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Reisz JA, Bansal N, Qian J, Zhao W, Furdui CM. Effects of ionizing radiation on biological molecules--mechanisms of damage and emerging methods of detection. Antioxid Redox Signal 2014; 21:260-92. [PMID: 24382094 PMCID: PMC4060780 DOI: 10.1089/ars.2013.5489] [Citation(s) in RCA: 414] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/07/2013] [Accepted: 01/01/2014] [Indexed: 12/13/2022]
Abstract
SIGNIFICANCE The detrimental effects of ionizing radiation (IR) involve a highly orchestrated series of events that are amplified by endogenous signaling and culminating in oxidative damage to DNA, lipids, proteins, and many metabolites. Despite the global impact of IR, the molecular mechanisms underlying tissue damage reveal that many biomolecules are chemoselectively modified by IR. RECENT ADVANCES The development of high-throughput "omics" technologies for mapping DNA and protein modifications have revolutionized the study of IR effects on biological systems. Studies in cells, tissues, and biological fluids are used to identify molecular features or biomarkers of IR exposure and response and the molecular mechanisms that regulate their expression or synthesis. CRITICAL ISSUES In this review, chemical mechanisms are described for IR-induced modifications of biomolecules along with methods for their detection. Included with the detection methods are crucial experimental considerations and caveats for their use. Additional factors critical to the cellular response to radiation, including alterations in protein expression, metabolomics, and epigenetic factors, are also discussed. FUTURE DIRECTIONS Throughout the review, the synergy of combined "omics" technologies such as genomics and epigenomics, proteomics, and metabolomics is highlighted. These are anticipated to lead to new hypotheses to understand IR effects on biological systems and improve IR-based therapies.
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Affiliation(s)
- Julie A Reisz
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
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52
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McCall AS, Cummings CF, Bhave G, Vanacore R, Page-McCaw A, Hudson BG. Bromine is an essential trace element for assembly of collagen IV scaffolds in tissue development and architecture. Cell 2014; 157:1380-1392. [PMID: 24906154 PMCID: PMC4144415 DOI: 10.1016/j.cell.2014.05.009] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/14/2014] [Accepted: 03/25/2014] [Indexed: 11/30/2022]
Abstract
Bromine is ubiquitously present in animals as ionic bromide (Br(-)) yet has no known essential function. Herein, we demonstrate that Br(-) is a required cofactor for peroxidasin-catalyzed formation of sulfilimine crosslinks, a posttranslational modification essential for tissue development and architecture found within the collagen IV scaffold of basement membranes (BMs). Bromide, converted to hypobromous acid, forms a bromosulfonium-ion intermediate that energetically selects for sulfilimine formation. Dietary Br deficiency is lethal in Drosophila, whereas Br replenishment restores viability, demonstrating its physiologic requirement. Importantly, Br-deficient flies phenocopy the developmental and BM defects observed in peroxidasin mutants and indicate a functional connection between Br(-), collagen IV, and peroxidasin. We establish that Br(-) is required for sulfilimine formation within collagen IV, an event critical for BM assembly and tissue development. Thus, bromine is an essential trace element for all animals, and its deficiency may be relevant to BM alterations observed in nutritional and smoking-related disease. PAPERFLICK:
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Affiliation(s)
- A Scott McCall
- Department of Pharmacology, Vanderbilt University School of Medicine, 451 Preston Research Building, Nashville, TN 37232, USA
| | - Christopher F Cummings
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University School of Medicine, D-3100 Medical Center North, Nashville, TN 37232, USA
| | - Gautam Bhave
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University School of Medicine, D-3100 Medical Center North, Nashville, TN 37232, USA
| | - Roberto Vanacore
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University School of Medicine, D-3100 Medical Center North, Nashville, TN 37232, USA; Center for Matrix Biology, Vanderbilt University Medical Center, 1161 21st Avenue South, Nashville, TN 37232, USA
| | - Andrea Page-McCaw
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, U-3218 Medical Research Building III, Nashville, TN 37232, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, 691 Preston Research Building, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Billy G Hudson
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University School of Medicine, D-3100 Medical Center North, Nashville, TN 37232, USA; Center for Matrix Biology, Vanderbilt University Medical Center, 1161 21st Avenue South, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, C-3322 Medical Center North, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, 896 Preston Research Building, Nashville, TN 37232, USA.
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53
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Dong Q, Yan X, Kilpatrick LE, Liang Y, Mirokhin YA, Roth JS, Rudnick PA, Stein SE. Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA). Mol Cell Proteomics 2014; 13:2435-49. [PMID: 24889059 DOI: 10.1074/mcp.o113.037135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This work presents a method for creating a mass spectral library containing tandem spectra of identifiable peptide ions in the tryptic digestion of a single protein. Human serum albumin (HSA(1)) was selected for this purpose owing to its ubiquity, high level of characterization and availability of digest data. The underlying experimental data consisted of ∼3000 one-dimensional LC-ESI-MS/MS runs with ion-trap fragmentation. In order to generate a wide range of peptides, studies covered a broad set of instrument and digestion conditions using multiple sources of HSA and trypsin. Computer methods were developed to enable the reliable identification and reference spectrum extraction of all peptide ions identifiable by current sequence search methods. This process made use of both MS2 (tandem) spectra and MS1 (electrospray) data. Identified spectra were generated for 2918 different peptide ions, using a variety of manually-validated filters to ensure spectrum quality and identification reliability. The resulting library was composed of 10% conventional tryptic and 29% semitryptic peptide ions, along with 42% tryptic peptide ions with known or unknown modifications, which included both analytical artifacts and post-translational modifications (PTMs) present in the original HSA. The remaining 19% contained unexpected missed-cleavages or were under/over alkylated. The methods described can be extended to create equivalent spectral libraries for any target protein. Such libraries have a number of applications in addition to their known advantages of speed and sensitivity, including the ready re-identification of known PTMs, rejection of artifact spectra and a means of assessing sample and digestion quality.
