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Abstract
This paper is based upon an extensive review of 71 willingness-to-pay (WTP) surveys of health and health care published in English during the period 1985--1998. The aim of the paper is to outline the arguments advanced for the superiority of WTP over quality-adjusted-life-years (QALYs) as a measure of benefit of health care programmes, and to review how empirical WTP studies adhere to their implications. An important argument is that WTP enables a more comprehensive valuation of benefits than QALYs. Our main focus is therefore to provide a careful review of the scenario descriptions used in the surveys, according to which types of benefits are being valued, and how comprehensively the descriptions are presented. Furthermore, the 'cost-benefit argument', that WTP can assist in improving social efficiency, is discussed before we inquire into the extent to which the studies actually compare WTP with social costs.
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Smith RD, Malley JD, Schechter AN. Quantitative analysis of globin gene induction in single human erythroleukemic cells. Nucleic Acids Res 2000; 28:4998-5004. [PMID: 11121491 PMCID: PMC115244 DOI: 10.1093/nar/28.24.4998] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mechanisms involved in the normal developmental regulation of globin gene expression, and the response to pharmacological agents that elevate fetal hemoglobin, may be expected to involve either changes in each cell or a selection process affecting subsets of differentiating erythroid cells. To study these mechanisms we have developed assays to measure mRNA levels in single erythroid cells. The assay involved the use of globin-specific probes, with no detectable cross-reactivity, in real-time, fluorescence-based quantitative PCR (Q-PCR). We had previously used this Q-PCR method to measure globin mRNA levels in cultures of primary erythroid cells demonstrating that drugs like hydroxyurea, 5-azacytidine and butyric acid each yielded increases in gamma/( gamma + ss) mRNA ratios, with differential effects on ss-globin levels. We have now extended this approach to measure globin mRNA levels in single K562 cells, a human erythroleukemic cell line, with and without 30 microM hemin treatment. Hemin exposure increases total hemoglobin levels by approximately 9-fold and total alpha-, epsilon- and gamma-globin mRNA levels by 1.5-2.3-fold. Single cell analyses showed initial wide distributions of each of the three individual globin mRNA levels with most cells having detectable but very low levels of each globin transcript. Hemin induction shifted the distributions to higher levels, with a tendency to residual left skewing as some cells remained with very low expression levels despite the effect of hemin in increasing expression in most of these low expressing cells. Thus transcriptional heterogeneity remains a crucial variable, even in this extensively used model of human erythroid biology, and clearly influences strongly the response to inducing agents. These methods may enable us to define better possible molecular and/or cellular models of globin gene modulation.
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Olivares-Reyes JA, Jayadev S, Hunyady L, Catt KJ, Smith RD. Homologous and heterologous phosphorylation of the AT(2) angiotensin receptor by protein kinase C. Mol Pharmacol 2000; 58:1156-61. [PMID: 11040065 DOI: 10.1124/mol.58.5.1156] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The angiotensin AT(2) receptor is an atypical seven transmembrane domain receptor that is coupled to activation of tyrosine phosphatase and inhibition of MAP kinase, and does not undergo agonist-induced internalization. An investigation of the occurrence and nature of AT(2) receptor phosphorylation revealed that phorbol ester-induced activation of protein kinase C (PKC) in HA-AT(2) receptor-expressing COS-7 cells caused rapid and specific phosphorylation of a single residue (Ser(354)) located in the cytoplasmic tail of the receptor. Agonist activation of AT(2) receptors by angiotensin II (Ang II) also caused rapid PKC-dependent phosphorylation of Ser(354) that was prevented by the AT(2) antagonist, PD123177, and by inhibitors of PKC. In cells coexpressing AT(1) and AT(2) receptors, Ang II-induced phosphorylation of the AT(2) receptor was reduced by either PD123177 or the AT(1) receptor antagonist, DuP753, and was abolished by treatment with both antagonists or with PKC inhibitors. These findings indicate that the AT(2) receptor is rapidly phosphorylated via PKC during homologous activation by Ang II, and also undergoes heterologous PKC-dependent phosphorylation during activation of the AT(1) receptor. The latter process may regulate the counteracting effects of AT(2) receptors on growth responses to AT(1) receptor activation.
