprotein (LDL) lowering. Using ion-pairing (IP) reversed-phase (RP) liquid chromatography ultra-high resolution (UHR) tandem mass spectrometry (IP-RPLC-MS/MS), a combination of accurate mass measurements and collision-induced dissociation enabled in-depth characterization of Apo C3 LNA/DNA oligonucleotide, in particular the inherent impurities following synthesis and degradation products after exposure to stress conditions. In this study, oligonucleotide samples were stressed under different pH and UV exposure conditions. The primary impurities in Apo C3 LNA/DNA were losses of nucleotide moieties from both the 5'- and 3'-terminus leading to n-1, n-2, etc. species. Desulfurization and depurination were observed in Apo C3 LNA/DNA after a week under UV light stress conditions at low pH. Guanine oxidation and dimerization were the primary degradation products detected under UV light exposure for 1 week at high pH. The effect of antioxidants on the levels of these degradation products was evaluated under neutral pH conditions. In the presence of all antioxidants, levels of guanine oxidation and desulfurization under tested conditions were the same as those in the unstressed sample, except for sodium ascorbate. The thorough understanding of the Apo C3 LNA/DNA oligonucleotide structure, its impurities, and degradation products laid the foundation for the successful formulation development of this novel biotherapeutic modality.
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Affiliation(s)
- Olga V Friese
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA.
| | - Justin B Sperry
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Yan He
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Liji Joseph
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - James A Carroll
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Jason C Rouse
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, Andover, Massachusetts, USA
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5
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Jud L, Micura R. An Unconventional Acid-Labile Nucleobase Protection Concept for Guanosine Phosphoramidites in RNA Solid-Phase Synthesis. Chemistry 2017; 23:3406-3413. [PMID: 27943429 DOI: 10.1002/chem.201605056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Indexed: 12/14/2022]
Abstract
We present an innovative O6 -tert-butyl/N2 -tert-butyloxycarbonyl protection concept for guanosine (G) phosphoramidites. This concept is advantageous for 2'-modified G building blocks because of very efficient synthetic access when compared with existing routes that usually employ O6 -(4-nitrophenyl)ethyl/N2 -acyl protection or that start from 2-aminoadenosine involving enzymatic transformation into guanosine later on in the synthetic path. The new phosphoramidites are fully compatible with 2'-O-tBDMS or TOM phosphoramidites in standard RNA solid-phase synthesis and deprotection, and provide excellent quality of tailored RNAs for the growing range of applications in RNA biophysics, biochemistry, and biology.
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Affiliation(s)
- Lukas Jud
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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6
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Eeltink S, Wouters S, Dores-Sousa JL, Svec F. Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides. J Chromatogr A 2017; 1498:8-21. [PMID: 28069168 DOI: 10.1016/j.chroma.2017.01.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/22/2016] [Accepted: 01/02/2017] [Indexed: 11/27/2022]
Abstract
This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown.
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Affiliation(s)
- Sebastiaan Eeltink
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Sam Wouters
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - José Luís Dores-Sousa
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Frantisek Svec
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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7
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Graphene oxide decorated monolithic column as stationary phase for capillary electrochromatography. J Chromatogr A 2016; 1452:27-35. [DOI: 10.1016/j.chroma.2016.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/23/2016] [Accepted: 05/01/2016] [Indexed: 12/14/2022]
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8
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Moravcová D, Rantamäki AH, Duša F, Wiedmer SK. Monoliths in capillary electrochromatography and capillary liquid chromatography in conjunction with mass spectrometry. Electrophoresis 2016; 37:880-912. [PMID: 26800083 DOI: 10.1002/elps.201500520] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 12/29/2022]
Abstract
Here, we have reviewed separation studies utilizing monolithic capillary columns for separation of compounds preceding MS analysis. The review is divided in two parts according to the used separation method, namely CEC and capillary LC (cLC). Based on our overview, monolithic CEC-MS technique have been more focused on the syntheses of highly specialized and selective separation phase materials for fast and efficient separation of specific types of analytes. In contrast, monolithic cLC-MS is more widely used and is often employed, for instance, in the analysis of oligonucleotides, metabolites, and peptides and proteins in proteomic studies. While poly(styrene-divinylbenzene)-based and silica-based monolithic capillaries found their place in proteomic analyses, the other laboratory-synthesized monoliths still wait for their wider utilization in routine analyses. The development of new monolithic materials will most likely continue due to the demand of more efficient and rapid separation of increasingly complex samples.
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Affiliation(s)
- Dana Moravcová
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
| | | | - Filip Duša
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
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9
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Close ED, Nwokeoji AO, Milton D, Cook K, Hindocha DM, Hook EC, Wood H, Dickman MJ. Nucleic acid separations using superficially porous silica particles. J Chromatogr A 2016; 1440:135-144. [PMID: 26948761 PMCID: PMC4801196 DOI: 10.1016/j.chroma.2016.02.057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 01/31/2023]
Abstract
Ion pair reverse-phase liquid chromatography has been widely employed for nucleic acid separations. A wide range of alternative stationary phases have been utilised in conjunction with ion pair reverse-phase chromatography, including totally porous particles, non-porous particles, macroporous particles and monolithic stationary phases. In this study we have utilised superficially porous silica particles in conjunction with ion pair reverse-phase liquid chromatography for the analysis of nucleic acids. We have investigated a range of different pore-sizes and phases for the analysis of a diverse range of nucleic acids including oligonucleotides, oligoribonucleotides, phosphorothioate oligonucleotides and high molecular weight dsDNA and RNA. The pore size of the superficially porous silica particles was shown to significantly affect the resolution of the nucleic acids. Optimum separations of small oligonucleotides such as those generated in RNase mapping experiments were obtained with 80Å pore sizes and can readily be interfaced with mass spectrometry analysis. Improved resolution of larger oligonucleotides (>19mers) was observed with pore sizes of 150Å. The optimum resolution for larger dsDNA/RNA molecules was achieved using superficially porous silica particles with pore sizes of 400Å. Furthermore, we have utilised 150Å pore size solid-core particles to separate typical impurities of a fully phosphorothioated oligonucleotide, which are often generated in the synthesis of this important class of therapeutic oligonucleotide.
