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Study on memapsin 2 cleavage properties and its interacting proteinsLi, Xiaoman. January 2010 (has links) (PDF)
Thesis (Ph. D.)--University of Oklahoma. / Bibliography: leaves 122-136.
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Biodisponibilidade comparativa de duas formulações de ramipril em voluntarios sadios apos administração de dose unica / Comparative bioavailability of two ramipril formulations in health human volunteers after a single dose administrationSanfelice, Andre Tasso Dantas 20 December 2005 (has links)
Orientador: Gilberto de Nucci / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-07T09:06:01Z (GMT). No. of bitstreams: 1
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Previous issue date: 2005 / Resumo: Objetivo: Avaliar a bioequivalência de uma formulação de ramipril 5 mg (formulação teste de ramipril dos laboratórios Biossintética Ltda. e a formulação de referência padrão Triatec@ da Aventis Pharma) em vinte e seis voluntários de ambos os sexos. Método: O estudo foi conduzido usando um estudo aberto, randomizado, cruzado de duas fases com um intervalo de washout de 2 semanas. As amostras de plasma foram obtidas sobre um período de 36 horas. As concentrações plasmáticas de ramipril e ramiprilato foram analisadas por cromatografia líquida acoplada à espectrometria de massa (LC-MS-MS), com modo de ionização electrospray positivo usando o monitoramento de múltiplas reações (MRM). Das curvas de concentração plasmática versus o tempo para ramipril e ramiprilato, os seguintes parâmetros farmacocinéticos foram obtidos: ASCo-36h ASCIast, ASC(}...infe Cmax. Resultados: O limite de quantificação foi 0.2 ng.mL-1 e 1.0 ng.mL-1 para ramipril e ramiprilato, respectivamente. A média geométrica e a respectivo intervalo de confiança de 90% para RamipriIJTriatec@ e Ramiprilatol Triatec@ foram respectivamente: 104.69".10 (90% IC= 93.210/0-117.59%) para Cmax" 102.49% (90% IC= 92.76%-113.24%) para ASClast" 102.97% (90% IC= 93.21%-113.74%) para ASCO-36h" 103.60% (90% IC= 93.56%-114.73%) para ASCinf;, 108.48% (90% IC= 98.86%-119.03%) para Cmax, 105.88% (90% IC= 101.55%-110.39%) para ASClast,105.81% (90% IC= 101.53%-110.27%) para ASCo.36h, 97.30% (90% IC= 90.17%-104.99%) para ASCinf. Conclusão: Desde que o IC de 90% para ASCtast, ASCO-36h, ASCO-inf e Cmax apresentou-se dentro do intervalo de 80-125% proposto pelo FDA (US), foi concluído que a formulação ramipril elaborada pelo laboratório Biosintética Ltda é bioequivalente para a formulação Triatec@ para taxa e velocidade de absorção / Abstract: Objective: To assess the bioequivalence of one ramipril 5 mg tablet formulation (ramipril test formulation from Laboratórios Biosintética Ltda and Triatec$ from Aventis Pharma standard reference formulation) in 26 healthy volunteers ofboth sexes. Methods: The study was conducted using an open, randomized, two-period crossover design with a 2-week washout interval. Plasma samples were obtained over a 36 h period. Plasma ramipril and ramiprilat concentrations were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS-MS) with positive ion electrospray ionization using multiple reaction monitoring (MRM). From the ramipril and ramiprilat plasma concentration vs time curves, the following pharmacokinetic parameters were obtained: ASCO-36h ASClast, ASCo-infand Cmax. Results: The limit of quantification was 0.2 ng.mL-1 and 1.0 ng.mL-1 for ramipril and ramiprilat, respectively. The geometric mean and respective 90% confidence interval (CI) RamipriVTriatec@ and Ramiprilat/ Triatec@ percent ratios were respectively: 104.69% (90% CI= 93.21%-117.59%) for Crnax,1O2.49% (90% CI= 92.76%-113.24%) for ASCIast,1O2.97% (90% CI= 93.21%-113.74%) for ASCo-36h,103.60% (90% CI= 93.56%-114.73%) for ASCnf)08.48% (9001Ó CI= 98.86%-119.03%) for Crnax,1O5.88% (90% CI= 101.55%-110.39%) for ASClast,105.81% (90% CI= 101.53%-110.27%) for ASCO-36h, 97.30% (9001Ó CI= 90.17%-104.99%) for ASCinf. Conclusion: Since the 90% CI for ASClast, ASCO-36h, ASCO-inf and Cmax ratios were within the 80-125% interval proposed by the US FDA, it was concluded that ramipril formulation elaborated by Laboratórios Biosintética Ltda is bioequivalent to Triatec@ formulation for both the rate and the extent of absorption / Mestrado / Clinica Medica / Mestre em Clinica Medica