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Affiliation(s)
- Qian Dong
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Xinjian Yan
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Lisa E Kilpatrick
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Yuxue Liang
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Yuri A Mirokhin
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Jeri S Roth
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Paul A Rudnick
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Stephen E Stein
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
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Poulsen K, Bahl JM, Simonsen AH, Hasselbalch SG, Heegaard NH. Distinct transthyretin oxidation isoform profile in spinal fluid from patients with Alzheimer's disease and mild cognitive impairment. Clin Proteomics 2014; 11:12. [PMID: 24678637 PMCID: PMC3973606 DOI: 10.1186/1559-0275-11-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 02/10/2014] [Indexed: 11/20/2022] Open
Abstract
Background Transthyretin (TTR), an abundant protein in cerebrospinal fluid (CSF), contains a free, oxidation-prone cysteine residue that gives rise to TTR isoforms. These isoforms may reflect conditions in vivo. Since increased oxidative stress has been linked to neurodegenerative disorders such as Alzheimer’s disease (AD) it is of interest to characterize CSF-TTR isoform distribution in AD patients and controls. Here, TTR isoforms are profiled directly from CSF by an optimized immunoaffinity-mass spectrometry method in 76 samples from patients with AD (n = 37), mild cognitive impairment (MCI, n = 17)), and normal pressure hydrocephalus (NPH, n = 15), as well as healthy controls (HC, n = 7). Fractions of three specific oxidative modifications (S-cysteinylation, S-cysteinylglycinylation, and S-glutathionylation) were quantitated relative to the total TTR protein. Results were correlated with diagnostic information and with levels of CSF AD biomarkers tau, phosphorylated tau, and amyloid β1-42 peptide. Results Preliminary data highlighted the high risk of artifactual TTR modification due to ex vivo oxidation and thus the samples for this study were all collected using strict and uniform guidelines. The results show that TTR is significantly more modified on Cys(10) in the AD and MCI groups than in controls (NPH and HC) (p ≤ 0.0012). Furthermore, the NPH group, while having normal TTR isoform distribution, had significantly decreased amyloid β peptide but normal tau values. No obvious correlations between levels of routine CSF biomarkers for AD and the degree of TTR modification were found. Conclusions AD and MCI patients display a significantly higher fraction of oxidatively modified TTR in CSF than the control groups of NPH patients and HC. Quantitation of CSF-TTR isoforms thus may provide diagnostic information in patients with dementia symptoms but this should be explored in larger studies including prospective studies of MCI patients. The development of methods for simple, robust, and reproducible inhibition of in vitro oxidation during CSF sampling and sample handling is highly warranted. In addition to the diagnostic information the possibility of using TTR as a CSF oxymeter is of potential value in studies monitoring disease activity and developing new drugs for neurodegenerative diseases.
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Affiliation(s)
| | | | | | | | - Niels Hh Heegaard
- Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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Drazic A, Winter J. The physiological role of reversible methionine oxidation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1367-82. [PMID: 24418392 DOI: 10.1016/j.bbapap.2014.01.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/17/2013] [Accepted: 01/02/2014] [Indexed: 01/04/2023]
Abstract
Sulfur-containing amino acids such as cysteine and methionine are particularly vulnerable to oxidation. Oxidation of cysteine and methionine in their free amino acid form renders them unavailable for metabolic processes while their oxidation in the protein-bound state is a common post-translational modification in all organisms and usually alters the function of the protein. In the majority of cases, oxidation causes inactivation of proteins. Yet, an increasing number of examples have been described where reversible cysteine oxidation is part of a sophisticated mechanism to control protein function based on the redox state of the protein. While for methionine the dogma is still that its oxidation inhibits protein function, reversible methionine oxidation is now being recognized as a powerful means of triggering protein activity. This mode of regulation involves oxidation of methionine to methionine sulfoxide leading to activated protein function, and inactivation is accomplished by reduction of methionine sulfoxide back to methionine catalyzed by methionine sulfoxide reductases. Given the similarity to thiol-based redox-regulation of protein function, methionine oxidation is now established as a novel mode of redox-regulation of protein function. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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Affiliation(s)
- Adrian Drazic
- Center for Integrated Protein Science Munich (CiPS(M)) at the Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Jeannette Winter
- Center for Integrated Protein Science Munich (CiPS(M)) at the Department Chemie, Technische Universität München, 85747 Garching, Germany.
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56
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Li G, Yin Y, Huang G. Increased disulfide peptide sequence coverage via “cleavage ON/OFF” switch during nanoelectrospray. RSC Adv 2014. [DOI: 10.1039/c4ra12386g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Disulfide peptide sequence coverage could be increased via switching “cleavage ON/OFF” modes between conventional and induced nanoelectrospray MS within 1 min.
