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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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2
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Castleberry CM, Rodicio LP, Limbach PA. Electrospray ionization mass spectrometry of oligonucleotides. ACTA ACUST UNITED AC 2009; Chapter 10:Unit 10.2. [PMID: 19085982 DOI: 10.1002/0471142700.nc1002s35] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Because of the high molecular weights and thermal lability of biomolecules such as nucleic acids and protein, they can be difficult to analyze by mass spectrometry. Such analyses require a "soft" ionization method that is capable of generating intact molecular ions. In addition, most mass analyzers have a limited upper mass range that is not sufficient for studying these large molecules. ESI-MS can be used to analyze molecules with a molecular weight that is larger than the mass-to-charge ratio limit of the analyzer. This unit describes how ESI allows for analysis of high-molecular-weight compounds through the generation of multiply charged ions in the gas phase. It discusses analyzer configurations and solvent selection, and gives protocols for sample preparation. For applications of ESI-MS, the unit discusses molecular weight determination, sequencing, and analysis of oligonucleotide mixtures by LC-MS.
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Affiliation(s)
- Colette M Castleberry
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
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3
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Pitterl F, Niederstätter H, Huber G, Zimmermann B, Oberacher H, Parson W. The next generation of DNA profiling - STR typing by multiplexed PCR - ion-pair RP LC-ESI time-of-flight MS. Electrophoresis 2008; 29:4739-50. [DOI: 10.1002/elps.200800209] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Feng X, Liu X, Luo Q, Liu BF. Mass spectrometry in systems biology: an overview. MASS SPECTROMETRY REVIEWS 2008; 27:635-660. [PMID: 18636545 DOI: 10.1002/mas.20182] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future.
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Affiliation(s)
- Xiaojun Feng
- The Key Laboratory of Biomedical Photonics of MOE, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Castleberry CM, Chou CW, Limbach PA. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of oligonucleotides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2008; Chapter 10:Unit 10.1. [PMID: 18551426 DOI: 10.1002/0471142700.nc1001s33] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
MALDI-MS is one of the most useful techniques available for determining biomolecule mass. It offers high mass accuracy, good sensitivity, simplicity, and speed. Because singly charged ions of oligonucleotides are typically observed, MALDI-MS spectra are easy to interpret. This unit presents protocols for sample preparation and purification, matrix preparation, and matrix/analyte sample preparation. It provides an introduction to the instrumentation and its calibration, and a discussion of some of the useful applications of MALDI-MS analysis in the study of oligonucleotides. This technique is typically used for 120-mer or smaller oligonucleotides.
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6
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On the use of different mass spectrometric techniques for characterization of sequence variability in genomic DNA. Anal Bioanal Chem 2008; 391:135-49. [DOI: 10.1007/s00216-008-1929-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 01/25/2008] [Accepted: 01/31/2008] [Indexed: 10/22/2022]
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Fukui K, Takahata Y, Nakagawa N, Kuramitsu S, Masui R. Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry. Nucleic Acids Res 2007; 35:e100. [PMID: 17686785 PMCID: PMC1976465 DOI: 10.1093/nar/gkm575] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Electrospray ionization with Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FT ICR MS) is a powerful tool for analyzing the precise structural features of biopolymers, including oligonucleotides. Here, we described the detailed characterization of a newly discovered nuclease activity of the C-terminal domain of Thermus thermophilus MutS2 (ttMutS2). Using this method, the length, nucleotide content and nature of the 5'- and 3'-termini of the product oligonucleotides were accurately identified. It is revealed that the C-terminal domain of ttMutS2 incised the phosphate backbone of oligodeoxynucleotides non-sequence-specifically at the 3' side of the phosphates. The simultaneous identification of the innumerable fragments was achieved by the extremely high-accuracy of ESI-FT ICR MS.