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Diagnóstico bioquímico das síndromes de deficiência de creatina / Biochemical diagnosis of creatine deficiency syndromesMarlene de Freitas Madeira 21 May 2010 (has links)
Recentemente, foi descrito um grupo de alterações no metabolismo da creatina denominado Síndromes de Deficiência de Creatina. Há três formas da doença geneticamente determinadas que cursam com deficiência de creatina, seja por comprometimento de sua síntese ou por defeito na proteína transportadora. O espectro de apresentação clínica dessa condição é inespecífico e inclui atraso ou estagnação do desenvolvimento neuromotor, hipotonia muscular, movimentos involuntários do tipo coreoatetose, retardo ou ausência do desenvolvimento da fala, retardo mental de grau variável, comportamento autista e epilepsia. Neste trabalho, foi desenvolvida e validada uma alternativa metodológica àquelas disponíveis na literatura, com a utilização de extração por troca catiônica forte e separação e detecção por cromatografia líquida de interação hidrofílica acoplada a espectrometria de massas em tandem em que foram exploradas as características químicas das moléculas de creatina e guanidinoacetato, metabólito intermediário da síntese de creatina. Os valores de referência para o método foram definidos pela sua aplicação a 150 amostras de urina e 197 amostras de soro de indivíduos de ambos os sexos e idades entre 0 e 16 anos. Foram também analisadas amostras de urina, soro e plasma de 54 pacientes com clínica compatível com a síndrome de deficiência de creatina sendo que 3 deles apresentaram perfil bioquímico característico de uma das formas dessa condição / Recently, a new group of inborn errors of metabolism, collectively named as creatine deficiency syndrome, was identified. Three genetically determined presentations are currently known, affecting both creatine synthesis and transport. Clinical presentation spectrum is non-specific and includes developmental delay, hypotonia, involuntary movements as choreoathetosis, delay or lack of speech acquisition, mental retardation of variable severity, autistic behavior, and epilepsy. Herein, we developed and validated an innovative method for determination of creatine and of its metabolic intermediate, guanidinoacetate, based on cation-exchange solid-phase extraction and hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry. Reference values for the method were defined testing 150 urine and 197 serum samples in males and females with age ranging from 0 to 16 years. Urine and serum samples from 54 patients with some clinical features that might be attributable to creatine deficiency were also evaluated, and in three, biochemical profile characteristic of one of the disorders was detected
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Comparaison de deux méthodes de mesure de la vitamine D en post chirurgie bariatrique malabsorptive de type dérivation bilio-pancréatique / Comparison of two methods for measuring 25-OH vitamin D in the follow-up of patients after bilio-pancreatic diversion bariatric surgeryChouiali, Ahlem January 2017 (has links)
Introduction: La prévalence de l'hypovitaminose D peut atteindre 90% chez les patients après une chirurgie bariatrique type dérivation bilio-pancréatique (DBP) malgré la supplémentation avec des méga-doses de vitamine D. Notre hypothèse est que la méthode de dosage immuno-compétitive courante de Roche pourrait ne pas reconnaître de façon équimolaire les deux formes de la 25-OH vitamine D (25-OH-D2 et 25-OH-D3), surestimant ainsi la prévalence du déficit en vitamine D et exposant ces patients, et plus particulièrement ceux supplémentés en D2, à un risque de toxicité à la vitamine D.