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Affiliation(s)
- Gongyu Li
- Department of Chemistry
- University of Science and Technology of China
- Hefei, P.R. China
| | - Yue Yin
- Department of Chemistry
- University of Science and Technology of China
- Hefei, P.R. China
| | - Guangming Huang
- Department of Chemistry
- University of Science and Technology of China
- Hefei, P.R. China
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57
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Gibson SC, Feigerle CS, Cook KD. Fluorometric Measurement and Modeling of Droplet Temperature Changes in an Electrospray Plume. Anal Chem 2013; 86:464-72. [DOI: 10.1021/ac402364g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen C. Gibson
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, 1420 Circle Drive, Knoxville, Tennessee 37996-1600, United States
| | - Charles S. Feigerle
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, 1420 Circle Drive, Knoxville, Tennessee 37996-1600, United States
| | - Kelsey D. Cook
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, 1420 Circle Drive, Knoxville, Tennessee 37996-1600, United States
- National Science Foundation, 4201
Wilson Boulevard, Arlington, Virginia 22230, United States
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58
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Serpa JJ, Makepeace KAT, Borchers TH, Wishart DS, Petrotchenko EV, Borchers CH. Using isotopically-coded hydrogen peroxide as a surface modification reagent for the structural characterization of prion protein aggregates. J Proteomics 2013; 100:160-6. [PMID: 24316355 DOI: 10.1016/j.jprot.2013.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/29/2013] [Accepted: 11/25/2013] [Indexed: 12/20/2022]
Abstract
UNLABELLED The conversion of the cellular prion protein (PrP(C)) into aggregated ß-oligomeric (PrP(ß)) and fibril (PrP(Sc)) forms is the central element in the development of prion diseases. Here we report the first use of isotopically-coded hydrogen peroxide surface modification combined with mass spectrometry (MS) for the differential characterization of PrP(C) and PrP(β). (16)O and (18)O hydrogen peroxide were used to oxidize methionine and tryptophan residues in PrP(C) and PrP(β), allowing for the relative quantitation of the extent of modification of each form of the prion protein. After modification with either light or heavy forms of hydrogen peroxide (H2(16)O2 and H2(18)O2), the PrP(C) and PrP(β) forms of the protein were then combined, digested with trypsin, and analysed by LC-MS. The (18)O/(16)O signal intensity ratios were used to determine the relative levels of oxidation of specific amino acids in the PrP(C) and PrP(β) forms. Using this approach we have detected several residues that are differentially-oxidized between the native and β-oligomeric prion forms, allowing determination of the regions of PrP(C) involved in the formation of PrP(β) aggregates. Modification of these residues in the β-oligomeric form is compatible with a flip of the β1-H1-β2 loop away from amphipathic helices 2 and 3 during conversion. BIOLOGICAL SIGNIFICANCE Surface modification using isotopically-coded hydrogen peroxide has allowed quantitative comparison of the exposure of methionine and tryptophan residues in PrP(C) and PrP(ß) forms of prion protein. Detected changes in surface exposure of a number of residues have indicated portions of the PrP structure which undergo conformational transition upon conversion. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Jason J Serpa
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Karl A T Makepeace
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Tristan H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada
| | - Evgeniy V Petrotchenko
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Christoph H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada; University of Victoria, Department of Biochemistry & Microbiology, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
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Siegel D, Permentier H, Reijngoud DJ, Bischoff R. Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 966:21-33. [PMID: 24326023 DOI: 10.1016/j.jchromb.2013.11.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/10/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022]
Abstract
This review deals with chemical and technical challenges in the analysis of small-molecule metabolites involved in central carbon and energy metabolism via liquid-chromatography mass-spectrometry (LC-MS). The covered analytes belong to the prominent pathways in biochemical carbon oxidation such as glycolysis or the tricarboxylic acid cycle and, for the most part, share unfavorable properties such as a high polarity, chemical instability or metal-affinity. The topic is introduced by selected examples on successful applications of metabolomics in the clinic. In the core part of the paper, the structural features of important analyte classes such as nucleotides, coenzyme A thioesters or carboxylic acids are linked to "problematic hotspots" along the analytical chain (sample preparation and-storage, separation and detection). We discuss these hotspots from a chemical point of view, covering issues such as analyte degradation or interactions with metals and other matrix components. Based on this understanding we propose solutions wherever available. A major notion derived from these considerations is that comprehensive carbon metabolomics inevitably requires multiple, complementary analytical approaches covering different chemical classes of metabolites.
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Affiliation(s)
- David Siegel
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar Permentier
- University of Groningen, Department of Pharmacy, Mass Spectrometry Core Facility, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- University Medical Center Groningen, Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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Liu H, Ponniah G, Neill A, Patel R, Andrien B. Accurate Determination of Protein Methionine Oxidation by Stable Isotope Labeling and LC-MS Analysis. Anal Chem 2013; 85:11705-9. [DOI: 10.1021/ac403072w] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hongcheng Liu
- Protein Characterization, Alexion Pharmaceuticals, Inc., 352 Knotter Drive, Cheshire, Connecticut 06410, United States
| | - Gomathinayagam Ponniah
- Protein Characterization, Alexion Pharmaceuticals, Inc., 352 Knotter Drive, Cheshire, Connecticut 06410, United States
| | - Alyssa Neill
- Protein Characterization, Alexion Pharmaceuticals, Inc., 352 Knotter Drive, Cheshire, Connecticut 06410, United States
| | - Rekha Patel
- Protein Characterization, Alexion Pharmaceuticals, Inc., 352 Knotter Drive, Cheshire, Connecticut 06410, United States
| | - Bruce Andrien
- Protein Characterization, Alexion Pharmaceuticals, Inc., 352 Knotter Drive, Cheshire, Connecticut 06410, United States
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Antonakis MM, Tsirigotaki A, Kanaki K, Milios CJ, Pergantis SA. Bipolar mass spectrometry of labile coordination complexes, redox active inorganic compounds, and proteins using a glass nebulizer for sonic-spray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1250-1259. [PMID: 23761045 DOI: 10.1007/s13361-013-0668-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/08/2013] [Accepted: 04/30/2013] [Indexed: 06/02/2023]
Abstract
In this study, we report on the development of a novel nebulizer configuration for sonic-spray ionization (SSI) mass spectrometry (MS), more specifically for a version of SSI that is referred to as Venturi easy ambient sonic-spray ionization (V-EASI) MS. The developed nebulizer configuration is based on a commercially available pneumatic glass nebulizer that has been used extensively for aerosol formation in atomic spectrometry. In the present study, the nebulizer was modified in order to achieve efficient V-EASI-MS operation. Upon evaluating this system, it has been demonstrated that V-EASI-MS offers some distinct advantages for the analysis of coordination compounds and redox active inorganic compounds over the predominantly used electrospray ionization (ESI) technique. Such advantages, for this type of compounds, are demonstrated here for the first time. More specifically, a series of labile heptanuclear heterometallic [Cu(II) 6Ln(III)] clusters held together with artificial amino acid ligands, in addition to easily oxidized inorganic oxyanions of selenium and arsenic, were analyzed. The observed advantages pertain to V-EASI appearing to be a "milder" ionization source than ESI, not requiring electrical potentials for gas phase ion formation, thus eliminating the possibility of unwanted redox transformations, allowing for the "simultaneous" detection of negative and positive ions (bipolar analysis) without the need to change source ionization conditions, and also not requiring the use of syringes and delivery pumps. Because of such features, especially because of the absence of ionization potentials, EASI can be operated with minimal requirements for source parameter optimization. We observed that source temperature and accelerating voltage do not seem to affect labile compounds to the extent they do in ESI-MS. In addition, bipolar analysis of proteins was demonstrated here by acquiring both positive and negative ion mass spectra from the same protein solutions, without the need to independently adjust solution and source conditions in each mode. Finally, the simple and efficient operation of a dual-nebulizer configuration was demonstrated for V-EASI-MS for the first time.