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Affiliation(s)
- Elizabeth D Close
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Alison O Nwokeoji
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Dafydd Milton
- Thermo Fisher Scientific, Stafford House, Boundary Way, Hemel Hempstead HP2 7GE, UK
| | - Ken Cook
- Thermo Fisher Scientific, Stafford House, Boundary Way, Hemel Hempstead HP2 7GE, UK
| | - Darsha M Hindocha
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Elliot C Hook
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Helen Wood
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK.
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10
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Erb R, Oberacher H. Comparison of mobile-phase systems commonly applied in liquid chromatography-mass spectrometry of nucleic acids. Electrophoresis 2013; 35:1226-35. [PMID: 24123202 DOI: 10.1002/elps.201300269] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 11/08/2022]
Abstract
LC-MS represents an important technology for the qualitative and quantitative analysis of nucleic acids. For MS, ESI in negative ion mode is used. The chromatographic method of choice is ion-pair (IP) RP chromatography. Chromatographic separations are usually accomplished by gradients of an organic modifier in aqueous solutions of IP reagents. Commonly applied IP reagents are 2.3 mM triethylamine/400 mM 1,1,1,3,3,3-hexafluoro-2-propanol (TEA/HFIP, pH 7.0) and 10-25 mM cyclohexyldimethylammonium acetate (CycHDMAA, pH 8.4). Direct comparison of mass spectrometric performance of the two solvent systems revealed that the TEA/HFIP system offers better detection sensitivity than the CycHDMAA system. This is mainly attributable to the depletion of HFIP during droplet formation and solvent evaporation. Removal of the anionic counterion facilitates oligonucleotide ionization, and the oligonucleotides are desorbed as highly charged ions into the gas phase. TEA/HFIP-based mobile phases are recommended for developing quantitative assays targeting defined oligonucleotides. The CycHDMAA system allows the formation of cyclohexyldimethylammonium adducts. These adducts are cleaved in the gas phase, and this decomposition gives rise to charge state reduction. Ammonium adduct formation is of particular importance in preventing adducting with metal ions. Thus, adducts with metal ions are efficiently suppressed with CycHDMAA. For the TEA/HFIP system, however, such adducting represents a severe problem particularly if large oligonucleotides are analyzed. Thus, CycHDMAA-based mobile phases are recommended for qualitative assays such as LC-MS-based genotyping.
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Affiliation(s)
- Robert Erb
- Institute of Legal Medicine and Core Facility Metabolomics, Innsbruck Medical University, Innsbruck, Austria
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11
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Yamauchi Y, Taoka M, Nobe Y, Izumikawa K, Takahashi N, Nakayama H, Isobe T. Denaturing reversed phase liquid chromatographic separation of non-coding ribonucleic acids on macro-porous polystyrene-divinylbenzene resins. J Chromatogr A 2013; 1312:87-92. [PMID: 24044980 DOI: 10.1016/j.chroma.2013.09.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 12/26/2022]
Abstract
The ability of denaturing ion-paired reversed phase LC to separate RNA was assessed using macro-porous polystyrene-divinylbenzene resins as the stationary phase. Using the three stationary phases with different pore size and a mobile phase containing phosphate, we separated RNAs of 20-8000 nucleotides with extremely high sensitivity, e.g., 50pg for an RNA 20 nucleotides in length, S/N=5. The method was used to separate non-coding RNAs obtained from biological sources and is suited for use with direct MS-based chemical characterization.
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Affiliation(s)
- Yoshio Yamauchi
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, Tokyo 192-0397, Japan
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12
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Sharma VK, Glick J, Liao Q, Shen C, Vouros P. GenoMass software: a tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:490-501. [PMID: 22689626 PMCID: PMC3375619 DOI: 10.1002/jms.2054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The analysis of DNA adducts is of importance in understanding DNA damage, and in the last few years mass spectrometry (MS) has emerged as the most comprehensive and versatile tool for routine characterization of modified oligonucleotides. The structural analysis of modified oligonucleotides, although routinely analyzed using mass spectrometry, is followed by a large amount of data, and a significant challenge is to locate the exact position of the adduct by computational spectral interpretation, which still is a bottleneck. In this report, we present an additional feature of the in-house developed GenoMass software, which determines the exact location of an adduct in modified oligonucleotides by connecting tandem mass spectrometry (MS/MS) to a combinatorial isomer library generated in silico for nucleic acids. The performance of this MS/MS approach using GenoMass software was evaluated by MS/MS data interpretation for an unadducted and its corresponding N-acetylaminofluorene (AAF) adducted 17-mer (5'OH-CCT ACC CCT TCC TTG TA-3'OH) oligonucleotide. Further computational screening of this AAF adducted 17-mer oligonucleotide (5'OH-CCT ACC CCT TCC TTG TA-3'OH) from a complex oligonucleotide mixture was performed using GenoMass. Finally, GenoMass was also used to identify the positional isomers of the AAF adducted 15-mer oligonucleotide (5'OH-ATGAACCGGAGGCCC-3'OH). GenoMass is a simple, fast, data interpretation software that uses an in silico constructed library to relate the MS/MS sequencing approach to identify the exact location of adduct on oligonucleotides.