Objectif: Notre objectif était de comparer deux méthodes de dosage sérique de la vitamine 25-OH-D totale : la méthode ECLIA de Roche et la méthode LC-MS/MS chez la population ayant eu une chirurgie bariatrique.
Méthode: Il s’agit d’une étude transversale et corrélationnelle avec dosage sérique de la 25-OH-D dans trois groupes : un groupe contrôle de 48 sujets apparemment sains choisis aléatoirement au laboratoire de biochimie clinique et deux groupes de patients post-dérivation bilio-pancréatique un supplémenté en vitamine D3 (n=44) et l’autre en vitamine D2 (n=30). Les patients ont été recrutés au cours de leur visite de suivi à la clinique de l'obésité au CHUS et à l’IUCPQ. Le nombre d'échantillons par groupe a été établi selon les recommandations du Clinical and Laboratory Standard Institute (EPO9-A2-IR). L'étude comparative (régression linéaire, régression de Deming et le graphique des différences de Bland-Altman) a été réalisée en utilisant le logiciel Analyse-it en considérant p <0,05 comme statistiquement significatif.
Résultats: La corrélation entre les deux méthodes était acceptable dans le groupe contrôle de sujets apparemment sains et dans le groupe post-DBP supplémenté en vitamine D3 avec des biais moyens respectifs de -1.7% et -9.2%. Cependant, cette corrélation était inacceptable dans le groupe post-DBP supplémenté en vitamine D2 avec un biais moyen de -45.3%. La méthode LC-MS/MS nous a permis de détecter quatre patients (13%) avec excès ou intoxication en vitamine D dans le groupe post-DBP supplémenté en D2, pour lesquels il était nécessaire d'arrêter la supplémentation en vitamine D.
Conclusion : Malgré la bonne corrélation apparente entre la méthode Roche et la méthode LC-MS/MS dans le groupe contrôle de sujets apparemment sains et dans le groupe de patients post-DBP supplémenté en vitamine D3, un biais considérable semble exister, en particulier en présence de la 25-OH-D2. La méthode Roche sous-estime la 25-OH-D totale sérique jusqu’à 95.7% et la spectrométrie de masse a conduit à un ajustement posologique pour plus d’un patient sur quatre. La méthode LC-MS/MS est donc la méthode la plus appropriée pour le suivi sécuritaire de la population bariatrique post-DBP supplémentée en vitamine D2. Il est à noter que nos résultats pourraient être généralisés à tous les types de chirurgie bariatrique et autres patients tels que les insuffisants rénaux. Ils permettraient également la mise à jour des recommandations du suivi post-chirurgie bariatrique et le changement des pratiques en optimisant le choix de suppléments en vitamine D (D2 vs D3) en fonction de la méthode de dosage disponible et d’orienter les laboratoires pour le choix de méthodes de dosage dépendamment de la clientèle servie. / Abstract : Introduction: The prevalence of hypovitaminosis D may reach 90 % in patients after BPD
despite supplementation with mega doses of vitamin D. Although LC-MS/MS is the gold
standard for vitamin D measurements, it is not routinely use in clinical practice. Our
hypothesis is that methods of assays currently used in laboratories of Medical Biochemistry
for evaluation of serum 25-hydroxyvitamin D may not recognize equimolarly the two
forms of 25-OH-D (D2 and D3) thus overestimating the prevalence of vitamin D deficiency
supplemented with D2 and exposing patients to the risk of toxicity.
Objective: Our objective was to compare the ECLIA from Roche versus the LC-MS/MS
method for quantitation of serum 25-hydroxy-vitamin D in patients who have undergone
bariatric surgery.