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Affiliation(s)
- Manolis M Antonakis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes Campus, Heraklion, 71003, Greece
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Timmes AG, Moore RA, Fischer ER, Priola SA. Recombinant prion protein refolded with lipid and RNA has the biochemical hallmarks of a prion but lacks in vivo infectivity. PLoS One 2013; 8:e71081. [PMID: 23936256 PMCID: PMC3728029 DOI: 10.1371/journal.pone.0071081] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/24/2013] [Indexed: 11/21/2022] Open
Abstract
During prion infection, the normal, protease-sensitive conformation of prion protein (PrPC) is converted via seeded polymerization to an abnormal, infectious conformation with greatly increased protease-resistance (PrPSc). In vitro, protein misfolding cyclic amplification (PMCA) uses PrPSc in prion-infected brain homogenates as an initiating seed to convert PrPC and trigger the self-propagation of PrPSc over many cycles of amplification. While PMCA reactions produce high levels of protease-resistant PrP, the infectious titer is often lower than that of brain-derived PrPSc. More recently, PMCA techniques using bacterially derived recombinant PrP (rPrP) in the presence of lipid and RNA but in the absence of any starting PrPSc seed have been used to generate infectious prions that cause disease in wild-type mice with relatively short incubation times. These data suggest that lipid and/or RNA act as cofactors to facilitate the de novo formation of high levels of prion infectivity. Using rPrP purified by two different techniques, we generated a self-propagating protease-resistant rPrP molecule that, regardless of the amount of RNA and lipid used, had a molecular mass, protease resistance and insolubility similar to that of PrPSc. However, we were unable to detect prion infectivity in any of our reactions using either cell-culture or animal bioassays. These results demonstrate that the ability to self-propagate into a protease-resistant insoluble conformer is not unique to infectious PrP molecules. They suggest that the presence of RNA and lipid cofactors may facilitate the spontaneous refolding of PrP into an infectious form while also allowing the de novo formation of self-propagating, but non-infectious, rPrP-res.
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Affiliation(s)
- Andrew G. Timmes
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Roger A. Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Elizabeth R. Fischer
- Electron Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Suzette A. Priola
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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Díaz-Moreno I, García-Heredia JM, González-Arzola K, Díaz-Quintana A, De la Rosa MÁ. Recent Methodological Advances in the Analysis of Protein Tyrosine Nitration. Chemphyschem 2013; 14:3095-102. [DOI: 10.1002/cphc.201300210] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Indexed: 01/20/2023]
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Silva CJ, Dynin I, Erickson ML, Requena JR, Balachandran A, Hui C, Onisko BC, Carter JM. Oxidation of methionine 216 in sheep and elk prion protein is highly dependent upon the amino acid at position 218 but is not important for prion propagation. Biochemistry 2013; 52:2139-47. [PMID: 23458153 DOI: 10.1021/bi3016795] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We employed a sensitive mass spectrometry-based method to deconstruct, confirm, and quantitate the prions present in elk naturally infected with chronic wasting disease and sheep naturally infected with scrapie. We used this approach to study the oxidation of a methionine at position 216 (Met216), because this oxidation (MetSO216) has been implicated in prion formation. Three polymorphisms (Ile218, Val218, and Thr218) of sheep recombinant prion protein were prepared. Our analysis showed the novel result that the proportion of MetSO216 was highly dependent upon the amino acid residue at position 218 (I > V > T), indicating that Ile218 in sheep and elk prion protein (PrP) renders the Met216 intrinsically more susceptible to oxidation than the Val218 or Thr218 analogue. We were able to quantitate the prions in the attomole range. The presence of prions was verified by the detection of two confirmatory peptides: GENFTETDIK (sheep and elk) and ESQAYYQR (sheep) or ESEAYYQR (elk). This approach required much smaller amounts of tissue (600 μg) than traditional methods of detection (enzyme-linked immunosorbent assay, Western blot, and immunohistochemical analysis) (60 mg). In sheep and elk, a normal cellular prion protein containing MetSO216 is not actively recruited and converted to prions, although we observed that this Met216 is intrinsically more susceptible to oxidation.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
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65
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Chen SH, Russell WK, Russell DH. Combining chemical labeling, bottom-up and top-down ion-mobility mass spectrometry to identify metal-binding sites of partially metalated metallothionein. Anal Chem 2013; 85:3229-37. [PMID: 23421923 DOI: 10.1021/ac303522h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Metalation and demetalation of human metallothionein-2A (MT) with Cd(2+) is investigated by using chemical labeling and "bottom-up" and "top-down" proteomics approaches. Both metalation and demetalation of MT-2A by Cd(2+) are shown to be domain specific and occur as two distinct processes. Metalation involves sequential addition of Cd(2+) to the α-domain resulting in formation of an intermediate, Cd4MT. Chemical labeling with N-ethylmaleimide (NEM) and tandem mass spectrometry experiments clearly show that the four metal ions are located in the α-domain. In the presence of excess Cd(2+), the Cd4MT intermediate reacts to add Cd(2+) to the β-domain to yield the fully metalated Cd7MT. Demetalation occurs in the reverse order, i.e., Cd(2+) is removed (by EDTA) first from the β-domain followed by Cd(2+) removal from the α-domain. Metalation of human MT-2A is shown to be metal ion specific by comparing relative metal ion binding constants for Cd(2+) and Zn(2+).