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Affiliation(s)
- Vaneet K Sharma
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - James Glick
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - Qing Liao
- Shenitech LLC, Acton, MA, 01720, USA
| | | | - Paul Vouros
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA, 02115, USA
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Fekete S, Veuthey JL, Guillarme D. New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications. J Pharm Biomed Anal 2012; 69:9-27. [PMID: 22475515 DOI: 10.1016/j.jpba.2012.03.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 12/22/2022]
Abstract
In the pharmaceutical field, there is considerable interest in the use of peptides and proteins for therapeutic purposes. There are various ways to characterize such complex samples, but during the last few years, a significant number of technological developments have been brought to the field of RPLC and RPLC-MS. Thus, the present review focuses first on the basics of RPLC for peptides and proteins, including the inherent problems, some possible solutions and some directions for developing a new RPLC method that is dedicated to biomolecules. Then the latest advances in RPLC, such as wide-pore core-shell particles, fully porous sub-2 μm particles, organic monoliths, porous layer open tubular columns and elevated temperature, are described and critically discussed in terms of both kinetic efficiency and selectivity. Numerous applications with real samples are presented that confirm the relevance of these different strategies. Finally, one of the key advantages of RPLC for peptides and proteins over other historical approaches is its inherent compatibility with MS using both MALDI and ESI sources.
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Affiliation(s)
- Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Bd d'Yvoy 20, 1211 Geneva 4, Switzerland.
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14
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Beverly MB. Applications of mass spectrometry to the study of siRNA. MASS SPECTROMETRY REVIEWS 2011; 30:979-998. [PMID: 20201110 DOI: 10.1002/mas.20260] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 08/13/2009] [Accepted: 08/13/2009] [Indexed: 05/28/2023]
Abstract
RNA interference (RNAi) has quickly become a well-established laboratory tool for regulating gene expression and is currently being explored for its therapeutic potential. The design and use of double-stranded RNA oligonucleotides as therapeutics to trigger the RNAi mechanism and a greater effort to understand the RNAi pathway itself is driving the development of analytical techniques that can characterize these oligonucleotides. Electrospray (ESI) and MALDI have been used routinely to analyze oligonucleotides and their ability to provide mass and sequence information has made them ideal for this application. Reviewed here is the work done to date on the use of ESI and MALDI for the study of RNAi oligonucleotides as well as the strategies and issues associated with siRNA analysis by mass spectrometry. While there is not a large body of literature on the specific application of mass spectrometry to RNAi, the work done in this area is a good demonstration of the range of experiments that can be conducted and the value that ESI and MALDI can provide to the RNAi field.
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Affiliation(s)
- Michael B Beverly
- RNA Therapeutics Department, Merck and Co., Inc., Boulder, CO 80301, USA.
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15
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McGinnis AC, Chen B, Bartlett MG. Chromatographic methods for the determination of therapeutic oligonucleotides. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 883-884:76-94. [PMID: 21945211 DOI: 10.1016/j.jchromb.2011.09.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/31/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
Both DNA and RNA are being explored for their therapeutic potential against a wide range of diseases. As these new drugs emerge, new demands arise for the analysis and quantitation of these biomolecules. Pharmacokinetic and pharmacodynamic analysis requirements for drug approval place enormous challenges on the methods for analyzing these therapeutics. This review will focus on bioanalytical methods for DNA antisense and aptamers as well as small-interfering RNA (siRNA) therapeutics. Chromatography methods employing ultraviolet (UV), fluorescence and mass spectrometric (MS) detection along with matrix-assisted laser desorption/ionization (MALDI) will be covered. Sample preparation from biological matrices will be reviewed as well as metabolite analysis and identification. All of these techniques are important contributions toward oligonucleotide therapeutic development. They will also be important in microRNA (miRNA) biomarker discovery and RNomics in general, as more non-coding RNAs are inevitably discovered.
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Affiliation(s)
- A Cary McGinnis
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
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16
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Abstract
Therapeutic oligonucleotides (OGNTs) are important biopharmaceutical drugs for the future, due to their ability to selectively reduce or knockout the expression of target genes. For the development of OGNTs, reliable and relatively high-throughput bioanalytical methods are required to perform the quantitative bioanalysis of OGNTs and their metabolites in biological fluids (e.g., plasma, urine and tissue). Although immunoaffinity methods, especially ELISA, are currently widely applied for this purpose, the potential of LC-MS in OGNT analysis is under investigation. Owing to its inherent ability to monitor the individual target OGNTs as well as their metabolites, LC-MS is now evolving into the method-of-choice for the bioanalysis of OGNTs. In this paper, the state-of-the-art of bioanalytical LC-MS of OGNTs and their metabolites in biological fluids is critically reviewed and its advantages and limitations highlighted. Finally, the future perspective of bioanalytical LC-MS, that is, lower detection levels and potential generic LC-MS methodology, is discussed.
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17
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Yuan Y, Xiao XC. Synthesis of monolithic columns based on poly(styrene-co-divinylbenzene) with the capillary-like flow-through pore diameter by template method. POLYMER SCIENCE SERIES B 2011. [DOI: 10.1134/s1560090411070086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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High-resolution separations of protein isoforms with liquid chromatography time-of-flight mass spectrometry using polymer monolithic capillary columns. J Chromatogr A 2011; 1218:5504-11. [DOI: 10.1016/j.chroma.2011.06.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/16/2011] [Accepted: 06/10/2011] [Indexed: 11/22/2022]
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Nikcevic I, Wyrzykiewicz TK, Limbach PA. DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY - HIGH RESOLUTION MASS SPECTROMETRY. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 304:98-104. [PMID: 21811394 PMCID: PMC3146765 DOI: 10.1016/j.ijms.2010.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described.Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3'-terminal phosphate monoester and 3'-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N(3) (2-cyanoethyl) adducts of the full length product. When compared with low resolution LC-MS, ~60% more impurities can be identified when charge state and isotopic distribution information is available and used for impurity profiling.
