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Zhu L, Yin L, Xue J, Wang Z, Nie Z. Mass Spectrometry Genotyping of Human Papillomavirus Based on High-Efficiency Selective Enrichment of Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2018; 10:41178-41184. [PMID: 30406990 DOI: 10.1021/acsami.8b16694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This work developed a novel spermine-modified nanodiamonds (SP-NDs)-based method to selectively enrich oligonucleotides for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of human papillomavirus (HPV) virus. Our results showed that SP-NDs can effectively extract and enrich DNA oligonucleotides from sodium dodecyl sulfonate and urea solution. In addition, SP-NDs can also selectively extract oligonucleotides from enzymes digestion products of polymerase chain reaction-restriction fragment mass polymorphism (PCR-RFMP) of HPV virus. Then, the extract can be detected by MALDI-TOF MS directly without further purification. According to the MS results, the HPV genotyping can be achieved. More importantly, with SP-NDs extraction, clinical samples infected with HPV genotype 16 and 18 can be identified. The described method shows great advantages of simplicity, high selectivity, and good reliability in real clinical samples. Due to our methods improvement on DNA enrichment, extraction and purification, the PCR-based MALDI-TOF MS for the analysis of oligonucleotides maybe become more rapid, sensitive, and high-throughput, is promising for analysis for DNA methylation, single-nucleotide polymorphisms, and other virus typing.
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Affiliation(s)
- Li Zhu
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , Beijing 100029 , China
- National Institutes for Food and Drug Control , Beijing 102629 , China
| | - Lihui Yin
- National Institutes for Food and Drug Control , Beijing 102629 , China
| | - JinJuan Xue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Zhihua Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
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Ivanova B, Spiteller M. A quantitative solid-state Raman spectroscopic method for control of fungicides. Analyst 2012; 137:3355-64. [DOI: 10.1039/c2an35174a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Ivanova B, Spiteller M. Conformation, optical properties, and absolute configuration of 2′,3′-isopropylideneadenosines: Theoretical vs. experimental study. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.08.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Abstract
Mass spectrometry imaging (MSI), a rapidly growing subfield of chemical imaging, employs mass spectrometry (MS) technologies to create single- and multi-dimensional localization maps for a variety of atoms and molecules. Complimentary to other imaging approaches, MSI provides high chemical specificity and broad analyte coverage. This powerful analytical toolset is capable of measuring the distribution of many classes of inorganics, metabolites, proteins, and pharmaceuticals in chemically and structurally complex biological specimens in vivo, in vitro, and in situ. The MSI approaches highlighted in this Methods in Molecular Biology volume provide flexibility of detection, characterization, and identification of multiple known and unknown analytes. The goal of this chapter is to introduce investigators who may be unfamiliar with MS to the basic principles of the mass spectrometric approaches as used in MSI. In addition to guidelines for choosing the most suitable MSI method for specific investigations, cross-references are provided to the chapters in this volume that describe the appropriate experimental protocols.
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Tu T, Gross ML. Miniaturizing sample spots for matrix-assisted laser desorption/ionization mass spectrometry. Trends Analyt Chem 2009; 28:833-841. [PMID: 20161086 PMCID: PMC2744082 DOI: 10.1016/j.trac.2009.03.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The trend of miniaturization in bioanalytical chemistry is shifting from technical development to practical application. In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), progress in miniaturizing sample spots has been driven by the needs to increase sensitivity and speed, to interface with other analytical microtechnologies, and to develop miniaturized instrumentation.We review recent developments in miniaturizing sample spots for MALDI-MS. We cover both target modification and microdispensing technologies, and we emphasize the benefits with respect to sensitivity, throughput and automation.We hope that this review will encourage further method development and application of miniaturized sample spots for MALDI-MS, so as to expand applications in analytical chemistry, protein science and molecular biology.
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Affiliation(s)
- Tingting Tu
- Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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Fu Y, Xu S, Pan C, Ye M, Zou H. 3,4-diaminobenzophenone matrix for analysis of oligonucleotides by MALDI-TOF mass spectrometry. ACTA ACUST UNITED AC 2008; Chapter 10:Unit 10.12. [PMID: 18428967 DOI: 10.1002/0471142700.nc1012s31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit contains procedures for analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry with 3,4-diaminobenzophenone (DABP) as a matrix. This new matrix has demonstrated advantages in the analysis of oligonucleotides. With DABP as a matrix, intact oligonucleotide ions can be readily produced with lower laser powers, resulting in better detection limits, less fragmentation, and fewer alkali-metal ion adducts compared with results obtained using conventional matrices. Minimal fragmentation and fewer alkali-metal ion adducts were seen even at low oligonucleotide concentrations. It was also found that samples prepared with DABP are highly homogenous, therefore reducing the need to find "sweet spots" in MALDI. Finally, excellent shot-to-shot reproducibility, resolution, and signal-to-noise ratio are observed using the DABP matrix.