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104
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Martinović S, Berger SJ, Pasa-Tolić L, Smith RD. Separation and detection of intact noncovalent protein complexes from mixtures by on-line capillary isoelectric focusing-mass spectrometry. Anal Chem 2000; 72:5356-60. [PMID: 11080887 DOI: 10.1021/ac0004557] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Separation and mass spectrometric analysis of intact noncovalent protein-protein complexes from mixtures is described. Protein complexes were separated using isoelectric focusing in a capillary under native conditions. During the mobilization, molecular masses of the intact complexes were measured on-line (as they emerged from the capillary) using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. An FTICR "in-trap" ion cleanup procedure was necessary for some complexes to reduce high levels of adduction and to obtain accurate molecular mass measurements. Optimization of the conditions for analysis of different intact complexes is discussed. We have shown that either the intact noncovalent complexes or their constituent protein subunits can be detected by variation of sheath liquid (i.e., NH4OAc vs HOAc) added at the electrospray-mass spectrometer interface. Thus, two successive experiments permit a fast and efficient characterization of intact complex stoichiometry, the individual complex subunits and the possible presence of metal or other adducted species.
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105
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Southall DP, Burr S, Smith RD, Bull DN, Radford A, Williams A, Nicholson S. The Child-Friendly Healthcare Initiative (CFHI): Healthcare provision in accordance with the UN Convention on the Rights of the Child. Child Advocacy International. Department of Child and Adolescent Health and Development of the World Health Organization (WHO). Royal College of Nursing (UK). Royal College of Paediatrics and Child Health (UK). United Nations Children's Fund (UNICEF). Pediatrics 2000; 106:1054-64. [PMID: 11061775 DOI: 10.1542/peds.106.5.1054] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Although modern medical technology and treatment regimens in well-resourced countries have improved the survival of sick or injured children, most of the world's families do not have access to adequate health care. Many hospitals in poorly resourced countries do not have basic water and sanitation, a reliable electricity supply, or even minimal security. The staff, both clinical and nonclinical, are often underpaid and sometimes undervalued by their communities. In many countries there continues to be minimal, if any, pain control, and the indiscriminate use of powerful antibiotics leads to a proliferation of multiresistant pathogens. Even in well-resourced countries, advances in health care have not always been accompanied by commensurate attention to the child's wider well-being and sufficient concerns about their anxieties, fears, and suffering. In accordance with the United Nations Convention on the Rights of the Child,(1) the proposals set out in this article aim to develop a system of care that will focus on the physical, psychological, and emotional well-being of children attending health care facilities, particularly as inpatients. DESIGN OF THE PROGRAM To develop in consultation with local health care professionals and international organizations, globally applicable standards that will help to ensure that practices in hospitals and health centers everywhere respect children's rights, not only to survival and avoidance of morbidity, but also to their protection from unnecessary suffering and their informed participation in treatment. Child Advocacy International will liase closely with the Department of Child and Adolescent Health and Development of the World Health Organization (WHO) and the United Nations Children's Fund (UNICEF) in the implementation of the pilot scheme in 6 countries. In hospitals providing maternity and newborn infant care, the program will be closely linked with the Baby Friendly Hospital Initiative of WHO/UNICEF that aims to strengthen support for breastfeeding. United Nations Children's Fund, United Nations Convention on the Rights of the Child, child protection, breastfeeding, pain control, palliative care, child abuse.