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Affiliation(s)
- Irena Nikcevic
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172
| | | | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172
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Noll B, Seiffert S, Vornlocher HP, Roehl I. Characterization of small interfering RNA by non-denaturing ion-pair reversed-phase liquid chromatography. J Chromatogr A 2011; 1218:5609-17. [PMID: 21737080 DOI: 10.1016/j.chroma.2011.06.057] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/31/2011] [Accepted: 06/11/2011] [Indexed: 01/27/2023]
Abstract
Small interfering RNAs (siRNA) are emerging as a novel therapeutic modality for the specific inhibition of target gene expression. siRNA are typically formed by annealing of two complementary single stranded oligoribonucleotides. Compared to purity determination of non-hybridized single strands by denaturing chromatographic methods, characterization of the hybridized duplex is challenging. Here we are reporting a non-denaturing ion pairing-reversed phase (IP-RP) chromatography method capable of separating optimal duplex (full-length single strands only) from non-optimal duplex variants (containing shortmers, longmers and 2',5'-isomers) using ultraviolet- and mass spectrometric detection. The impact of different annealing conditions on siRNA composition was investigated. Optimized annealing conditions lead to a significant increase in optimal duplex, while total duplex content remained constant. The non-denaturing method reported herein showed high mass spectrometric sensitivity and superior separation efficiencies compared to other IP-RP buffer systems. The method is useful for in-process control and release testing of therapeutic double stranded nucleic acids such as siRNA.
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21
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Beer B, Erb R, Pitterl F, Niederstätter H, Maroñas O, Gesteira A, Carracedo A, Piatkov I, Oberacher H. CYP2D6 genotyping by liquid chromatography-electrospray ionization mass spectrometry. Anal Bioanal Chem 2011; 400:2361-70. [DOI: 10.1007/s00216-010-4597-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/10/2010] [Accepted: 12/12/2010] [Indexed: 10/25/2022]
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22
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Beer B, Plattner S, Hubalek M, Oberguggenberger A, Sztankay M, Meraner V, Achleitner R, Oberacher H. CYP2D6 genotyping in breast cancer patients by liquid chromatography-electrospray ionization mass spectrometry. Horm Mol Biol Clin Investig 2011; 6:247-53. [DOI: 10.1515/hmbci.2011.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 02/21/2011] [Indexed: 11/15/2022]
Abstract
AbstractThe application of cytochrome P450 2D6 (CYP2D6) genotyping to allow a personalized treatment approach for breast cancer patients undergoing endocrine therapy has been repeatedly discussed. However, the actual clinical relevance of the CYP2D6 genotype in the endocrine treatment of breast cancer still remains to be elucidated. A major prerequisite for the successful and valid evaluation of the CYP2D6 genotype with regard to its pharmacokinetic and clinical relevance is the availability of a comprehensive, accurate and cost-effective CYP2D6 genotyping strategy. Herein we present a CYP2D6 genotyping assay employing polymerase chain reaction (PCR)-ion pair reversed-phase high-performance liquid chromatography-electrospray ionization time-of-flight mass spectrometry (ICEMS). The genotyping strategy involves the simultaneous amplification of nine variable regions within the CYP2D6 gene by a two-step PCR protocol and the direct analysis of the generated PCR amplicons by ICEMS. The nucleotide composition profiles generated by ICEMS enable the differentiation of 37 of the 80 reported CYP2D6 alleles. The assay was applied to type the CYP2D6 gene in 199 Austrian individuals including 106 breast cancer patients undergoing tamoxifen treatment. The developed method turned out to be a highly applicable, robust and cost-effective approach, enabling an economical CYP2D6 testing for large patient cohorts.
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23
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Taoka M, Ikumi M, Nakayama H, Masaki S, Matsuda R, Nobe Y, Yamauchi Y, Takeda J, Takahashi N, Isobe T. In-Gel Digestion for Mass Spectrometric Characterization of RNA from Fluorescently Stained Polyacrylamide Gels. Anal Chem 2010; 82:7795-803. [DOI: 10.1021/ac101623j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Masato Taoka
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Maki Ikumi
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Hiroshi Nakayama
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Shunpei Masaki
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Ryozo Matsuda
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Jun Takeda
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Nobuhiro Takahashi
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan, Biomolecular Characterization Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan, and Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of
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Curtis M, Minier MA, Chitranshi P, Sparkman OD, Jones PR, Xue L. Direct analysis in real time (DART) mass spectrometry of nucleotides and nucleosides: elucidation of a novel fragment [C5H5O]+ and its in-source adducts. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1371-1381. [PMID: 20451406 DOI: 10.1016/j.jasms.2010.03.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 02/04/2010] [Accepted: 03/30/2010] [Indexed: 05/29/2023]
Abstract
Direct analysis in real time (DART) mass spectrometry is a recently developed innovative technology, which has shown broad applications for fast and convenient analysis of complex samples. Due to the ease of sample preparation, we have recently initiated an investigation of the feasibility of detecting nucleotides and nucleosides using the DART-AccuTOF instrument, which we will refer to as the DART mass spectrometer. Our experimental results reveal that the ions representing the intact molecules of nucleotides are not detectable in either positive-ion or negative-ion mode. Instead, all four natural nucleotides fragment in the DART ion source, and a common fragment ion, [C(5)H(5)O](+) (1), is observed, which is probably formed via multiple-elimination reactions. Interestingly, 1 can form adducts with nucleobases in different molar ratios in the DART ion source. In contrast to nucleotides, the ions representing the intact molecules of nucleosides are detected in both positive-ion and negative-ion mode using DART mass spectrometry. Surprisingly, the fragmentation pattern of nucleosides is different from that of nucleotides in the DART ion source. In the cases of nucleosides (under positive-ion conditions), the production of 1 is not observed, indicating that the phosphate group plays an important role for the multiple eliminations observed in the spectra of nucleotides. The in-source reactions described in the present work show the complexity of the conditions in the DART ion source, and we hope that our results illustrate a better understanding about DART mass spectrometry.