Design and methods: Cross-sectional and correlational study was performed on three
different groups for the 25-OH-D levels quantitated by both methods. The control group of
apparently healthy subjects (n=48) was randomly selected in a clinical chemistry
laboratory. Test groups were patients who had undergone bilio-pancreatic diversion (BPD)
and were supplemented either with vitamin D2 (n=30) or with vitamin D3 (n=44). Patients
were recruited during their follow-up visit to the obesity clinics at the CHUS and at the
IUCPQ. The number of samples per group was established according to the Clinical and
Laboratory Standard Institute recommendation protocol (EPO9-A2-IR). The study
comparing methods (linear regression, Deming and Bland-Altman bias) was performed
using the Analyse-it software program considering p < 0.05 as statistically significant.
Results: The agreement of LC-MS/MS with the Roche method was acceptable in the
apparently healthy subjects group and in the post-BPD D3-supplemented group with an
average bias of -1.7% and -9.2%, respectively. However, this agreement was unacceptable
in the post-BPD D2-supplemented group with an average bias of -45.3%. The LC-MS/MS
enabled us to detect four patients (13%) who had excess vitamin D or intoxication with vitamin D for which it was necessary to stop the supplementation with vitamin D in the D2
-supplemented group.
Conclusion: Despite the apparent good agreement between the Roche method and LCMS/MS
in the healthy subjects group and in the post-DBP D3-supplemented patient group,
a considerable bias seems to exist, particularly in the presence of D2. Results showed that
the routine method underestimated total vitamin D ad 95.7% in patients post BPD
supplemented with D2. The LC-MS/MS method is therefore the most accurate method to
follow the vitamin D2-supplemented bariatric population.
This study could generalize the results to all types of bariatric surgeries and other patients
such as renal impairment. The study could also update the recommendations of the postbariatric
surgery monitoring, and suggest making changes to the clinical practices so as to
optimize the choices of vitamin D supplements (D2 vs D3) depending on the assay method
available. It could also guide laboratories in choosing methods depending on dosage of
clients served.
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Combined tandem mass spectrometry and ion mobility spectrometry in proteome analysesChawner, Ross January 2013 (has links)
Proteomic studies aim to identify, quantify and characterise the full complement of proteins in a cell or organism under a defined set of conditions, and are important to our understanding of cellular mechanisms. However, such studies represent a major analytical challenge. A typical proteome analysis involves enzyme-mediated digestion of complex protein mixtures to yield an even more complex mixture of peptides. Combined reverse-phase liquid chromatography and tandem mass spectrometry is then traditionally utilised to ascertain sequence information from the characteristic peptide sequences. Analytical data derived for the peptides are employed as search terms in database searching of protein sequences derived from gene sequences. The extreme complexity of the peptide mixtures analysed means that additional novel approaches are required to fully interrogate the vast number of tandem mass spectra generated, assigning peptide identity and thereby helping to address demanding biological questions. The research reported here aims to further our understanding of both gas phase peptide/peptide fragment ion structure and peptide fragmentation behaviour using a combination of tandem mass spectrometry and ion mobility measurement.To facilitate the determination of peptide ion collision cross section, a novel standard, QCAL-IM, produced using the QconCAT strategy, has been developed to enable calibration of drift time in Travelling Wave Ion Mobility instruments. The standard facilitates empirical determination of the rotationally averaged collision cross section of any peptide/peptide fragment ion that lies within the calibration range encompassed. QCAL-IM was subsequently utilised to determine the collision cross section of a range of peptide ions produced by Lys-C and Lys-N proteolysis of ‘standard’ proteins. Data produced allowed the effect upon gas phase ion conformation through changing the location of the basic residue lysine within a peptide sequence to be assessed.The fragmentation behaviour of peptide ions produced by a variety of digestion regimes during both collision-induced dissociation (CID) and electron transfer dissociation (ETD) has also been extensively studied. The proteases trypsin and Lys-C are those typically utilised during proteomic studies and peptides produced by each have either the basic residues arginine or lysine at their carboxy-terminus. Secondary enzymatic treatment with the exoprotease carboxypeptidase B cleaves these basic residues from the C-terminus. Tandem mass spectrometric analysis of both tryptic/Lys-C peptides and their CBPB truncated analogue highlights that the dominant fragment ion series observed during both CID and ETD is determined, at least in part, by the location of such basic residues.Finally, studies were undertaken to investigate the factors which may promote/inhibit scrambling of peptide fragment ion sequence, which has recently been shown to take place during CID. The effect of modifying the gas phase basicity of the N-terminal amino acid residue is studied through a combination of derivatisation and synthesis of alternative peptide sequences. Increasing the gas phase basicity is shown to inhibit the observed sequence scrambling while promoting concomitant rearrangement/retention of a carboxyl oxygen at the C-terminus to give enhanced formation of bn+H2O product ion species.