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Affiliation(s)
- Kenji Fukui
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 and Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yoshio Takahata
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 and Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Noriko Nakagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 and Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Seiki Kuramitsu
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 and Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ryoji Masui
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 and Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- *To whom correspondence should be addressed.+81 06 6850 5433+81 06 6850 5442
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Oberacher H, Niederstätter H, Parson W. Liquid chromatography-electrospray ionization mass spectrometry for simultaneous detection of mtDNA length and nucleotide polymorphisms. Int J Legal Med 2006; 121:57-67. [PMID: 16955300 DOI: 10.1007/s00414-006-0117-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 07/05/2006] [Indexed: 10/24/2022]
Abstract
We demonstrate the applicability of ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization time-of-flight mass spectrometry (ICEMS) for the simultaneous characterization of length and nucleotide polymorphisms. Two sections within the first (HVS-I) and second (HVS-II) hypervariable segments of the mitochondrial (mt)DNA control region were selected as targets, both containing poly-cytosine (C) tracts, which display length heteroplasmy at a substantial frequency in the population. The two mtDNA sections were simultaneously amplified and analyzed by ICEMS in 90 maternally unrelated mother-offspring pairs from Austria. The findings were confirmed by direct sequencing of the polymerase chain reaction products. For the detailed characterization of present-length heteroplasmic variants, the results retrieved through ICEMS were more informative compared with those derived from direct sequencing. Hence, ICEMS represents an interesting option for successful application in forensic science.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, 6020, Innsbruck, Austria
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9
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Zhang Z, Jackson GW, Fox GE, Willson RC. Microbial identification by mass cataloging. BMC Bioinformatics 2006; 7:117. [PMID: 16524471 PMCID: PMC1488874 DOI: 10.1186/1471-2105-7-117] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 03/08/2006] [Indexed: 01/23/2023] Open
Abstract
Background The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample. Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms. Results Ribonuclease T1 and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T1 of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individual fragments or combinations thereof can be used to recognize the presence of specific organisms in a complex sample. In this regard, 140 strains out of 1,921 organisms (7.3%) could be identified by the presence of a unique RNase T1-generated oligoribonucleotide mass. Combinations of just two and three oligoribonucleotide masses allowed 54% and 72% of the specific strains to be identified, respectively. An initial algorithm for recovering likely organisms present in complex samples is also described. Conclusion The use of catalogs of compositions (masses) of characteristic oligoribonucleotides for microbial identification appears extremely promising. RNase T1 is more useful than ribonuclease A in generating characteristic masses, though RNase A produces oligomers which are more readily distinguished due to the large mass difference between A and G. Identification of multiple species in mixtures is also feasible. Practical applicability of the method depends on high performance mass spectrometric determination, and/or use of methods that increase the one dalton (Da) mass difference between uracil and cytosine.
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Affiliation(s)
- Zhengdong Zhang
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204-5001, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - George W Jackson
- Department of Chemical Engineering, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204-4004, USA
- BioTex, Inc., 8058 El Rio St., Houston, TX 77054, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204-5001, USA
- Department of Chemical Engineering, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204-4004, USA
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204-5001, USA
- Department of Chemical Engineering, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204-4004, USA
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10