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Affiliation(s)
- Matthew Curtis
- Department of Chemistry, University of the Pacific, Stockton, California 95211, USA
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25
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Eeltink S, Dolman S, Vivo-Truyols G, Schoenmakers P, Swart R, Ursem M, Desmet G. Selection of Column Dimensions and Gradient Conditions to Maximize the Peak-Production Rate in Comprehensive Off-Line Two-Dimensional Liquid Chromatography Using Monolithic Columns. Anal Chem 2010; 82:7015-20. [DOI: 10.1021/ac101514d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastiaan Eeltink
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, The Netherlands, and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Sebastiaan Dolman
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, The Netherlands, and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Gabriel Vivo-Truyols
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, The Netherlands, and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Peter Schoenmakers
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, The Netherlands, and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Remco Swart
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, The Netherlands, and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Mario Ursem
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, The Netherlands, and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Gert Desmet
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium, Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, The Netherlands, and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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26
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Metal ion-mobilizing additives for comprehensive detection of femtomole amounts of phosphopeptides by reversed phase LC-MS. Amino Acids 2010; 41:311-20. [DOI: 10.1007/s00726-010-0647-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 05/31/2010] [Indexed: 02/02/2023]
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27
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Deng P, Chen X, Zhang G, Zhong D. Bioanalysis of an oligonucleotide and its metabolites by liquid chromatography-tandem mass spectrometry. J Pharm Biomed Anal 2010; 52:571-9. [PMID: 20153130 DOI: 10.1016/j.jpba.2010.01.040] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 01/22/2010] [Accepted: 01/22/2010] [Indexed: 01/15/2023]
Abstract
An ion-pair reversed phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been developed for the quantification of a phosphorothioate oligonucleotide (PS-OGN) PF-ODN and its metabolites 5'N-1/3'N-1, 5'N-2 and 5'N-3 in rat plasma. Plasma samples were prepared with an initial phenol/dichloromethane liquid-liquid extraction followed by a solid phase extraction. Chromatographic separation was performed with a gradient system on a Phenomenex Gemini C(18) column using hexafluoro-2-propanol/triethylamine buffer and methanol as the mobile phase at a flow rate of 0.5mL/min. Except for 5'N-1 and 3'N-1, which were coeluted and could not be differentiated by mass spectrometer, the other analytes were separated chromatographically and mass spectrometrically. The detection was carried out in multiple reaction monitoring (MRM) mode using a negative electrospray ionization (ESI) interface. The lower limit of quantification (LLOQ) achieved was 4.0ng/mL for PF-ODN and its four metabolites with acceptable precision and accuracy. Inter-day and intra-day RSD for three quality control (QC) levels across validation runs were less than 12.0% and the accuracy ranged from -9.6% to 6.0% for the analytes. This validated LC-MS/MS method was applied to a preliminary pharmacokinetic study of PF-ODN in rats.
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Affiliation(s)
- Pan Deng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 646 Songtao Road, Shanghai 201203, China
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28
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Taoka M, Yamauchi Y, Nobe Y, Masaki S, Nakayama H, Ishikawa H, Takahashi N, Isobe T. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes. Nucleic Acids Res 2010; 37:e140. [PMID: 19740761 PMCID: PMC2790879 DOI: 10.1093/nar/gkp732] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.
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Affiliation(s)
- Masato Taoka
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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29
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Oberacher H. Frontiers of mass spectrometry in nucleic acids analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:351-365. [PMID: 20530841 DOI: 10.1255/ejms.1045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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30
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Saunders KC, Ghanem A, Boon Hon W, Hilder EF, Haddad PR. Separation and sample pre-treatment in bioanalysis using monolithic phases: A review. Anal Chim Acta 2009; 652:22-31. [DOI: 10.1016/j.aca.2009.05.043] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 05/29/2009] [Accepted: 05/30/2009] [Indexed: 10/20/2022]
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31
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Schlemmer B, Bandari R, Rosenkranz L, Buchmeiser MR. Electron beam triggered, free radical polymerization-derived monolithic capillary columns for high-performance liquid chromatography. J Chromatogr A 2009; 1216:2664-70. [DOI: 10.1016/j.chroma.2008.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 08/28/2008] [Accepted: 09/02/2008] [Indexed: 10/21/2022]
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32
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Farand J, Beverly M. Sequence confirmation of modified oligonucleotides using chemical degradation, electrospray ionization, time-of-flight, and tandem mass spectrometry. Anal Chem 2008; 80:7414-21. [PMID: 18729471 DOI: 10.1021/ac8011158] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report the sequencing of highly modified oligonucleotides containing a mixture of 2'-deoxy, 2'-fluoro, 2'-O-methyl, abasic, and ribonucleotides. The passenger and guide strands each containing 48% and 86% of modified nucleotides, respectively, are representative sequences of synthetic short interfering RNAs (siRNAs). We describe herein the sequence confirmation of both strands using a series of robust chemical reactions, followed by analysis via ESI-TOF and ion trap mass spectrometry (ITMS). The following method enables the rapid sequence confirmation of highly modified oligonucleotides.
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Affiliation(s)
- Julie Farand
- Department of Process Research, Merck Research Laboratories, 2950 Wilderness Place, Boulder, Colorado 80301, USA.