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Affiliation(s)
- Shu-Hua Chen
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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66
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Bonvin G, Schappler J, Rudaz S. Capillary electrophoresis–electrospray ionization-mass spectrometry interfaces: Fundamental concepts and technical developments. J Chromatogr A 2012; 1267:17-31. [DOI: 10.1016/j.chroma.2012.07.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/04/2012] [Accepted: 07/06/2012] [Indexed: 01/24/2023]
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67
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Bachi A, Dalle-Donne I, Scaloni A. Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises. Chem Rev 2012. [DOI: 10.1021/cr300073p] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Angela Bachi
- Biological Mass Spectrometry Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
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68
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Plattner S, Erb R, Chervet JP, Oberacher H. Ascorbic acid for homogenous redox buffering in electrospray ionization-mass spectrometry. Anal Bioanal Chem 2012; 404:1571-9. [PMID: 22772139 PMCID: PMC3426670 DOI: 10.1007/s00216-012-6196-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
Abstract
Electrospray ionization (ESI) involves the dispersion of a liquid containing analytes of interest into a fine aerosol by applying a high potential difference to the sample solution with respect to a counter electrode. Thus, from the electrochemical point of view, the ESI source represents a two-electrode controlled-current electrochemical flow cell. The electroactive compounds part of the solvent sprayed may be altered by occurring electrolysis (oxidation in positive ion mode and reduction in negative ion mode). These reactions can be troublesome in the context of unknown identification and quantification. In the search for a simple, inexpensive, and efficient way to suppress electrochemical oxidation in positive ESI, the usability of ascorbic acid, hydroquinone, and glutathione for homogenous redox buffering was tested. Performance of the antioxidants was assessed by analyzing pharmaceutical compounds covering a broad range of functional groups prone to oxidation. Different emitter setups were applied for continuous infusion, flow injection, and liquid chromatography/mass spectrometry experiments. Best performance was obtained with ascorbic acid. In comparison to hydroquinone and glutathione, ascorbic acid offered superior antioxidant activity, a relatively inert oxidation product, and hardly any negative effect on the ionization efficiency of analytes. Furthermore, ascorbic acid suppressed the formation of sodiated forms and was able to induce charge state reduction. Only in the very special case of analyzing a compound isobaric to ascorbic acid, interference with the low-abundant [ascorbic acid+H](+) signal may become a point of attention.
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Affiliation(s)
- Sabine Plattner
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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69
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Wu L, White DE, Ye C, Vogt FG, Terfloth GJ, Matsuhashi H. Desulfurization of phosphorothioate oligonucleotides via the sulfur-by-oxygen replacement induced by the hydroxyl radical during negative electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:836-844. [PMID: 22791250 DOI: 10.1002/jms.3022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
While the occurrence of desulfurization of phosphorothioate oligonucleotides in solution is well established, this study represents the first attempt to investigate the basis of the unexpected desulfurization via the net sulfur-by-oxygen (S-O) replacement during negative electrospray ionization (ESI). The current work, facilitated by quantitative mass deconvolution, demonstrates that considerable desulfurization can take place even under common negative ESI operating conditions. The extent of desulfurization is dependent on the molar phosphorothioate oligonucleotide-to-hydroxyl radical ratio, which is consistent with the corona discharge-induced origin of the hydroxyl radical leading to the S-O replacement. This hypothesis is supported by the fact that an increase of the high-performance liquid chromatography (HPLC) flow rate and the on-column concentration of a phosphorothioate oligonucleotide, as well as a decrease of the electrospray voltage reduce the degree of desulfurization. Comparative LC-tandem mass spectrometry (MS/MS) sequencing of a phosphorothioate oligonucleotide and its corresponding desulfurization product revealed evidence that the S-O replacement occurs at multiple phosphorothioate internucleotide linkage sites. In practice, the most convenient and effective strategy for minimizing this P = O artifact is to increase the LC flow rate and the on-column concentration of phosphorothioate oligonucleotides. Another approach to mitigate possible detrimental effects of the undesired desulfurization is to operate the ESI source at a very low electrospray voltage to diminish the corona discharge; however this will significantly compromise sensitivity when analyzing the low-level P = O impurities in phosphorothioate oligonucleotides.
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Affiliation(s)
- Lianming Wu
- API Chemistry and Analysis, Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA.
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70
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Grasso G. The use of mass spectrometry to study amyloid-β peptides. MASS SPECTROMETRY REVIEWS 2011; 30:347-365. [PMID: 21500241 DOI: 10.1002/mas.20281] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/06/2009] [Accepted: 11/06/2009] [Indexed: 05/30/2023]
Abstract
Amyloid-β peptide (Aβ) varies in size from 39 to 43 amino acids and arises from sequential β- and γ-secretase processing of the amyloid precursor protein. Whereas the non-pathological role for Aβ is yet to be established, there is no disputing that Aβ is now widely regarded as central to the development of Alzheimer's disease (AD). The so named "amyloid cascade hypothesis" states that disease progression is the result of an increased Aβ burden in affected areas of the brain. To elucidate the Aβ role in AD, many analytical approaches have been proposed as suitable tools to investigate not only the total Aβ load but also many other issues that are considered crucial for AD, such as: (i) the aggregation state in which Aβ is present; (ii) its interaction with other species or metals; (iii) its ability to induce oxidative stress; and (iv) its degradative pathways. This review provides an insight into the use of mass spectrometry (MS) in the field of Aβ investigation aimed to assess its role in AD. In particular, the different MS-based approaches applied in vitro and in vivo that can provide detailed information on the above-mentioned issues are reviewed. Moreover, the advantages offered by the MS methods over all the other techniques are highlighted, together with the recent developments and uses of combined analytical approaches to detect and characterize Aβ.
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Affiliation(s)
- Giuseppe Grasso
- Chemistry Department, Università di Catania, Viale Andrea Doria 6, Catania 95125, Italy.