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Oberacher H, Niederstätter H, Casetta B, Parson W. Some guidelines for the analysis of genomic DNA by PCR-LC-ESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:124-9. [PMID: 16406562 DOI: 10.1016/j.jasms.2005.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 09/29/2005] [Accepted: 09/29/2005] [Indexed: 05/06/2023]
Abstract
Ion-pair reversed-phase high-performance liquid chromatography online hyphenated to electrospray ionization mass spectrometry (ICEMS) represents an efficient method for the characterization of nucleic acids amplified by polymerase chain reaction (PCR). Since sample preparation is limited to PCR, the optimization of its solution conditions is of utmost importance for efficient mass spectrometric detection. The compatibility of a number of different commercially available PCR components including DNA polymerases, deoxynucleotide triphosphates, bovine serum albumin, enhancer, and ionic buffers was evaluated. These experiments revealed that higher concentration of enhancer and detergents such as Tween-20 or Nonidet P-40 impairs the mass spectrometric detection of nucleic acids and should be avoided within the PCR mixture. The optimized analytical platform was applied to the characterization of PCR products covering parts of the first hypervariable region of the noncoding mitochondrial control region. Truncated amplicons were detected attributable to the use of low quality primers. Furthermore, due to the proofreading activity of the applied polymerase system, mismatches between the primer and the target sequence located at the last or the second last base at the 3'-end of primers were corrected and detected within the corresponding amplicons.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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11
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Maziarz III EP, Baker GA, Wood TD. Electrospray ionization Fourier transform mass spectrometry of polycyclic aromatic hydrocarbons using silver(I)-mediated ionization. CAN J CHEM 2005. [DOI: 10.1139/v05-195] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, a methodology employing doped Ag(I) salt as an in situ cationization reagent for efficient ionization of nonpolar molecules within a conventional electrospray ionization source is described. The effectiveness of Ag(I)-mediated ionization is demonstrated using ESI Fourier transform mass spectrometry for the rapid detection and identification of priority pollutant polyaromatic hydrocarbon (PAH) species. In contrast to earlier coordination ESI-MS reports employing silver salts, argentated species are not typically observed for PAH species. Instead, oxidation of the PAH occurs to produce only the [PAH]+· odd-electron molecular parent ion, simplifying spectral analysis. In addition, the method demonstrates linear quantitative performance. The Ag(I) reagent provides quantifiable PAHs (not ordinarily amenable to ESI-MS) from 64 ppb, and suggests the immediate potential for sampling and on-line monitoring of complex, real world, and otherwise intractable environmental samples. Finally, the high mass accuracy of ESI Fourier transform mass spectrometry further allows unequivocal identification of molecular formulas within PAH mixtures.Key words: electrospray ionization, nonpolar, hydrocarbons, polyaromatic, Fourier transform mass spectrometry.
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Willems AV, Deforce DL, Lambert WE, Van Peteghem CH, Van Bocxlaer JF. Rapid characterization of oligonucleotides by capillary liquid chromatography-nano electrospray quadrupole time-of-flight mass spectrometry. J Chromatogr A 2005; 1052:93-101. [PMID: 15527125 DOI: 10.1016/j.chroma.2004.08.108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A fast quality control method is developed allowing the desalting and characterization of oligonucleotides by capillary liquid chromatography and on-line nano-electrospray ionization quadrupole time-of-flight mass spectrometry using column switching. The influence of addition of ammonium acetate, trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid, formic acid or acetic acid to the sample, addition of ammonium acetate to the trapping solvent and variation of the trapping time on the further reduction of cation adduction was studied. Final conditions were the addition of 0.1 M ammonium acetate to the sample, the use of a trapping solvent consisting of 0.4 M aqueous 1,1,1,3,3,3-hexafluoro-2-propanol (HFLP) adjusted to pH 7.0 with triethylamine plus 10 mM ammonium acetate during 8 min and the elution of the oligonucleotides with 0.4 M HFIP in 50% methanol. The potential of the optimized procedure is demonstrated for different synthetic oligonucleotides.
