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Dissertations / Theses on the topic 'MALDI matrix'

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Published: 22 December 2023

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1

Krüger, Ralf. "Untersuchungen zum Einbau von Analytionen in MALDI-Matrizes sowie zur Ionisation und Adduktbildung in der MALDI-Massenspektrometrie." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969681682.

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2

Bouschen, Werner. "Ortsaufgelöste MALDI-Massenspektrometrie an biologischen und synthetischen Oberflächen." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=971766886.

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3

Jacksén, Johan. "Improved techniques for CE-MALDI-MS off-line coupling and MALDI-MS analysis of primarily hydrophobic proteins and peptides." Licentiate thesis, KTH, Chemistry, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4599.

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Due to the hydrophobic nature of integral membrane proteins (IMP) they give rise to several difficulties concerning handling and analysis, which is not the case for the most water soluble proteins. New analysis methods are needed, where the insolubility problems of the hydrophobic proteins due to aggregation and adhesion are tackled. Those problems also affect digestion performance and equipment compatibility for the analysis.

Protocols for analysis and separation specified for IMP are presented in Paper I and III.

The instrumentation used in this work was capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Both instruments are suitable for peptide/proteins analysis.

In Paper I, protocols for a CE separation of bacteriorhodopsin (BR) peptides as model IMP peptides are established. Also, a partially automated manufacturing procedure of a concentration MALDI-target is presented, suitable for fractions from CE. The MS analysis detected 9 out of 10 cyanogen bromide (CNBr) digested BR peptides. A novel technique for the off-line integration of CE to MALDI-MS using a closed-open-closed system is presented in Paper II, where the open part is a microcanal functioning as a MALDI target window. Investigation of the microcanal electro-osmotic flow (EOF) properties and band broadening characteristics was performed. A protein separation was obtained and detected with MALDI-MS analysis in the microcanal. Different protein digestion methods were evaluated using BR in Paper III through MALDI-MS. Several digestion methods as well as MS media were investigated alongside different MALDI matrices. For example, matrices as the hydrophobic 2,6-dihydroxyacetophenone (DHAP) and 2-Hydroxy-3-methoxybenzoic acid (2H3MBA) or 2-Hydroxy-5-methoxybenzoic acid (2H5MBA) mixed with DHB, appeared to be promising matrices for analysis of BR.


Med anledning av integrala membranproteiners (IMP) hydrofoba egenskaper uppstår flera svårigheter vid hantering och analys av IMP, vilket inte är fallet för vattenlösliga proteiner. Nya analysmetoder krävs, som löser löslighetsproblemen för de hydrofoba proteinerna som tex flockning och adsorbtion. Dessa problem påverkar även klyvningsgrad och kompatibilitet med analysutrustningen.

I Artikel I och Artikel III presenteras protokoll för analys och separation specifikt för IMP. Instrumenteringen som har använts i detta arbete är kapillärelektrofores (CE) och matris-assisterad laserdesorptions-joniserings-masspektrometri (MALDI-MS). Båda instrumenten är lämpade för peptid/protein analyser.

I Artikel I, presenteras protokoll för en CE separation av peptider från bacteriorhodopsin (BR), som användes som modellpeptider för IMP. En delvis automatiserat tillverkningsprocedur för en koncentrerande MALDI-platta, som är anpassad för CE fraktionerna beskrivs också. MS-analysen detekterade 9 av 10 BR-peptider från cyanobromid-klyvning (CNBr). En ny teknik för off line-integrering av CE till MALDI-MS genom ett slutet-öppet-slutet system presenteras i Artikel II, där den öppna delen är en mikrokanal som fungerar som detektionsfönster i MALDI. Undersökning av mikrokanalens egenskaper som tex det elektroosmotiska flödet (EOF) och bandbreddningen utvärderades. En proteinseparation genomfördes och detekterades med MALDI–MS i mikrokanalen. Olika proteinklyvningsmetoder för BR undersöktes i Artikel III med MALDI-MS. Flera proteinklyvningsmetoder samt MS-medier utvärderades tillsammans med olika MALDI-matriser. Den hydrofoba matrisen 2,6-dihydroxyacetophenone (DHAP) och 2-Hydroxy-3-methoxybenzoic acid (2H3MBA) eller 2-Hydroxy-5-methoxybenzoic acid (2H5MBA) blandade med DHB, visade sig exempelvis vara lovande matriser för BR-analyser.