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34
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Development of capillary electrochromatography with poly(styrene-divinylbenzene-vinylbenzenesulfonic acid) monolith as the stationary phase. J Chromatogr A 2008; 1190:263-70. [PMID: 18358481 DOI: 10.1016/j.chroma.2008.02.105] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 02/17/2008] [Accepted: 02/29/2008] [Indexed: 10/22/2022]
Abstract
A new polystyrene-based monolithic stationary phase, which was prepared by single step in situ copolymerization of styrene, divinylbenzene and vinylbenzenesulfonic acid (VBSA), was developed as a separation column for capillary electrochromatography, in which VBSA was employed as the charge-bearing monomer. Polymerization time of the polystyrene-based monolith had slightly influenced the separation time of the tested analytes, but it effectively altered their separation resolutions. Furthermore, baseline separation for a wider range of acetonitrile levels of mobile phase was achieved when a monolithic column prepared by a longer polymerization time was used. This novel polystyrene-based monolithic column provided an adequate electroosmotic flow either in basic or acidic mobile phase when VBSA level was maintained at 2.6% (w/w). Finally, this proposed polystyrene-based column allowed seven tested analytes to achieve a reproducible baseline separation within 2.2 min with theoretical plate numbers higher than 164 000 plates/m.
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35
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Smith NW, Jiang Z. Developments in the use and fabrication of organic monolithic phases for use with high-performance liquid chromatography and capillary electrochromatography. J Chromatogr A 2008; 1184:416-40. [DOI: 10.1016/j.chroma.2007.09.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Revised: 09/11/2007] [Accepted: 09/13/2007] [Indexed: 10/22/2022]
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36
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Forensic DNA fingerprinting by liquid chromatography-electrospray ionization mass spectrometry. Biotechniques 2007; 43:vii-xiii. [PMID: 18019345 DOI: 10.2144/000112581] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The determination of the molecular mass of a DNA sequence has several benefits over conventional fragment-length analysis that are advantageous to the forensic field: (i) sequence variation is captured that increases the power of discrimination compared with that obtained by conventional fragment-length analysis. First experiments showed that this increase makes up to 20%-30% for STR analysis. The new technical approach does not invalidate established developments and data, but adds to this information with additional discriminative categories. (ii) ICEMS is faster and cheaper than electrophoresis, does not require internal size standards, allelic ladders, or spectral calibration, which are necessary for fluorescence-based electrophoresis. (iii) ICEMS can unequivocally detect any single sequence variation in DNA molecules with lengths up to 250 nucleotides. This allows for maximum discrimination of forensically relevant DNA fragments, covering all sorts of STRs, SNPs, and also the analysis of the hypervariable segments of mtDNA. More effort, however, needs to be put into software development that escorts the analysis and data interpretation processes to make this technology manageable for the practical user.
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37
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Bandari R, Elsner C, Knolle W, Kühnel C, Decker U, Buchmeiser MR. Separation behavior of electron-beam curing derived, acrylate-based monoliths. J Sep Sci 2007; 30:2821-7. [DOI: 10.1002/jssc.200700364] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gu C, Lin L, Chen X, Jia J, Ren J, Fang N. Fabrication of a poly(styrene-octadecene-divinylbenzene) monolithic column and its comparison with a poly(styrene-divinylbenzene) monolithic column for the separation of proteins. J Sep Sci 2007; 30:1005-12. [PMID: 17566334 DOI: 10.1002/jssc.200600397] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, a poly(styrene-octadecene-divinylbenzene) (PS-OD-DVB) monolithic column was prepared in one step by introducing a C18 carbon chain as monomer. N,N-Dimethylformamide and decanol served as porogens to make a homogeneous polymerization mixture in a fused silica capillary (320 microm inner diameter). Its physical and chromatographic properties were compared with those of poly(styrene-divinylbenzene) (PS-DVB) monolithic column, which was also fabricated by in-situ polymerization in a fused silica capillary with the same inner diameter. Six standard proteins were used to evaluate the columns and their potential application for the separation of human hemoglobin was also discussed. It was shown that the PS-OD-DVB and PS-DVB monoliths appeared to have similar efficiency for rapid separation of six proteins within 3.5 min. The PS-OD-DVB monolith was found to have higher loading capacity and higher resolution for the separation of alpha and beta chains of hemoglobin because of the introduction of C18 carbon chains, and shows great potential for the separation of bio-macromolecules.
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Affiliation(s)
- Congying Gu
- College of Environmental Science & Engineering, Shanghai Jiaotong University, Shanghai, China
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40
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Yoo C, Patwa TH, Kreunin P, Miller FR, Huber CG, Nesvizhskii AI, Lubman DM. Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:312-34. [PMID: 17206599 PMCID: PMC3426914 DOI: 10.1002/jms.1163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A comprehensive platform that integrates information from the protein and peptide levels by combining various MS techniques has been employed for the analysis of proteins in fully malignant human breast cancer cells. The cell lysates were subjected to chromatofocusing fractionation, followed by tryptic digestion of pH fractions for on-line monolithic RP-HPLC interfaced with linear ion trap MS analysis for rapid protein identification. This unique approach of direct analysis of pH fractions resulted in the identification of large numbers of proteins from several selected pH fractions, in which approximately 1.5 microg of each of the pH fraction digests was consumed for an analysis time of ca 50 min. In order to combine valuable information retained at the protein level with the protein identifications obtained from the peptide level information, the same pH fraction was analyzed using nonporous (NPS)-RP-HPLC/ESI-TOF MS to obtain intact protein MW measurements. In order to further validate the protein identification procedures from the fraction digest analysis, NPS-RP-HPLC separation was performed for off-line protein collection to closely examine each protein using MALDI-TOF MS and MALDI-quadrupole ion trap (QIT)-TOF MS, and excellent agreement of protein identifications was consistently observed. It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis.
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Affiliation(s)
- Chul Yoo
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Tasneem H. Patwa
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Paweena Kreunin
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Fred R. Miller
- Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Christian G. Huber
- Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrucken, Germany
| | - Alexey I. Nesvizhskii
- Department of Pathology, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - David M. Lubman
- Department of Surgery, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Correspondence to: David M. Lubman, University of Michigan Medical Center, Department of Surgery, MSRBI, A510B, Box 0658, Ann Arbor, MI 48109, USA.