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Affiliation(s)
- An V Willems
- Laboratory of Medical Biochemistry and Clinical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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13
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Laskin J, Futrell JH. Activation of large ions in FT-ICR mass spectrometry. MASS SPECTROMETRY REVIEWS 2005; 24:135-167. [PMID: 15389858 DOI: 10.1002/mas.20012] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The advent of soft ionization techniques, notably electrospray and laser desorption ionization methods, has enabled the extension of mass spectrometric methods to large molecules and molecular complexes. This both greatly extends the applications of mass spectrometry and makes the activation and dissociation of complex ions an integral part of these applications. This review emphasizes the most promising methods for activation and dissociation of complex ions and presents this discussion in the context of general knowledge of reaction kinetics and dynamics largely established for small ions. We then introduce the characteristic differences associated with the higher number of internal degrees of freedom and high density of states associated with molecular complexity. This is reflected primarily in the kinetics of unimolecular dissociation of complex ions, particularly their slow decay and the higher energy content required to induce decomposition--the kinetic shift (KS). The longer trapping time of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) significantly reduces the KS, which presents several advantages over other methods for the investigation of dissociation of complex molecules. After discussing general principles of reaction dynamics related to collisional activation of ions, we describe conventional ways to achieve single- and multiple-collision activation in FT-ICR MS. Sustained off-resonance irradiation (SORI)--the simplest and most robust means of introducing the multiple collision activation process--is discussed in greatest detail. Details of implementation of this technique, required control of experimental parameters, limitations, and examples of very successful application of SORI-CID are described. The advantages of high mass resolving power and the ability to carry out several stages of mass selection and activation intrinsic to FT-ICR MS are demonstrated in several examples. Photodissociation of ions from small molecules can be effected using IR or UV/vis lasers and generally requires tuning lasers to specific wavelengths and/or utilizing high flux, multiphoton excitation to match energy levels in the ion. Photodissociation of complex ions is much easier to accomplish from the basic physics perspective. The quasi-continuum of vibrational states at room temperature makes it very easy to pump relatively large amounts of energy into complex ions and infrared multiphoton dissociation (IRMPD) is a powerful technique for characterizing large ions, particularly biologically relevant molecules. Since both SORI-CID and IRMPD are slow activation methods they have many common characteristics. They are also distinctly different because SORI-CID is intrinsically selective (only ions that have a cyclotron frequency close to the frequency of the excitation field are excited), whereas IRMPD is not (all ions that reside on the optical path of the laser are excited). There are advantages and disadvantages to each technique and in many applications they complement each other. In contrast with these slow activation methods, the less widely appreciated activation method of surface induced dissociation (SID) appears to offer unique advantages because excitation in SID occurs on a sub-picosecond time scale, instantaneously relative to the observation time of any mass spectrometer. Internal energy deposition is quite efficient and readily adjusted by altering the kinetic energy of the impacting ion. The shattering transition--instantaneous decomposition of the ion on the surface--observed at high collision energies enables access to dissociation channels that are not accessible using SORI-CID or IRMPD. Finally, we discuss some approaches for tailoring the surface to achieve particular aims in SID.
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Affiliation(s)
- Julia Laskin
- Fundamental Science Directorate, Pacific Northwest National Laboratory, P.O. Box 999 (K8-88), Richland, Washington 99352, USA.
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Hofstadler SA, Sannes-Lowery KA, Hannis JC. Analysis of nucleic acids by FTICR MS. MASS SPECTROMETRY REVIEWS 2005; 24:265-285. [PMID: 15389854 DOI: 10.1002/mas.20016] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fourier transform ion cyclotron resonance (FTICR) mass spectrometry represents a unique platform with which to study nucleic acids and non-covalent complexes containing nucleic acids moieties. In particular, systems in which very high mass measurement accuracy is required, very complex mixtures are to be analyzed, or very limited amounts of sample are available may be uniquely suited to interrogation by FTICR mass spectrometry. Although the FTICR platform is now broadly deployed as an integral component of many high-end proteomics-based research efforts, momentum is still building for the application of the platform towards nucleic acid-based analyses. In this work, we review fundamental aspects of nucleic acid analysis by FTICR, focusing primarily on the analysis of DNA oligonucleotides but also describing applications related to the characterization of RNA constructs. The goal of this review article is to give the reader a sense of the breadth and scope of the status quo of FTICR analysis of nucleic acids and to summarize a few recently published reports in which researchers have exploited the performance attributes of FTICR to characterize nucleic acids in support of basic and applied research disciplines including genotyping, drug discovery, and forensic analyses.
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Affiliation(s)
- Steven A Hofstadler
- Ibis Therapeutics, A Division of Isis Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, California 92008, USA.