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Method Development for the Analysis of Smokeless Powders and Organic Gunshot Residue by Ultra Performance Liquid Chromatography with Tandem Mass SpectrometryThomas, Jennifer L. 12 November 2013 (has links)
The goal of this project was to develop a rapid separation and detection method for analyzing organic compounds in smokeless powders and then test its applicability on gunshot residue (GSR) samples. In this project, a total of 20 common smokeless powder additives and their decomposition products were separated by ultra performance liquid chromatography (UPLC) and confirmed by tandem mass spectrometry (MS/MS) using multiple reaction monitoring mode (MRM). Some of the targeted compounds included diphenylamines, centralites, nitrotoluenes, nitroglycerin, and various phthalates. The compounds were ionized in the MS source using simultaneous positive and negative electrospray ionization (ESI) with negative atmospheric pressure chemical ionization (APCI) in order to detect all compounds in a single analysis. The developed UPLC/MS/MS method was applied to commercially available smokeless powders and gunshot residue samples recovered from the hands of shooters, spent cartridges, and smokeless powder retrieved from unfired cartridges. Distinct compositions were identified for smokeless powders from different manufacturers and from separate manufacturing lots. The procedure also produced specific chemical profiles when tested on gunshot residues from different manufacturers. Overall, this thesis represents the development of a rapid and reproducible procedure capable of simultaneously detecting the widest possible range of components present in organic gunshot residue.
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Determinação de hormônios em águas bruta e tratada via EFS-CL-EM/EM : eficiências de degradação com ozonização e cloroamoniação / Determination of hormones in raw water and treated via SPE-LC-MS/MS : degradation efficiencies with ozonation and chloroamoniationOliveira, André Felipe de, 1978- 27 August 2018 (has links)
Orientador: Maria Aparecida Carvalho de Medeiros / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Tecnologia / Made available in DSpace on 2018-08-27T02:18:56Z (GMT). No. of bitstreams: 1
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Previous issue date: 2015 / Resumo: Há uma preocupação crescente na área de Saneamento Ambiental com relação a qualidade das águas dos corpos hídricos, tendo em vista que pesquisas têm revelado que os sistemas de tratamentos convencionais de esgotos e de água para abastecimento público não possuem eficiências adequadas para remoção de compostos orgânicos classificados como Desreguladores Endócrinos (DE). Nesta classe de compostos são destacados os estrógenos naturais 17 ß-estradiol (E2), estriol (E3), estrona (E1) e o sintético 17 ?-etinilestradiol (EE2). Os efeitos destes hormônios sexuais, que são compostos extremamente ativos biologicamente, têm sido citados como agentes etiológicos de feminilização em peixes e também de vários tipos de cânceres. Neste sentido, trabalhos aplicando tecnologias avançadas de tratamento destes DE estão sendo desenvolvidos por vários grupos de pesquisas. Apesar de que as Legislações ambientais relacionadas aos parâmetros de lançamento (RESOLUÇÃO CONAMA no. 430 de 2011) e de parâmetros de potabilidade (Portaria no. 2914 de 2011) não contemplarem estes compostos DE, sendo que diversos trabalhos têm sido publicados com quantificação destes compostos em água da ordem de ng L-1. Neste contexto, o presente trabalho teve como objetivos: (1) adaptação e validação de metodologia analítica para confirmar e quantificar simultaneamente os hormônios E1, E2, E3 e EE2, nas águas bruta e tratada do rio Atibaia, manancial que abastece o município de Campinas, utilizando a técnica de extração em fase sólida (EFS), juntamente com a técnica de Cromatografia