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71
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Braz VA, Barkley MD, Jockusch RA, Wintrode PL. Efavirenz binding site in HIV-1 reverse transcriptase monomers. Biochemistry 2010; 49:10565-73. [PMID: 21090588 DOI: 10.1021/bi101480z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Efavirenz (EFV) is a potent nonnucleoside reverse transcriptase inhibitor (NNRTI) used in the treatment of AIDS. NNRTIs bind in a hydrophobic pocket located in the p66 subunit of reverse transcriptase (RT), which is not present in crystal structures of RT without an inhibitor. Recent studies showed that monomeric forms of the p66 and p51 subunits bind efavirenz with micromolar affinity. The effect of efavirenz on the solution conformations of p66 and p51 monomers was studied by hydrogen-deuterium exchange mass spectrometry (HXMS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). HXMS data reveal that five peptides, four of which contain efavirenz contact residues seen in the crystal structure of the RT-EFV complex, exhibit a reduced level of exchange in monomer-EFV complexes. Moreover, peptide 232-246 undergoes slow cooperative unfolding-refolding in the bound monomers, but at a rate much slower than that observed in the p66 subunit of the RT heterodimer [Seckler, J. M., Howard, K. J., Barkley, M. D., and Wintrode, P. L. (2009) Biochemistry 48, 7646-7655]. These results suggest that the efavirenz binding site on p66 and p51 monomers is similar to the NNRTI binding pocket in the p66 subunit of RT. Nanoelectrospray ionization FT-ICR mass spectra indicate that the intact monomers each have (at least) two different conformations. In the presence of efavirenz, the mass spectra change significantly and suggest that p51 adopts a single, more compact conformation, whereas p66 undergoes facile, electrospray-induced cleavage. The population shift is consistent with a selected-fit binding mechanism.
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Affiliation(s)
- Valerie A Braz
- Department of Chemistry, Case Western Reserve University,10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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72
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Roeser J, Bischoff R, Bruins AP, Permentier HP. Oxidative protein labeling in mass-spectrometry-based proteomics. Anal Bioanal Chem 2010; 397:3441-55. [PMID: 20155254 PMCID: PMC2911539 DOI: 10.1007/s00216-010-3471-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 01/07/2023]
Abstract
Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)-mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade.
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Affiliation(s)
- Julien Roeser
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Andries P. Bruins
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar P. Permentier
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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73
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Perdivara I, Deterding LJ, Przybylski M, Tomer KB. Mass spectrometric identification of oxidative modifications of tryptophan residues in proteins: chemical artifact or post-translational modification? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1114-7. [PMID: 20219394 PMCID: PMC2900464 DOI: 10.1016/j.jasms.2010.02.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/01/2010] [Accepted: 02/05/2010] [Indexed: 05/08/2023]
Abstract
Oxidative modification of tryptophan to kynurenine (KYN) and N-formyl kynurenine (NFK) has been described in mitochondrial proteins associated with redox metabolism, and in human cataract lenses. To a large extent, however, previously reported identifications of these modifications were performed using peptide mass fingerprinting and/or tandem-MS data of proteins separated by gel electrophoresis. To date, it is uncertain whether NFK and KYN may represent sample handling artifacts or exclusively post-translational events. To address the problem of the origin of tryptophan oxidation, we characterized several antibodies by liquid chromatography-tandem mass spectrometry, with and without the use of electrophoretic separation of heavy and light chains. Antibodies are not normally expected to undergo oxidative modifications, however, several tryptophan (Trp) residues on both heavy and light chains were found extensively modified to both doubly oxidized Trp and KYN following SDS-PAGE separation and in-gel digestion. In contrast, those residues were observed as non-modified upon in-solution digestion. These results indicate that Trp oxidation may occur as an artifact in proteins separated by SDS-PAGE, and their presence should be carefully interpreted, especially when gel electrophoretic separation methods are employed.
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Affiliation(s)
- Irina Perdivara
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
- Laboratory of Analytical Chemistry and Biopolymer Structure Analysis, University of Konstanz, 78457 Konstanz, Germany
| | - Leesa J. Deterding
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael Przybylski
- Laboratory of Analytical Chemistry and Biopolymer Structure Analysis, University of Konstanz, 78457 Konstanz, Germany
- Address reprint requests to: Dr. Kenneth B. Tomer, Laboratory of Structural Biology, National Institutes of Environmental Health Sciences, Phone: +1 919 541 1966, Fax: +1 919 541 0220, . Professor Dr. Michael Przybylski, Department of Chemistry, University of Konstanz, Phone:++49-7531-882249, Fax: ++49-7531-3097,
| | - Kenneth B. Tomer
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
- Address reprint requests to: Dr. Kenneth B. Tomer, Laboratory of Structural Biology, National Institutes of Environmental Health Sciences, Phone: +1 919 541 1966, Fax: +1 919 541 0220, . Professor Dr. Michael Przybylski, Department of Chemistry, University of Konstanz, Phone:++49-7531-882249, Fax: ++49-7531-3097,
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Alberici RM, Simas RC, Sanvido GB, Romão W, Lalli PM, Benassi M, Cunha IBS, Eberlin MN. Ambient mass spectrometry: bringing MS into the "real world". Anal Bioanal Chem 2010; 398:265-94. [PMID: 20521143 DOI: 10.1007/s00216-010-3808-3] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 04/26/2010] [Accepted: 04/29/2010] [Indexed: 11/26/2022]
Abstract
Mass spectrometry has recently undergone a second contemporary revolution with the introduction of a new group of desorption/ionization (DI) techniques known collectively as ambient mass spectrometry. Performed in an open atmosphere directly on samples in their natural environments or matrices, or by using auxiliary surfaces, ambient mass spectrometry (MS) has greatly simplified and increased the speed of MS analysis. Since its debut in 2004 there has been explosive growth in the applications and variants of ambient MS, and a very comprehensive set of techniques based on different desorption and ionization mechanisms is now available. Most types of molecules with a large range of masses and polarities can be ionized with great ease and simplicity with the outstanding combination of the speed, selectivity, and sensitivity of MS detection. This review describes and compares the basis of ionization and the concepts of the most promising ambient MS techniques known to date and illustrates, via typical analytical and bioanalytical applications, how ambient MS is helping to bring MS analysis deeper than ever into the "real world" open atmosphere environment--to wherever MS is needed.