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15
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Yeboah FK, Konishi Y. Mass Spectrometry of Biomolecules: Functional Foods, Nutraceuticals, and Natural Health Products. ANAL LETT 2003. [DOI: 10.1081/al-120026571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Benson LM, Null AP, Muddiman DC. Advantages of Thermococcus kodakaraenis (KOD) DNA Polymerase for PCR-mass spectrometry based analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:601-604. [PMID: 12781461 DOI: 10.1016/s1044-0305(03)00148-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The advantages of the thermostable DNA polymerase from Thermococcus kodakaraensis (KOD) are demonstrated for PCR amplification with subsequent detection by mass spectrometry. Commonly used DNA polymerases for PCR amplification include those from Thermus aquaticus (Taq) and Pyrococcus furiosus (Pfu). A 116 base-pair PCR product derived from a vWA locus was amplified by Taq, Pfu, or KOD DNA polymerase and compared by agarose gel electrophoresis and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). KOD DNA polymerase demonstrated a 2- to 3-fold increase in PCR product formation compared to Pfu or Taq, respectively, and generated blunt-ended PCR product which allows facile interpretation of the mass spectrum. Additionally, we demonstrate the advantage of using high magnetic fields to obtain unit resolution of the same 116 base pair (approximately 72 kDa) PCR product at high m/z.
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Affiliation(s)
- Linda M Benson
- Department of Biochemistry and Molecular Biology and the W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
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Null AP, Muddiman DC. Determination of a correction to improve mass measurement accuracy of isotopically unresolved polymerase chain reaction amplicons by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1714-1722. [PMID: 12872276 DOI: 10.1002/rcm.1111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The experimental determination of average mass by mass spectrometry is limited for large molecules due to the negative bias introduced by the natural distribution of isotopic abundances. This results in the measurement of the top-of-centroid (ToC) as opposed to the true centroid. We have developed a practical correction factor that is applied to the ToC measurement to largely remove the systematic bias introduced by nature. The correction factor is calculated easily using the average molecular mass (<100 kDa) of the analyte molecule and the full-width half maximum resolving power (<3,500) of the measurement. In addition, an approach to calculating resolving power is described that accurately predicts resolving power achievable for Fourier transform ion cyclotron resonance (FT-ICR) mass analysis of large molecules. A combination of internal calibration with a dual-electrospray source and application of the correction factor to average mass measurements improved the mass error from 192.5 to -35.0 ppm for a 44 kDa PCR amplicon.
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Affiliation(s)
- Allison P Null
- Department of Biochemistry and Molecular Biology and the W.M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic and Foundation, Rochester, MN 55905, USA
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18
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Null AP, Benson LM, Muddiman DC. Enzymatic strategies for the characterization of nucleic acids by electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:2699-2706. [PMID: 14673816 DOI: 10.1002/rcm.1255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a powerful technique used for the identification and characterization of DNA polymorphisms. Continual improvement in instrument design assures high mass measurement accuracy, sensitivity, and resolving power. This work describes an eclectic array of enzymatic strategies we have invoked in order to detect single-nucleotide polymorphisms by ESI-MS, although other applications may be envisioned. One strategy combines the use of two enzymes, exonuclease III and lambda exonuclease, to provide a ladder of single-stranded DNA fragments for straightforward sequence identification by mass spectrometry. A second strategy combines restriction enzymes to screen for polymorphisms present within specific amplicons. Finally, we describe the use of stable-isotope-labeled nucleotides for the determination of length and base composition of a PCR product.
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Affiliation(s)
- Allison P Null
- W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, and Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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Koomen JM, Russell WK, Tichy SE, Russell DH. Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:357-371. [PMID: 11948842 DOI: 10.1002/jms.312] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.