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Huang HY, Lin HY, Lin SP. CEC with monolithic poly(styrene-divinylbenzene-vinylsulfonic acid) as the stationary phase. Electrophoresis 2006; 27:4674-81. [PMID: 17080486 DOI: 10.1002/elps.200600125] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study, poly(styrene-divinylbenzene-vinylsulfonic acid) monolithic columns, prepared by singlestep in situ polymerization, were first used as separation columns for CEC in which vinylsulfonic acid was employed as the charge-bearing monomer. The effects of the polymerization conditions (compositions of monomer and porogenic solvent, and polymerization time) on the chromatographic property of the polystyrene-based monolithic column were examined. Furthermore, an increase in water content of the porogenic solvent markedly altered the retention behaviors of these analytes, where the monolithic column was able to be produced in a higher ratio of vinylsulfonic acid. Finally, the study demonstrated that acidic analytes could be successfully separated by the polystyrene-based monolithic column under an acidic mobile phase.
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Affiliation(s)
- Hsi-Ya Huang
- Department of Chemistry and Center for Nanotechnology, Chung Yuan Christian University, Chung-Li, Taiwan, ROC
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Stulík K, Pacáková V, Suchánková J, Coufal P. Monolithic organic polymeric columns for capillary liquid chromatography and electrochromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 841:79-87. [PMID: 16714153 DOI: 10.1016/j.jchromb.2006.04.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 04/13/2006] [Accepted: 04/20/2006] [Indexed: 11/30/2022]
Abstract
This review briefly summarizes the present state of the preparation and use of capillary monolithic columns for liquid chromatography (LC) and electrochromatography (EC). Most important approaches to the preparation of monolithic stationary phases based on organic polymers are outlined and the properties of the monoliths obtained are compared with those of classical particulate phases. A few selected applications of monolithic columns are shown to demonstrate the most important advantages of monolithic capillary columns. It is concluded that both the monolithic and particulate capillary columns are important and that judicious choice of the type suitable for a particular application requires careful consideration of the purpose of the separation and the properties of the solutes to be separated. Monolithic columns are substantially younger than packed ones and thus will require further theoretical and experimental study to further improve their preparation and to enable reliable prediction of their properties and applicability; nevertheless, they are very promising for the future.
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Affiliation(s)
- Karel Stulík
- Department of Analytical Chemistry, Charles University, Hlavova 2030, 128 40 Prague 2, Czech Republic
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Huang HY, Huang IY, Lin HY. Separation of parabens in capillary electrochromatography using poly(styrene-divinylbenzene-methacrylic acid) monolithic column. J Sep Sci 2006; 29:2038-48. [PMID: 17017017 DOI: 10.1002/jssc.200600071] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this study, a series of poly(styrene-divinylbenzene-methacrylic acid) monolithic capillaries was used as the separation column of CEC for the analyses of parabens in commercial pharmaceutical and cosmetic products. The results showed that the chromatographic characteristics of these analytes were strongly affected by the preparation condition of the monolithic column including monomer content, porogenic solvent composition, and polymerization time. Baseline separations were markedly sped up by lowering the polymerization time without any obvious loss of resolution. Furthermore, mobile-phase composition (pH, ACN, and electrolyte concentration) was also able to effectively improve the separation behavior. Similar to the influence of lowering the polymerization time, retention times for all analytes were significantly shortened in the CEC method by decreasing the electrolyte concentration in the mobile phase.
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Affiliation(s)
- Hsi-Ya Huang
- R&D Center for Membrane Technology, CYCU, Department of Chemistry, Chung Yuan Christian University, Chung-Li, Taiwan, ROC.
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Elhawary NA, Shawky RM, Elsayed N. High-precision DNA microsatellite genotyping in Duchenne muscular dystrophy families using ion-pair reversed-phase high performance liquid chromatography. Clin Biochem 2006; 39:758-61. [PMID: 16765929 DOI: 10.1016/j.clinbiochem.2006.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 02/24/2006] [Accepted: 03/12/2006] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Genetic typing of the intronic (CA)n loci within the dystrophin gene was exploited for linkage analysis and diagnosis of carrier status. DESIGN AND METHODS IP-RP-HPLC was developed for genotyping of 98 chromosomes. RESULTS The typing of 2-bp STRs with mean SD of +/- 0.43 bp ensured an allele's identity with 99.7% confidence. CONCLUSION The automation enabled the accurate sizing of unlabeled alleles with an excellent reproducibility of 100% with significant labor saving and reduced reagent costs.
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Yoo C, Pal M, Miller FR, Barder TJ, Huber C, Lubman DM. Toward high sequence coverage of proteins in human breast cancer cells using on-line monolith-based HPLC-ESI-TOF MS compared to CE MS. Electrophoresis 2006; 27:2126-38. [PMID: 16637017 DOI: 10.1002/elps.200500651] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A method is developed toward high sequence coverage of proteins isolated from human breast cancer MCF10 cell lines using a 2-D liquid separations. Monolithic-capillary columns prepared by copolymerizing styrene with divinylbenzene are used to achieve high-resolution separation of peptides from protein digests. This separation is performed with minimal sample preparation directly from the 2-D liquid fractionation of the cell lysate. The monolithic column separation is directly interfaced to ESI-TOF MS to obtain a peptide map. The protein digests were also analyzed by MALDI-TOF MS and an accurate M(r) of the intact protein was obtained using an HPLC-ESI-TOF MS. The result is that these techniques provide complementary information where nearly complete sequence coverage of the protein is obtained and can be compared to the experimental M(r) value. The high sequence coverage provides information on isoforms and other post-translational modifications that would not be available from methods that result in low sequence coverage. The results from the use of monolithic columns are compared to that obtained by CE-MS. The monolithic column separations provide a rugged and highly reproducible method for separating protein digests prior to MS analysis and is suited to confidently identify biomarkers associated with cancer progression.