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106
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Catt KJ, Olivares Reyes AJ, Zhang M, Smith RD, Hunyady L. Activation and phosphorylation of angiotensin AT1 and AT2 receptors. Endocr Res 2000; 26:559-60. [PMID: 11196428 DOI: 10.3109/07435800009048570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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107
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Citterio F, Corradini L, Smith RD, Bertorelli R. Nociceptin attenuates opioid and gamma-aminobutyric acid(B) receptor-mediated analgesia in the mouse tail-flick assay. Neurosci Lett 2000; 292:83-6. [PMID: 10998554 DOI: 10.1016/s0304-3940(00)01448-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Nociceptin (NC) and the opioid receptor like-1 receptors are widely distributed in areas of the neuraxis that are part of the descending modulatory pain system. We used the tail-flick assay in mice to assess the interaction between NC and other analgesic compounds acting on different areas of the descending pathway. Given by intracerebroventricular injection, NC induced hyperalgesia at 10 nmol (39% of reduction vs. control group). The same dose of NC reversed analgesia induced by distinct classes of analgesia-producing compounds such as morphine, dynorphin A or baclofen. NC caused a reduction of their antinociceptive effects: 61, 41 and 27%, respectively. Thus, NC at the supraspinal level appears to interact with both opioid and gamma-aminobutyric acid(B) systems producing anti-analgesic effects probably through the descending pathway for pain control.
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Abstract
In the present work, capillary isoelectric focusing (CIEF) methods were developed for the separation and identification of yeast cells. Yeast cells (approximately 4-microm diameter) cultured to various phases of growth were shown to be reproducibly resolved by CIEF using 100-microm-i.d. fused-silica capillaries coated with hydroxypropyl methylcellulose. Separation efficiencies corresponding to peak capacities of >4000 were obtained. The suitable cell concentration range for obtaining repeatable elution in CIEF separations was found to be quite low (<3 cells/microL). CIEF experiments showed that yeast cell populations at early log, mid log, and stationary growth phases differ in isoelectric point, with values ranging from 5.2 to 6.4. The broader application of CIEF are projected for microorganism identification and separation based upon growth conditions.
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Manolis AJ, Grossman E, Jelakovic B, Jacovides A, Bernhardi DC, Cabrera WJ, Watanabe LA, Barragan J, Matadamas N, Mendiola A, Woo KS, Zhu JR, Mejia AD, Bunt T, Dumortier T, Smith RD. Effects of losartan and candesartan monotherapy and losartan/hydrochlorothiazide combination therapy in patients with mild to moderate hypertension. Losartan Trial Investigators. Clin Ther 2000; 22:1186-203. [PMID: 11110230 DOI: 10.1016/s0149-2918(00)83062-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVE The goal of this multicenter, double-blind, randomized, parallel-group study was to compare the effects of losartan potassium (hereafter referred to as losartan), candesartan cilexitil (hereafter referred to as candesartan), and losartan/hydrochlorothiazide (HCTZ) in patients with mild to moderate hypertension (sitting diastolic blood pressure [SiDBP] 95-115 mm Hg). METHODS A total of 1161 patients were randomized in a 2:2:1 ratio to 12 weeks of treatment with losartan 50 mg QD, possibly titrated to 100 mg QD (n = 461); candesartan 8 mg QD, possibly titrated to 16 mg QD (n = 468); or losartan 50 mg QD, possibly titrated to losartan 50 mg plus HCTZ 12.5 mg QD (n = 232). At 6 weeks, the regimens of patients not reaching a goal SiDBP <90 mm Hg were titrated as described, whereas patients achieving this goal continued with low-dose monotherapy. The single primary end point at 12 weeks tested the equivalence of the 2 monotherapy regimens, predefined as a maximum between-treatment difference in the mean change from baseline trough SiDBP of 2.5 mm Hg. RESULTS At 12 weeks, changes in SiDBP/sitting systolic blood pressure (SiSBP) of -12.4/-14.4 mm Hg with losartan 50 mg/100 mg and -13.1/-15.8 mm Hg with candesartan 8 