Líquida acoplada à espectrometria de massas em tandem (CL-EM/EM), (2) aplicação de tecnologias de degradação destes compostos E1, E2, E3 e EE2 em escala piloto, pelos processos de ozonização e cloroamoniação, visando contribuir com as determinação das dosagens, do tempo de contato e da eficiências de remoção. Os resultados obtidos nas análises via EFS-LC-MS/MS mostraram a ocorrência do hormônio sexual natural E1, na água bruta do rio Atibaia com concentração de 17 ng L-1, sendo que para os demais E2 e E3 os valores obtidos foram inferiores ao limite de quantificação 2 ng L-1 e para o EE2 inferior a 5 ng L-1. As técnicas de oxidação ozonização e cloroamoniação utilizadas nos ensaios demonstraram eficiências de degradação em média, maiores do que 95% dos DE estudados, com exceção de E1, cuja eficiência de remoção ficou entre 87% a 93%, dependendo da faixa de fortificação / Abstract: There is growing concern in the field of Environmental Sanitation regarding the water quality of water bodies, given that research has shown that systems of conventional treatments of sewage and public water supply does not have adequate efficiencies to removal of some organic compounds Endocrine Disruptors (DE). In this class of compounds are included the natural estrogens 17 ß-estradiol (E2), estriol (E3), estrone (E1) and the synthetic 17 ?-ethinylestradiol (EE2). The effects of these sex hormones, which are highly biologically active compounds, have been cited as etiological agents of feminization in fish and various types of cancers. In this regard, several works by applying advanced technologies for treating these DE are being developed by many research groups. Although the environmental legislations related to the parameters of launch (CONAMA RESOLUTION. 430 of 2011) and potability parameters (Ordinance no. 2914 2011) does not address these DE compounds, several studies have been published with quantification of these compounds in the order of ng L-1. In this context, the aimsmof this paper were: (1) adaptation and validation of the analytical methodology to confirm and to quantify simultaneously the E1, E2, E3 and EE2 hormones, raw water and treated in the Atibaia River, a source that supplies the municipality Campinas, using the technique of solid phase extraction (EFS) with the technique of Liquid Chromatography coupled to mass spectrometry in tandem (LC-MS/MS), (2) applying degradation technologies of these compounds E1, E2, E3 and EE2 in pilot scale, by using the processes of ozonation and cloroamoniation, to contribute to the determination of dosage, contact time and degradation efficiencies. The results obtained in this study via EFS-LC-MS / MS showed the occurrence of natural sex hormone E1 in the Atibaia River raw water with a concentration of 17 ng L-1, and for the other E2 and E3 the values were lower the quantification limit of 2 ng L-1 and EE2 less than 5 ng L-1. The ozonation and chloroamoniation oxidation techniques used for the degradation tests were with efficiencies on average more than 95% of the studied DE, except E1, the removal efficiency was between 87% to 93% depending on the fortification range, by using ozonation in pre oxidation and cloroamoniation and the disinfection step / Mestrado / Tecnologia e Inovação / Mestre em Tecnologia
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2ND TIER ASSAY FOR THE DETECTION OF CONGENITAL ADRENAL HYPERPLASIA BY VIRGINIA’S NEWBORN SCREENING LABORATORY: STEROID PROFILE BY HPLC-MS/MSNixon, Christopher E 01 January 2019 (has links)
Congenital Adrenal Hyperplasia (CAH) encompasses several disorders related to disruptions in the adrenal steroid production pathway. These disruptions may cause virilization of the external female sex organs, incorrect gender assignment, precocious puberty, and in the most severe form, may cause life-threatening salt wasting and adrenal crisis if not detected and treated early in the newborn period.