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4

Priyasantha, Kandalama KD. "DEVELOPMENT OF A NOVEL MATRIX ASSISTED LASER DESORPTION / IONIZATION (MALDI) BASED PEPTIDE QUANTITATION APPROACH." OpenSIUC, 2015. https://opensiuc.lib.siu.edu/dissertations/989.

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Matrix Assisted Laser Desorption / Ionization (MALDI) Mass Spectrometry (MS) has emerged as an important tool in the field of proteomics mainly because it is simple, quick and efficient. The identification and quantitation of biomarkers, protein targets for drugs, and metabolites are some of the important fields in proteomics research. Although MALDI MS is an important tool in proteomics research there are drawbacks of the technique that need further development in order for the approach to be used in clinical laboratories. One major limitation of MALDI MS is the generally poor reproducibility of ion signal intensities, which negatively impacts the quantitation of peptides and protein by MALDI MS. A considerable amount of research has been performed in an effort to improve the ion signal reproducibility in MALDI MS. However, many of the approaches developed have introduced specific drawbacks with respect to the traditional dried-droplet sample preparation technique, negating many of the advantages of the MALDI MS approach. This project has focused on the development of a novel approach to quantify peptides by MALDI MS while preserving traditional known advantages of the technique. The studies performed show that an approach in which the ion signal base widths are manipulated to match that of a reference ion signal, through adjustments in desorption laser intensity, leads to much higher reproducibility in the integrated ion signal intensities. A standard curve acquired using the constant ion signal base width approach showed lower average RSDs (< 10.00% vs.> 39.00%) and improved R2 values (> 0.9600 vs. < 0.809) as compared to the conventional constant desorption laser intensity approach. Subsequent work also revealed that the peptide hydrophobic / hydrophilic properties influenced the applicability of the quantitation approach to mixtures of peptides. Specifically, the data revealed that peptides with differing hydrophobic / hydrophilic properties appear to co-crystallize with the MALDI matrix differently leading to an inability to use a hydrophobic peptide signal to quantitate a hydrophilic peptide, and vice versa. This latter conclusion was further supported in similar studies performed on the mixture of peptides resulting from tryptic digestion of the protein bovine serum albumin.
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5

Allwood, Daniel Anthony. "Characterisation and ionisation modelling of matrices in MALDI mass spectrometry." Thesis, University of Hull, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301477.

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6

PENG, LIJUAN. "MATRIX-ASSISTED LASER DESORPTION/IONIZATION (MALDI) TARGET MODIFICATION FOR ENHANCED PROTEOMICS ANALYSIS AND PLASMA POLYMER CHARACTERIZATION BY MALDI MASS SPECTROMETRY." OpenSIUC, 2010. https://opensiuc.lib.siu.edu/dissertations/207.