mg/16 mg demonstrated equivalence between the 2 monotherapy regimens (95% CI for difference in SiDBP, -1.6 to 0.2). At 12 weeks, the losartan 50 mg/50 mg plus HCTZ 12.5 mg regimen had reduced SiDBP/SiSBP significantly more (-14.3/-18.0 mm Hg) than either the candesartan 8 mg/16 mg (SiDBP, P = 0.045; SiSBP, P = 0.017) or losartan 50 mg/100 mg regimen (SiDBP and SiSBP, P = 0.001). During the last 6 weeks, patients whose regimen had been titrated to losartan 50 mg plus HCTZ 12.5 mg (n = 114) showed a greater reduction in SiDBP/SiSBP (-14.5/ -18.7 mm Hg) than did those whose regimen had been titrated to either losartan 100 mg (-10.5/-12.3 mm Hg; n = 211) or candesartan 16 mg (-11.5/-13.2 mm Hg; n = 206), representing a clinically meaningful > or = 2.5-mm Hg) difference. All 3 treatments were well tolerated, with few patients experiencing drug-related adverse events (6.9% losartan 50 mg/100 mg, 7.5% candesartan 8 mg/16 mg, 3.0% losartan 50 mg/ 50 mg plus HCTZ 12.5 mg). Candesartan 8 mg/16 mg increased serum uric acid levels (0.13 mg/dL; 95% CI, 0.04 to 0.23), whereas losartan 50 mg/100 mg decreased them (-0.14 mg/dL; 95% CI, -0.24 to -0.04), and losartan 50 mg/50 mg plus HCTZ 12.5 mg left them unchanged (0.06 mg/dL; 95% CI, -0.07 to 0.20). CONCLUSIONS Losartan 50 mg/100 mg and candesartan 8 mg/16 mg were comparable treatments in terms of blood pressure reduction. After titration, losartan 50 mg plus HCTZ 12.5 mg was superior to either candesartan 16 mg or losartan 100 mg in reducing hypertension. Losartan, but not candesartan, lowered serum uric acid levels and attenuated the expected increase in uric acid levels with HCTZ 12.5 mg.
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110
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Watt SD, Gu X, Smith RD, Spitzer NC. Specific frequencies of spontaneous Ca2+ transients upregulate GAD 67 transcripts in embryonic spinal neurons. Mol Cell Neurosci 2000; 16:376-87. [PMID: 11085875 DOI: 10.1006/mcne.2000.0871] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Spontaneous Ca2+ transients expressed prior to synaptogenesis regulate the developmental appearance of GABA in cultured Xenopus spinal neurons. We find that glutamic acid decarboxylase (GAD) immunoreactivity is also Ca(2+)-dependent and parallels the appearance of GABA. We show that xGAD 67 transcripts first appear in the embryonic spinal cord during the period in which these Ca2+ spikes are generated, in a pattern that is temporally and spatially appropriate to account for differentiation of GABAergic interneurons. RNase protection and competitive quantitative RT-PCR demonstrate that transcript levels are approximately threefold greater when neurons are cultured in the presence of extracellular Ca2+ that permits generation of transients than when cultured in its absence. The frequency of spontaneous Ca2+ spikes plays a crucial role in the regulation of transcripts, since reimposition of Ca2+ transients at the frequency generated in cultured neurons rescues normal expression. We conclude that naturally occurring low frequencies of these Ca2+ transients regulate levels of xGAD 67 mRNA in differentiating neurons.
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112
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Abstract
Excitability has long been recognized as the basis for rapid signaling in the mature nervous system, but roles of channels and receptors in controlling slower processes of differentiation have been identified only more recently. Voltage-dependent and transmitter-activated channels are often expressed at early stages of development prior to synaptogenesis, and allow influx of Ca(2+). Here we examine the functions of spontaneous transient elevations of intracellular Ca(2+) in embryonic neurons. These Ca(2+) transients abruptly raise levels of Ca(2+) as much as tenfold, for brief periods, repeatedly, and can be highly localized. Like cloudbursts on the developing landscape, Ca(2+) transients modulate growth and stimulate differentiation, in a frequency-dependent manner, probably by changes in phosphorylation or proteolysis of regulatory and structural proteins in local regions. We review the mechanisms by which Ca(2+) transients are generated and their effects in regulating motility via the cytoskeleton and differentiation via transcription.