17α-Hydroxyprogesterone (17-OHP) is the primary target for immunofluorescence detection of CAH from dried blood spots in newborn screening (NBS). Unfortunately, current immunoassay techniques for the detection of CAH suffer from high false positive rates. The primary factors contributing to false positive determinations can include the natural increase of 17-OHP due to stress stimuli as well as cross-reactivity of the immunoassay antibody with other hormones and endogenous compounds in blood.
Analysis of the adrenal steroid profile and corresponding analyte ratios using high performance liquid chromatography (HPLC)or ultra-high pressure liquid chromatography (UHPLC)combined with tandem mass spectrometry (MS/MS) has been shown to be a sensitive and selective technique for the significant reduction of the false positive reporting rate for CAH in newborn screening.
In working toward optimization, validation, and implementation of an HPLC-MS/MS steroid profile for use by Virginia’s Newborn Screening laboratory as a 2nd tier analysis for CAH screening, a commercially-available core-shell HPLC column with a biphenyl stationary phase was determined to offer adequate retention and selectivity to achieve baseline resolution of isobaric target analytes under rapid reversed phase gradient conditions. Method linearity, precision, and accuracy were assessed using enriched dried blood spot materials. Double-blinded analyses of over 300 newborn dried blood spot specimens were used to determine clinical sensitivity and specificity of the assay, which is projected to substantially reduce the false positive reporting rate for CAH screening while meeting target sample turnaround times.
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Podobnostní vyhledávání v databázích hmotnostních spekter / Similarity search in Mass Spectra DatabasesNovák, Jiří January 2013 (has links)
Shotgun proteomics is a widely known technique for identification of protein and peptide sequences from an "in vitro" sample. A tandem mass spectrometer generates tens of thousands of mass spectra which must be annotated with peptide sequences. For this purpose, the similarity search in a database of theoretical spectra generated from a database of known protein sequences can be utilized. Since the sizes of databases grow rapidly in recent years, there is a demand for utilization of various database indexing techniques. We investigate the capabilities of (non)metric access methods as the database indexing techniques for fast and approximate similarity retrieval in mass spectra databases. We show that the method for peptide sequences identification is more than 100x faster than a sequential scan over the entire database while more than 90% of spectra are correctly annotated with peptide sequences. Since the method is currently suitable for small mixtures of proteins, we also utilize a precursor mass filter as the database indexing technique for complex mixtures of proteins. The precursor mass filter followed by ranking of spectra by a modification of the parametrized Hausdorff distance outperforms state-of-the-art tools in the number of identified peptide sequences and the speed of search. The...
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Využití LC-MS/MS v diagnostice kongenitální adrenální hyperplasie / Utilization of LC-MS/MS in diagnosis of congenital adrenal hyperplasiaGrúlová, Kristýna January 2020 (has links)
Congenital adrenal hyperplasia (CAH) is an autosomal recessive disease that causes a disorder of steroidogenesis in the adrenal cortex. This disease is a part of a panel of diseases searched in preclinical nationwide neonatal screening. The methodology is based on measuring the concentration of 17-hydroxyprogesterone (17-OHP) in a dried blood spot using fluorescence immunoassay (FIA). However, this determination is not entirely specific and generates a high rate of false positive results (up to 4.3 %). In this diploma thesis the LC-MS / MS method was developed. This method measures selected steroid hormones involved in cortisol metabolism with respect to the diagnosis of CAH disease. The method was validated and applied to clinical samples, it identified CAH patients from negative controls and significantly reduced the false positivity of neonatal screening results. Compared to the FIA results, the LC-MS / MS method reduced false positivity up to 50 % by evaluating the concentration of 17-OHP. Moreover, by extending the diagnostic algorithm with other measured markers, the reduction was enhanced up to 98%. The developed method is also applicable for the measurement of serum and plasma samples, respectively, and has become a part of the confirmation tests for suspected CAH screening findings. Key...
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