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Affiliation(s)
- John M Koomen
- Laboratory for Biological Mass Spectrometry, Texas A&M University, College Station, Texas 77843, USA
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Null AP, George LT, Muddiman DC. Evaluation of sample preparation techniques for mass measurements of PCR products using ESI-FT-ICR mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:338-344. [PMID: 11951971 DOI: 10.1016/s1044-0305(02)00342-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Elimination of PCR buffer components and alkali metal cations (i.e., Na+, K+) is of critical importance to allow for accurate mass measurements of PCR products for genotyping and sequencing applications. Ethanol precipitation followed by microdialysis has been repeatedly shown to efficiently desalt PCR products for analysis by mass spectrometry and is considered the gold standard. Alternative cleanup techniques that are compatible with automation are explored here with the intent of expanding the bottleneck that exists between the production of PCR products and analysis by electrospray ionization mass spectrometry (ESI-MS). Numerous combinations of approaches were evaluated that included PCR purification kits and alcohol precipitations. The data shown here support alternative approaches to an ethanol precipitation followed by microdialysis that have comparable desalting efficiency and can be utilized for cleanup of PCR products generated from single reactions.
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Affiliation(s)
- Allison P Null
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284, USA
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Mangrum JB, Flora JW, Muddiman DC. Solution composition and thermal denaturation for the production of single-stranded PCR amplicons: piperidine-induced destabilization of the DNA duplex? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:232-240. [PMID: 11908803 DOI: 10.1016/s1044-0305(01)00356-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Strategies to produce single-stranded PCR amplicons for detection by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) were investigated using modified electrospray solutions and by thermally denaturing the duplex structures with a resistively heated electrospray ionization source. A synthetic 20-mer oligonucleotide annealed to its complementary strand was used as a model system for initial experiments. Electrospray solutions were altered by varying the relative proportion of aqueous phase in efforts to induce destabilization of the double helix. When the electrospray solution contains a 25% aqueous content, the 20-mer oligonucleotide is detected in its double-stranded form. Increasing the proportion of aqueous phase in the electrospray solution to 60% destabilized the double helix, resulting in the detection of only single-stranded species. This strategy was extended to an 82-bp polymerase chain reaction (PCR) product derived from the human tyrosine hydroxylase gene (HUMTH01). In efforts to destabilize the 82-bp PCR product, electrospray solutions reaching 70% aqueous content were necessary to promote the detection of only single-stranded amplicons. Implementation of the resistively heated transfer line and an electrospray solution in which the oligonucleotide is on the threshold of duplex stability allowed for double-stranded and single-stranded species to be generated from the same ESI solutions at both ambient and elevated transfer line temperatures, respectively, without disruption of the electrospray process. The volatile base piperidine, present at 20 mM concentrations in the electrospray solution, was found to play a critical role in the formation of single-stranded species at the higher aqueous percentages and a duplex destabilization mechanism has been proposed.
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Affiliation(s)
- John B Mangrum
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284, USA
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Null AP, Muddima DC. CEPH family 1362 STR database: an online resource for characterization of PCR products using electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:89-90. [PMID: 11777204 DOI: 10.1016/s1044-0305(01)00326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An online database has been established in order to validate electrospray ionization mass spectrometry (ESI-MS) for genotyping and to publicize the procedures developed in our laboratory for the characterization of PCR products by ESI-MS. Genotypes derived from short tandem repeat (STR) loci that were obtained using ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) have been posted for fifteen members of the CEPH family 1362 pedigree. The website provides specific information such as PCR parameters, PCR product cleanup approaches, and ESI solution compositions to enable other laboratories to reproduce our data. Links are provided to related websites in an effort to integrate information regarding the CEPH family, STR genotyping, and mass spectrometry. The database, currently available at http://www.people.vcu.edu/ -dcmuddim/genotype/ will be routinely updated with genotypes from additional STR loci including PCR parameters as well as PCR cleanup strategies as further developments are completed.
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Affiliation(s)
- Allison P Null
- Department of Chemistry, Virginia Commonwealth University, Richmond, 23284, USA
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:976-987. [PMID: 11523099 DOI: 10.1002/jms.95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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