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113
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Krahmer MT, Walters JJ, Fox KF, Fox A, Creek KE, Pirisi L, Wunschel DS, Smith RD, Tabb DL, Yates JR. MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products. Anal Chem 2000; 72:4033-40. [PMID: 10994962 DOI: 10.1021/ac000142b] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ESI (electrospray ionization) MS and tandem mass spectrometry (MS/MS) were used for the analysis of single nucleotide polymorphisms (SNPs) and more complex genetic variations. Double-stranded (ds) PCR products were studied. PCR products of the proline [5'-x(G17)-x(C38)x-3'] and arginine variants [(5'-x(Gl7)-x(G38)x-3'] of the p53 gene are distinguished by an SNP (cytosine or guanine) and were discriminated using both quadrupole and quadrupole ion trap MS analysis. A 69 bp arginine mutant PCR product [5'-x(C17)-x(G38)x-3'] with a negating switch has the same mass as the proline variant but was readily distinguishable on ion trap MS/MS analysis; fragments containing the mutation site, but not the polymorphism, were identified. The 69 bp PCR products were restriction-enzyme-digested, to create 43 bp fragments. ESI quadrupole ion trap MS/MS analysis of the 43 bp product-ion spectra readily demonstrated both polymorphism and negating switch sites. MS and MS/MS are powerful and complementary techniques for analysis of DNA. MS can readily distinguish SNPs but MS/MS is required to differentiate isomeric PCR products (same nucleotide composition but different sequence).
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Cairney JM, Smith RD, Munroe PR. Transmission Electron Microscope Specimen Preparation of Metal Matrix Composites Using the Focused Ion Beam Miller. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2000; 6:452-462. [PMID: 11003680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Transmission electron microscope samples of two types of metal matrix composites were prepared using both traditional thinning methods and the more novel focused ion beam miller. Electropolishing methods were able to produce, very rapidly, thin foils where the matrix was electron transparent, but the ceramic reinforcement particles remained unthinned. Thus, it was not possible in these foils to study either the matrix-reinforcement interface or the microstructure of the reinforcement particles themselves. In contrast, both phases in the composites prepared using the focused ion beam miller thinned uniformly. The interfaces in these materials were clearly visible and the ceramic reinforcement was electron transparent. However, microstructural artifacts associated with ion beam damage were also observed. The extent of these artifacts and methods of minimizing their effect were dependent on both the materials and the milling conditions used.
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115
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Smith RD, Khoubehi B, Chandra A, Glass JM, Mee AD. Xanthogranulomatous pyelonephritis and renal malignancy: unusual fellows in the renal bed. BJU Int 2000; 86:558-9. [PMID: 10971292 DOI: 10.1046/j.1464-410x.2000.00817.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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116
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Conrads TP, Anderson GA, Veenstra TD, Pasa-Tolić L, Smith RD. Utility of accurate mass tags for proteome-wide protein identification. Anal Chem 2000; 72:3349-54. [PMID: 10939410 DOI: 10.1021/ac0002386] [Citation(s) in RCA: 228] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An enabling capability for proteomics would be the ability to study protein expression on a global scale. While several different separation and analysis options are being investigated to advance the practice of proteomics, mass spectrometry (MS) is rapidly becoming the core instrumental technology used to characterize the large number of proteins that constitute a proteome. To be most effective, proteomic measurements must be high-throughput, ideally allowing thousands of proteins to be identified on a time scale of hours. Most strategies of identification by MS rely on the analysis of enzymatically produced peptides originating from an isolated protein followed by either peptide mapping or tandem MS (MS/MS) to obtain sequence information for a single peptide. In the case of peptide mapping, several peptide masses are needed to unambiguously identify a protein with the typically achieved mass measurement accuracies (MMA). The ability to identify proteins based on the mass of a single peptide (i.e., an accurate mass tag; AMT) is proposed and is largely dependent on the MMA that can be achieved. To determine the MMA necessary to enable the use of AMTs for proteome-wide protein identification, we analyzed the predicted proteins and their tryptic fragments from Saccharomyces cerevisiae and Caenorhabditis elegans. The results show that low ppm (i.e., approximately 1 ppm) level measurements have practical utility for analysis of small proteomes. Additionally, up to 85% of the peptides predicted from these organisms can function as AMTs at sub-ppm MMA levels attainable using Fourier transform ion cyclotron resonance MS. Additional information, such as sequence constraints, should enable even more complex proteomes to be studied at more modest mass measurement accuracies. Once AMTs are established, subsequent high-throughput measurements of proteomes (e.g., after perturbations) will be greatly facilitated.