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Affiliation(s)
- Rosana M Alberici
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP 13083-970, Brazil.
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75
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Trimpin S. A perspective on MALDI alternatives-total solvent-free analysis and electron transfer dissociation of highly charged ions by laserspray ionization. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:471-485. [PMID: 20446310 DOI: 10.1002/jms.1737] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Progress in research is hindered by analytical limitations, especially in biological areas in which sensitivity and dynamic range are critical to success. Inherent difficulties of characterization associated with complexity arising from heterogeneity of various materials including topologies (isomeric composition) and insolubility also limit progress. For this reason, we are developing methods for total solvent-free analysis by mass spectrometry consisting of solvent-free ionization followed by solvent-free gas-phase separation. We also recently constructed a novel matrix-assisted laser desorption ionization (MALDI) source that provides a simple, practical and sensitive way of producing highly charged ions by laserspray ionization (LSI) or singly charged ions commonly observed with MALDI by choice of matrix or matrix preparation. This is the first ionization source with such freedom-an extremely powerful analytical 'switch'. Multiply charged LSI ions allow molecules exceeding the mass-to-charge range of the instrument to be observed and permit for the first time electron transfer dissociation fragment ion analysis.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
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76
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Silva CJ, Onisko BC, Dynin I, Erickson ML, Vensel WH, Requena JR, Antaki EM, Carter JM. Assessing the role of oxidized methionine at position 213 in the formation of prions in hamsters. Biochemistry 2010; 49:1854-61. [PMID: 20121218 DOI: 10.1021/bi901850n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prions are infectious proteins that are able to recruit a normal cellular prion protein and convert it into a prion. The mechanism of this conversion is unknown. Detailed analysis of the normal cellular prion protein and a corresponding prion has shown they possess identical post-translational modifications and differ solely in conformation. Recent work has suggested that the oxidized form of the methionine at position 213 (Met213) plays a role in the conversion of the normal cellular prion protein to the prion conformation and is a prion-specific covalent signature. We developed a sensitive method of quantitating the methionine sulfoxide present at position 213 (MetSO213) and used this method to measure the changes in MetSO213 over the time course of an intracranial challenge, using the 263K strain of hamster-adapted scrapie. These results indicate that the proportion of Met213 that is oxidized decreases over the course of the disease. We examined the quantity of MetSO213 in PrP(C) and compared it to the amount found in animals terminally afflicted with the 263K, 139H, and drowsy strains of hamster-adapted scrapie. These strains show only low levels of MetSO213 that is comparable to that of PrP(C). These data suggest that MetSO213 does not appear to be a prion-specific covalent signature.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture, Albany, California 94710, USA.
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77
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Maire F, Lange CM. Formation of unexpected ions from a first-generation polyamidoamine dendrimer by use of methanol: an artefact due to electrospray emitter corrosion? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:995-1000. [PMID: 20209661 DOI: 10.1002/rcm.4475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report the formation of unexpected ions during the analyses of a first-generation polyamidoamine dendrimer in negative ion mode using an ion trap equipped with an electrospray ionisation source. These surprising ions corresponded to an increase of 12 m/z units over those expected. The formation of the unexpected ions was dependent on the tuning of the solution flow rate and the capillary high voltage. In addition, measurements of unusual value of the current suggested that a reaction was occurring in the corona plasma. The influence of methanol in this phenomenon was demonstrated by using CD(3)OH in the sample preparation. We propose two structures to explain the observed adduct based on the results of MS(2) experiments and by referring to previous work dealing with 12 m/z units addition. We showed that a corona discharge caused by alterations taking place to the electrospray capillary emitter was the origin of these unexpected ions. Finally, we discuss the mechanism involved in the formation of the ions and we propose means to control such artefacts.
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Affiliation(s)
- Florian Maire
- Université de Rouen, IRCOF, rue Tesnière, 76130 Mont-Saint-Aignan, France
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78
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Trimpin S, Herath TN, Inutan ED, Wager-Miller J, Kowalski P, Claude E, Walker JM, Mackie K. Automated solvent-free matrix deposition for tissue imaging by mass spectrometry. Anal Chem 2010; 82:359-67. [PMID: 19968249 DOI: 10.1021/ac902065u] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ability to analyze complex (macro) molecules is of fundamental importance for understanding chemical, physical, and biological processes. Complexity may arise from small differences in structure, large dynamic range, as well as a vast range in solubility or ionization, imposing daunting tasks in areas as different as lipidomics and proteomics. Here, we describe a rapid matrix application that permits the deposition of matrix-assisted laser desorption/ionization (MALDI) matrix solvent-free. This solvent-free one-step automatic matrix deposition is achieved through vigorous movements of beads pressing the matrix material through a metal mesh. The mesh (20 mum) produces homogeneous coverage of <12 microm crystals (DHB, CHCA matrixes) in 1 min, as determined by optical microscopy, permitting fast uniform coverage of analyte and possible high-spatial resolution surface analysis. Homogenous tissue coverage of <5 microm sized crystals is achieved using a 3 microm mesh. Solvent-free MALDI analysis on a time-of-flight (TOF) mass analyzer of mouse brain tissue homogenously covered with CHCA matrix subsequently provides a homogeneous response in ion signal intensity. Total solvent-free analysis (TSA) by mass spectrometry (MS) of tissue sections is carried out by applying the MALDI matrix solvent-free for subsequent ionization and gas phase separation for decongestion of complexity in the absence of any solvent using ion mobility spectrometry (IMS) followed by MS detection. Isobaric compositions were well-delineated using TSA by MS.
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Affiliation(s)
- Sarah Trimpin
- Wayne State University, Department of Chemistry, Detroit, Michigan 48202, USA.