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MESH Headings
- Amino Acid Sequence
- Breast Neoplasms/chemistry
- Chromatography, High Pressure Liquid/instrumentation
- Chromatography, High Pressure Liquid/methods
- Electrophoresis, Capillary
- Female
- Humans
- Molecular Sequence Data
- Neoplasm Proteins/analysis
- Online Systems
- Peptide Mapping/methods
- Sequence Analysis, Protein/methods
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Chul Yoo
- Department of Chemistry, The University of Michigan, Ann Arbor, 48109, USA
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Umemura T, Ueki Y, Tsunoda KI, Katakai A, Tamada M, Haraguchi H. Preparation and characterization of methacrylate-based semi-micro monoliths for high-throughput bioanalysis. Anal Bioanal Chem 2006; 386:566-71. [PMID: 16685518 DOI: 10.1007/s00216-006-0425-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 03/13/2006] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Hexyl methacrylate (HMA)-based monolithic semi-micro columns were prepared by in situ polymerization within the confines of 1.02-mm-i.d. silicosteel tubing for reversed-phase and/or precipitation-redissolution liquid chromatography. Practically useful monolithic columns with adequate separation efficiency, high permeability, and good mechanical strength were successfully obtained using a polymerization mixture comprising 24% hexyl methacrylate (HMA), 6% ethylene dimethacrylate (EDMA), 44.5% 1-propanol, and 25.5% 1,4-butanediol. The column performance was evaluated through the separations of a series of alkylbenzenes. At a normal flow rate of 50 microL min(-1), the produced HMA-based monolithic columns typically exhibited 3,000 theoretical plates for a 20-cm-long column, and the pressure drop was generally less than 1 MPa per 20 cm. The monolithic columns were resistant to at least 15 MPa, and could be properly operated at 15-20 times higher flow rate than normal, reducing the separation time to 1/15-1/20. The HMA-based monolithic columns were applied to rapid and efficient separations of proteins such as ribonuclease A, cytochrome c, transferrin, and ovalbumin in the precipitation-redissolution mode. Using a CH(3)CN gradient elution at a flow rate of 1,000 microL min(-1), four proteins were baseline separated within 20 s.
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Affiliation(s)
- Tomonari Umemura
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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Ueki Y, Umemura T, Iwashita Y, Odake T, Haraguchi H, Tsunoda KI. Preparation of low flow-resistant methacrylate-based monolithic stationary phases of different hydrophobicity and the application to rapid reversed-phase liquid chromatographic separation of alkylbenzenes at high flow rate and elevated temperature. J Chromatogr A 2006; 1106:106-11. [PMID: 16443455 DOI: 10.1016/j.chroma.2005.08.041] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Revised: 07/29/2005] [Accepted: 08/12/2005] [Indexed: 11/18/2022]
Abstract
Low flow-resistant alkyl methacrylate-based monolithic stationary phases of different hydrophobicity were constructed for reversed-phase capillary liquid chromatography by thermally initiated radical polymerization of respective methacrylate ester monomer with different alkyl chain (C2, C4, C6, C12, C18) and ethylene glycol dimethacrylate (EDMA) in a 250 microm i.d. fused silica capillary. The hydrophobicity was basically controlled by changing the length and/or the density of the alkyl-chain, while the composition and the ratio of porogenic solvent were adjusted to obtain highly permeable rigid monoliths with adequate column efficiency. Among the prepared monolithic stationary phases, C18-methacrylate monoliths polymerized from a binary porogenic solvent of isoamyl alcohol and 1,4-buthandiol exhibited the most promising performance in terms of hydraulic resistance and column efficiency. The pressure drops of 20-cm long monolithic columns were below approximately 0.4 MPa at a normal linear velocity of 1mm/s (a flow rate of 3 microL/min), and the numbers of theoretical plates for alkylbenzenes mostly exceeded 3000 plates/20 cm. The produced monolithic columns had good mechanical strength for high pressure and temperature, and could be properly operated even at a temperature of 80 degrees C and at a pressure of at least 33 MPa. At 80 degrees C, the theoretical plate numbers reached 6000 plates/20 cm because of the enhanced mass transfer. Due to the novel hydraulic resistance and mechanical strength, the separation time could be reduced 120-fold simply by raising the flow rate and column temperature.
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Affiliation(s)
- Yuji Ueki
- Department of Chemistry, Faculty of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
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48
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Huck CW, Bonn GK. Poly(Styrene-Divinylbenzene) Based Media for Liquid Chromatography. Chem Eng Technol 2005. [DOI: 10.1002/ceat.200500265] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Nordborg A, Svec F, Fréchet JMJ, Irgum K. Extending the array of crosslinkers suitable for the preparation of polymethacrylate-based monoliths. J Sep Sci 2005; 28:2401-6. [PMID: 16350275 DOI: 10.1002/jssc.200500222] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The in situ preparation of monolithic capillary columns comprising copolymers of butyl methacrylate with ethylene dimethacrylate, diethylene glycol dimethacrylate, triethylene glycol dimethacrylate, and pentaerythritol tetraacrylate using thermal polymerization within 250 microm ID capillaries and their application for micro-HPLC separations of proteins has been studied. For all crosslinkers, optimization of the porogenic mixture consisting of 1-propanol and 1,4-butanediol yielded monoliths with pore sizes above 1 microm suitable for rapid separations at low back pressure. Very good separations were achieved for a protein mixture consisting of ribonuclease A, cytochrome c, myoglobin, and ovalbumin with all tested columns.
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Affiliation(s)
- Anna Nordborg
- Department of Chemistry, University of California, Berkeley 94720-1460, USA
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50
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1110-21. [PMID: 16106339 DOI: 10.1002/jms.809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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