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Martinović S, Masselon C, Jensen PK, Stone CL, Smith RD. Characterization of human alcohol dehydrogenase isoenzymes by capillary isoelectric focusing-mass spectrometry. Electrophoresis 2000; 21:2368-75. [PMID: 10939447 DOI: 10.1002/1522-2683(20000701)21:12<2368::aid-elps2368>3.0.co;2-f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The human liver alcohol dehydrogenase (ADH) isoenzymes are currently believed to play a major role in ethanol metabolism, accounting for most of the ethanol oxidized in the liver. They have similar molecular masses and similar isoelectric point (pI) values (the 13 possible isoenzymes having pIs in the range of 8.26-8.87), making their characterization a significant analytical challenge. Capillary isoelectric focusing (CIEF) coupled on-line with electrospray ionization - Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry was applied to separate and characterize mixtures of alphaalpha, beta1beta1 and beta3beta3 ADH isoenzymes. Seven different species were resolved by the separation in the pI 8.26-8.67 range. ESI-FTICR analysis of native ADHs revealed that each noncovalent ADH complex contains two monomeric protein units and four zinc atoms. The combination of CIEF separations with mass spectrometry appears well-suited for detailed characterization of ADH isozymes, and the attomole level sensitivity of FTICR should allow very small samples to be addressed.
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Xiang F, Anderson GA, Veenstra TD, Lipton MS, Smith RD. Characterization of microorganisms and biomarker development from global ESI-MS/MS analyses of cell lysates. Anal Chem 2000; 72:2475-81. [PMID: 10857623 DOI: 10.1021/ac991307n] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The capability for sensitive and accurate identification of microorganisms has potential applications that include the monitoring of industrial bioprocessing operations, food safety analyses, disease diagnosis, and detection of potential biological hazards. Efforts based upon matrix-assisted laser desorption/ionization mass spectrometry to detect and identify specific microorganisms have been actively pursued for several years. We report a new method being developed to select useful biomarkers for the identification of microorganisms based upon electrospray ionization (ESI)-ion trap mass spectrometry. Crude cell lysates are processed using a recently developed dualmicrodialysis device and then directly infused into an ion trap MS. The low ESI flow rate and precursor ion accumulation capability of the ion trap MS enables high-sensitivity MS/MS analyses. Precursor ions are automatically selected and analyzed using tandem MS (MS/MS) to produce "global" MS/MS surveys and processed to yield two-dimensional MS/MS spectral displays. Such global MS/MS surveys are demonstrated for Escherichia coli lysates. The distinctive MS/MS spectral patterns can be used to identify mass spectrometric-detected species useful as biomarkers, which then provide a basis for confident microorganism identification. The results presented demonstrate the application of this method for the identification of microorganisms, as well as for detection of bacteriophage MS2 in the presence of a large excess of E. coli.
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Abstract
Decision analysis is a process for systematically analyzing complex choices by considering all pertinent information. In this paper, we discuss how uncertainty associated with diagnostic testing can be included in a decision analysis using pay-off tables and decision trees (decision-flow diagrams). Variables associated with diagnostic test interpretation (such as pre-test and post-test probability of disease; test sensitivity, specificity and predictive values; fixed cut-offs versus continuous measurement scales; test dependence associated with the use of multiple tests) are considered. Several decision criteria and output measures are discussed (including MAXIMIN and MAXIMAX criteria, opportunity costs, expected monetary values, expected utility, sensitivity and risk-profile analysis, and threshold analysis). The application of decision analysis to diagnostic testing for Johne's disease and traumatic reticuloperitonitis of cattle, and for canine heartworm disease are used to illustrate both population- and patient-oriented applications and criteria for ranking the desirability of different outcomes.