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79
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Wu C, Qian K, Nefliu M, Cooks RG. Ambient analysis of saturated hydrocarbons using discharge-induced oxidation in desorption electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:261-267. [PMID: 19914089 DOI: 10.1016/j.jasms.2009.10.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 10/07/2009] [Accepted: 10/10/2009] [Indexed: 05/28/2023]
Abstract
Saturated nonfunctionalized hydrocarbons can be oxidized in situ by initiating an electrical discharge during desorption electrospray ionization (DESI) to generate the corresponding alcohols and ketones. This form of reactive DESI experiment can be utilized as an in situ derivatization method for rapid and direct analysis of alkanes at atmospheric pressure without sample preparation. Betaine aldehyde was incorporated into the DESI spray solution to improve the sensitivity of detecting the long-chain alcohol oxidation products. The limit of detection for alkanes (C(15)H(32) to C(30)H(62)) from pure samples is approximately 20 ng. Multiple oxidations and dehydrogenations occurred during the DESI discharge, but no hydrocarbon fragmentation was observed, even for highly branched squalane. Using exact mass measurements, the technique was successfully implemented for analysis of petroleum distillates containing saturated hydrocarbons.
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Affiliation(s)
- Chunping Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-1393, USA
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80
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Gibson GTT, Mugo SM, Oleschuk RD. Nanoelectrospray emitters: trends and perspective. MASS SPECTROMETRY REVIEWS 2009; 28:918-936. [PMID: 19479726 DOI: 10.1002/mas.20248] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The benefits of electrospray ionization are many, including sensitivity, robustness, simplicity and the ability to couple continuous flow methods with mass spectrometry. The technique has seen further improvement by lowering flow rates to the nanoelectrospray regime (<1,000 nL/min), where sample consumption is minimized and sensitivity increases. The move to nanoelectrospray has required a shift in the design of the electrospray source which has mostly involved the emitter itself. The emitter has seen an evolution in architecture as the shape and geometry of the device have proved pivotal in the formation of sufficiently small droplets for sensitive MS detection at these flow rates. There is a clear movement toward the development of emitters that produce multiple Taylor cones. Such multielectrospray emitters have been shown to provide enhanced sensitivity and sample utilization. This article reviews the development of nanoelectrospray emitters, including factors such as geometry and the manner of applying voltage. Designs for emitters that take advantage of multielectrospray are emphasized.
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Affiliation(s)
- Graham T T Gibson
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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81
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Moolayil JT, George M, Giblin D, Gross ML. 2-Nitrophenyl Aryl Sulfides Undergo Both Intramolecular and Electrospray-Induced Intermolecular Oxidation of Sulfur: An Experimental and Theoretical Case Study. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2009; 283:222-228. [PMID: 20161084 PMCID: PMC2743511 DOI: 10.1016/j.ijms.2009.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Aromatic sulfides bearing a nitro group undergo sulfur oxidation upon electrospray ionization in the positive-ion mode. For example, 2-nitrophenyl phenyl sulfide, its para nitro isomer, and its chloro and methyl substituted analogs pick up an oxygen atom to afford [M + H + O](+) and [M + Na + O](+) ions upon ESI. Elemental-composition determination and tandem mass spectrometry confirm the reactions. Another oxidation of the sulfur, by the ortho nitro group of the [M + H](+) ions, occurs as intramolecular oxygen-transfer processes, evidenced by characteristic losses of SO, SO(2) and SO(2)H(*), the latter yielding the carbazole radical cation, and the generation of the aryl-SO(+) product ion. The intramolecular oxidation via oxygen transfer from the nitro group to the sulfur was corroborated by molecular modeling. The results substantiate both inter- and intramolecular oxidation and provide more evidence that care must be taken when analyzing not only methionine-containing peptides but also small sulfides.
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Affiliation(s)
- Joseph T Moolayil
- Department of Chemistry, Sacred Heart College, Thevara, Cochin, Kerala, India 682013
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82
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Boys BL, Kuprowski MC, Noël JJ, Konermann L. Protein Oxidative Modifications During Electrospray Ionization: Solution Phase Electrochemistry or Corona Discharge-Induced Radical Attack? Anal Chem 2009; 81:4027-34. [DOI: 10.1021/ac900243p] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Brian L. Boys
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Mark C. Kuprowski
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - James J. Noël
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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83
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Marginean I, Kelly RT, Moore RJ, Prior DC, LaMarche BL, Tang K, Smith RD. Selection of the optimum electrospray voltage for gradient elution LC-MS measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:682-688. [PMID: 19196520 PMCID: PMC2692488 DOI: 10.1016/j.jasms.2008.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 12/03/2008] [Accepted: 12/07/2008] [Indexed: 05/27/2023]
Abstract
Changes in liquid composition during gradient elution liquid chromatography (LC) coupled to mass spectrometry (MS) analyses affect the electrospray operation. To establish methodologies for judicious selection of the electrospray voltage, we monitored in real time the effect of the LC gradient on the spray current. The optimum range of the electrospray voltage decreased as the concentration of organic solvent in the eluent increased during reversed-phase LC analyses. These results and related observations provided the means to rationally select the voltage to ensure effective electrospray operation throughout gradient-elution LC separations. For analyses in which the electrospray was operated at constant voltage, a small run-to-run variation in the spray current was observed, indicating a changing electric field resulting from fouling or degradation of the emitter. Algorithms using feedback from spray current measurements that can maintain the electrospray voltage within the optimum operating range throughout gradient elution LC-MS were evaluated. The electrospray operation with voltage regulation and at a constant, judiciously selected voltage during gradient elution LC-MS measurements produced data with similar reproducibility.
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Affiliation(s)
- Ioan Marginean
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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84
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Muñoz J, Fernández-Irigoyen J, Santamaría E, Parbel A, Obeso J, Corrales FJ. Mass spectrometric characterization of mitochondrial complex I NDUFA10 variants. Proteomics 2008; 8:1898-908. [DOI: 10.1002/pmic.200701085] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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85
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Potential pathogenic role of β-amyloid1–42–aluminum complex in Alzheimer's disease. Int J Biochem Cell Biol 2008; 40:731-46. [DOI: 10.1016/j.biocel.2007.10.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 10/09/2007] [Accepted: 10/09/2007] [Indexed: 11/20/2022]
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