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Affiliation(s)
- Yu Fu
- National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Dalian, China
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Hsu NY, Yang WB, Wong CH, Lee YC, Lee RT, Wang YS, Chen CH. Matrix-assisted laser desorption/ionization mass spectrometry of polysaccharides with 2',4',6'-trihydroxyacetophenone as matrix. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:2137-46. [PMID: 17546658 DOI: 10.1002/rcm.3072] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
So far, there have been only a few matrices reported for detection of polysaccharides with molecular weight higher than 3000 Daltons by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). In this work, we found that 2',4',6'-trihydroxyacetophenone (THAP) is a good matrix for MALDI time-of-flight MS analysis of polysaccharides with broad mass range. Large polysaccharides, dextrans, glycoproteins and polysialic acids have been successfully detected by MALDI-MS with THAP as matrix.
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Affiliation(s)
- Nien-Yeen Hsu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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Chang WC, Huang LCL, Wang YS, Peng WP, Chang HC, Hsu NY, Yang WB, Chen CH. Matrix-assisted laser desorption/ionization (MALDI) mechanism revisited. Anal Chim Acta 2006; 582:1-9. [PMID: 17386467 DOI: 10.1016/j.aca.2006.08.062] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/24/2006] [Accepted: 08/24/2006] [Indexed: 11/29/2022]
Abstract
Although matrix-assisted laser desorption/ionization (MALDI) was developed more than a decade ago and broad applications have been successfully demonstrated, detailed mechanism of MALDI is still not well understood. Two major models; namely photochemical ionization (PI) and cluster ionization (CI) mechanisms have been proposed to explain many of experimental results. With the photochemical ionization model, analyte ions are considered to be produced from a protonation or deprotonation process involving an analyte molecule colliding with a matrix ion in the gas phase. With the cluster ionization model, charged particles are desorbed with a strong photoabsorption by matrix molecules. Analyte ions are subsequently produced by desolvation of matrix from cluster ions. Nevertheless, many observations still cannot be explained by these two models. In this work, we consider a pseudo proton transfer process during crystallization as a primary mechanism for producing analyte ions in MALDI. We propose an energy transfer induced disproportionation (ETID) model to explain the observation of an equal amount of positive and negative ions produced in MALDI for large biomolecules. Some experimental results are used for comparisons of various models.
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Affiliation(s)
- Wei Chao Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Fu Y, Xu S, Pan C, Ye M, Zou H, Guo B. A matrix of 3,4-diaminobenzophenone for the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Nucleic Acids Res 2006; 34:e94. [PMID: 16885235 PMCID: PMC1540732 DOI: 10.1093/nar/gkl509] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 07/01/2006] [Accepted: 07/03/2006] [Indexed: 12/04/2022] Open
Abstract
A new matrix of 3,4-diaminobenzophenone (DABP) was demonstrated to be advantageous in the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. With DABP as a matrix, intact oligonucleotide ions can be readily produced with lower laser powers, resulting in better detection limits, less fragmentation and fewer alkali metal ion adducts compared with the results obtained with conventional matrices. Importantly, minimal fragmentation and fewer alkali metal ion adducts were seen even at low concentrations of oligonucleotides. It was also found that samples prepared with DABP are highly homogenous and therefore reducing the need for finding 'sweet' spots in MALDI. In addition, excellent shot-to-shot reproducibility, resolution and signal-to-noise ratio were seen with DABP as the matrix.
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Affiliation(s)
- Yu Fu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Songyun Xu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Chensong Pan
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Mingliang Ye
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Hanfa Zou
- To whom correspondence should be addressed. Tel: +86 411 843 79610; Fax: +86 411 843 79620;
| | - Baochuan Guo
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
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Edwards JR, Ruparel H, Ju J. Mass-spectrometry DNA sequencing. Mutat Res 2005; 573:3-12. [PMID: 15829234 DOI: 10.1016/j.mrfmmm.2004.07.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 07/15/2004] [Indexed: 11/15/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been explored widely for DNA sequencing. Compared to gel electrophoresis based sequencing systems, mass spectrometry produces very high resolution of sequencing fragments, rapid separation on microsecond time scales, and completely eliminates compressions associated with gel-based systems. While most of the research efforts have focused on using mass spectrometers to analyze the DNA products from Sanger sequencing or enzymatic digestion reactions, the read lengths attainable are currently insufficient for large-scale de novo sequencing. The advantage of mass-spectrometry sequencing is that one can unambiguously identify frameshift mutations and heterozygous mutations making it an ideal choice for resequencing projects. In these applications, DNA sequencing fragments that are the same length but with different base compositions are generated, which are challenging to consistently distinguish in gel-based sequencing systems. In contrast, MALDI-TOF MS produces mass spectra of these DNA sequencing fragments with nearly digital resolution, allowing accurate determination of the mixed bases. For these reasons mass spectrometry based sequencing has mainly been focused on the detection of frameshift mutations and single nucleotide polymorphisms (SNPs). More recently, assays have been developed to indirectly sequence DNA by first converting it into RNA. These assays take advantage of the increased resolution and detection ability of MALDI-TOF MS for RNA.
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Affiliation(s)
- John R Edwards
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, Room 405A, Russ Berrie Medical Science Pavilion, New York, NY 10032, USA
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