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Greiner M, Pfeiffer D, Smith RD. Principles and practical application of the receiver-operating characteristic analysis for diagnostic tests. Prev Vet Med 2000; 45:23-41. [PMID: 10802332 DOI: 10.1016/s0167-5877(00)00115-x] [Citation(s) in RCA: 1268] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We review the principles and practical application of receiver-operating characteristic (ROC) analysis for diagnostic tests. ROC analysis can be used for diagnostic tests with outcomes measured on ordinal, interval or ratio scales. The dependence of the diagnostic sensitivity and specificity on the selected cut-off value must be considered for a full test evaluation and for test comparison. All possible combinations of sensitivity and specificity that can be achieved by changing the test's cut-off value can be summarised using a single parameter; the area under the ROC curve. The ROC technique can also be used to optimise cut-off values with regard to a given prevalence in the target population and cost ratio of false-positive and false-negative results. However, plots of optimisation parameters against the selected cut-off value provide a more-direct method for cut-off selection. Candidates for such optimisation parameters are linear combinations of sensitivity and specificity (with weights selected to reflect the decision-making situation), odds ratio, chance-corrected measures of association (e. g. kappa) and likelihood ratios. We discuss some recent developments in ROC analysis, including meta-analysis of diagnostic tests, correlated ROC curves (paired-sample design) and chance- and prevalence-corrected ROC curves.
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Kim T, Tolmachev AV, Harkewicz R, Prior DC, Anderson G, Udseth HR, Smith RD. Design and implementation of a new electrodynamic ion funnel. Anal Chem 2000; 72:2247-55. [PMID: 10845370 DOI: 10.1021/ac991412x] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new electrodynamic (rf) ion funnel has been developed and evaluated for use in the interface regions (at approximately 1-10 Torr) of atmospheric pressure ion sources (e.g., electrospray ionization (ESI) for mass spectrometry). The ion funnel consists of a ring electrode ion guide with decreasing i.d. and with a superimposed dc potential gradient along the ring stack. The thicknesses of the ring electrodes and the spacings between them were reduced to 0.5 mm from 1.59 mm compared to those used for previous designs. The new ion funnel displays a significant improvement in low-mass transmission (m/z >200) and sensitivity compared to previous designs. The transmission efficiencies for electrosprayed peptides and proteins (ranging in mass from 200 to 17,000 Da) were typically 50-60% of total incoming currents from a heated capillary inlet. The transmitted ion currents were a factor of 30-56 greater than those of the standard interface for peptide samples and a factor of 18-22 greater than those for protein samples. The sensitivity gains realized at the MS detector were somewhat lower, possibly due to space charge effects in the octapole ion beam guide following the ion funnel. The improved ion transmission properties result primarily from the use of reduced spacings between ring electrodes. We also show that the ion funnel can be operated in two different modes, one using low-rf-amplitude scans, allowing fragile noncovalent complexes (as well as generally undesired adducts) to be transmitted, and the other using high-rf-amplitude scans, providing greater collisional activation and more effective adduct removal (or the dissociation of lower m/z species).
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Belov ME, Gorshkov MV, Udseth HR, Anderson GA, Smith RD. Zeptomole-sensitivity electrospray ionization--Fourier transform ion cyclotron resonance mass spectrometry of proteins. Anal Chem 2000; 72:2271-9. [PMID: 10845374 DOI: 10.1021/ac991360b] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods are being developed for ultrasensitive protein characterization based upon electrospray ionization (ESI) with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The sensitivity of a FTICR mass spectrometer equipped with an ESI source depends on the overall ion transmission, which combines the probability of ionization, transmission efficiency, and ion trapping in the FTICR cell. Our developments implemented in a 3.5 tesla FTICR mass spectrometer include introduction and optimization of a newly designed electrodynamic ion funnel in the ESI interface, improving the ion beam characteristics in a quadrupole-electrostatic ion guide interface, and modification of the electrostatic ion guide. These developments provide a detection limit of approximately 30 zmol (approximately 18,000 molecules) for proteins with molecular weights ranging from 8 to 20 kDa.
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Shen Y, Berger SJ, Anderson GA, Smith RD. High-efficiency capillary isoelectric focusing of peptides. Anal Chem 2000; 72:2154-9. [PMID: 10815979 DOI: 10.1021/ac991367t] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several approaches are presently being developed for global proteome characterization that are based upon the analysis of polypeptide mixtures resulting from digestion of (often complex) mixtures of proteins. Improved methods for peptide analysis are needed that provide for sample concentration, higher resolution separations, and direct compatibility with mass spectrometry. In this work, methods for the high-efficiency capillary isoelectric focusing (CIEF) separation of peptides have been developed that provide for simultaneous sample concentration and separation according to peptide isoelectric point. Under typical nondenaturing CIEF conditions, peptides are concentrated approximately 500-fold, and peptides present at < 1 ng/ microL were detectable using conventional UV detection. CIEF separations of peptides provided much faster measurements of isoelectric points compared with conventional isoelectric focusing in gels. Very small differences in peptide isoelectric points (deltapI approximately 0.01) could be resolved, High-efficiency CIEF separations for complex peptide mixtures from tryptic digestion of yeast cytosol fractions were obtained and showed significant improvement over those obtained using capillary zone electrophoresis and packed capillary reversed-phase liquid chromatography.
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Bruce JE, Anderson GA, Brands MD, Pasa-Tolic L, Smith RD. Obtaining more accurate Fourier transform ion cyclotron resonance mass measurements without internal standards using multiply charged ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:416-421. [PMID: 10790845 DOI: 10.1016/s1044-0305(00)00096-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Space-charge effects produce frequency shifts in Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and correction for these shifts is necessary for obtaining accurate mass measurements. We report a novel method for obtaining accurate mass calibration to correct for space-charge induced mass shifts without the requirement for internal calibrants. The new approach is particularly well suited for electrospray ionization-FTICR mass spectra that contain multiple charge states of the same molecular species. This method, deconvolution of Coulombic affected linearity (DeCAL), is described and presented with several examples demonstrating the increased mass measurement accuracy obtained. DeCAL provides the basis for more routinely obtaining higher mass accuracy measurements in conjunction with chromatographic separations for complex mixture analysis, and obviates the need for internal calibration in many applications.
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Masselon C, Anderson GA, Harkewicz R, Bruce JE, Pasa-Tolic L, Smith RD. Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Anal Chem 2000; 72:1918-24. [PMID: 10784162 DOI: 10.1021/ac991133+] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new tandem mass spectrometric approach for the improved identification of polypeptides from mixtures (e.g., using genomic databases). The approach involves the dissociation of several species simultaneously in a single experiment and provides both increased speed and sensitivity. The data analysis makes use of the known fragmentation pathways for polypeptides and highly accurate mass measurements for both the set of parent polypeptides and their fragments. The accurate mass information makes it possible to attribute most fragments to a specific parent species. We provide an initial demonstration of this multiplexed tandem MS approach using an FTICR mass spectrometer with a mixture of seven polypeptides dissociated using infrared irradiation from a CO2 laser. The peptides were added to, and then successfully identified from, the largest genomic database yet available (C. elegans), which is equivalent in complexity to that for a specific differentiated mammalian cell type. Additionally, since only a few enzymatic fragments are necessary to unambiguously identify a protein from an appropriate database, it is anticipated that the multiplexed MS/MS method will allow the more rapid identification of complex protein mixtures with on-line separation of their enzymatically produced polypeptides.
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