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The work described in this dissertation is divided into three sections. In the first section three surface modifications are used to produce MALDI targets having reduced surface-protein binding affinity with a goal of increasing peptide/protein MALDI ion signals and lowering the limits of detection (LODs) for proteins and peptides. The second section discusses a bioselective MALDI target, produced via radio frequency (rf) plasma deposited ethylenediamine (EDA), for on-target separation of complex protein mixtures. The third section develops a new approach for characterization of rf plasma-deposited bulk polymers by using MALDI MS. Previous studies in our group have shown that the analyte signal in a MALDI MS experiment is strongly influenced by the binding interactions between the target surface and the analyte. Specifically, the analyte signal increases with decreasing surface-analyte binding affinity, which has been attributed to more unbound analyte being available for incorporation within the MALDI matrix. In the presented studies MALDI targets are modified with polyethylene glycol (PEG)-like structures via chemical grafting of PEG onto polyurethane (PU) film and rf plasma polymerization of ethylene oxide vinyl ether (EO2) and tetraglyme. It is shown that there are enhancements in the protein MALDI ion signals on these modified targets and that the LOD for target proteins is decreased by a factor of 2-10 in comparison with the conventional stainless steel MALDI target. On-probe affinity capture (OPAC) MALDI MS, developed in our group, has shown that functional group modified MALDI targets can be used to rapidly and selectively isolate target analytes from complex samples. For applications involving analysis of complex peptide/protein mixtures, fractionation of the mixture on the basis of component pI can reduce MALDI ion suppression effects leading to efficient ionization of larger numbers of mixture components. In the present studies a MALDI target is modified by rf plasma deposition of polymerized EDA to yield an OPAC target suitable for capture of proteins with low pI (expected to be negatively charged at neutral pH). In subsequent MALDI MS analyses of both control and biological mixtures after fractionation on the OPAC target it is observed that a significant number of additional peptide/protein ion signals are detected. The results of these studies, along with studies of the effects of the density of the primary amine functionality on the bio-selective MALDI ion signals, are presented. The complex nature of the polymer films resulting from plasma polymerization makes it very difficult to characterize their molecular structures. The presented study is the first to use MALDI MS for characterization of rf plasma-deposited bulk polymers and for investigation of the rf plasma polymerization process. It is shown that the mass spectra of the soluble fraction of allyl alcohol, EO2 and ethylene glycol butyl vinyl ether -plasma polymers contain clear polymer series. Furthermore, it is found that the peaks of the EO2-plasma polymer series shift to higher molecular weight distribution with decreasing plasma duty cycle. In contrast to predictions based on conventional radical polymerization, the mass spectra of all three plasma polymers exhibit the same repeat unit of 44 Da, for which the most likely structure would be -(CH2CH2O)-.
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7

Walbrodt, Dirk [Verfasser]. "Das Ablationsverhalten von Matrix- und Analytneutralen im UV-MALDI-Prozess / Dirk Walbrodt." Kiel : Universitätsbibliothek Kiel, 2008. http://d-nb.info/101955360X/34.

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8

Tummala, Manorama. "Surfactant-Aided Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (SA-MALDI MS)." University of Cincinnati / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1100672049.

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9

Siricord, Cornelia Charito. "Detection of Phytophthora species by MALDI-TOF mass spectrometry." Thesis, Siricord, Cornelia Charito (2005) Detection of Phytophthora species by MALDI-TOF mass spectrometry. PhD thesis, Murdoch University, 2005. https://researchrepository.murdoch.edu.au/id/eprint/314/.

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Phytophthora diseases have caused worldwide economic, social and environmental impacts for decades. Once their presence is confirmed, they are difficult to eradicate. To reduce and manage the damage inflicted by the pathogen, fast and reliable disease management protocols are required. Tests that enable the rapid and reliable identification of the pathogen assist greatly in disease management. Phytophthora species are traditionally not only detected by baiting but also by plating of symptomatic tissue on selective media. Species can be identified by the characteristics of the mycelium growing out of the bait. However, the method is low throughput, labour intensive, and prone to false negatives. An alternative approach would be to detect the pathogen by the presence of its DNA. This involves amplification of the pathogen DNA using Polymerase Chain Reaction (PCR) and detection of the amplification product. Detection is usually by agarose gel electrophoresis. However, this is also a labour intensive process involving pouring, loading, running, and staining of the gels. The aim of this thesis is to explore the use of Matrix Assisted Laser Desorption/ Ionisation Time-of-Flight (MALDI-TOF) mass spectrometry for detection of PCR products. This procedure enables the analysis of large numbers of samples within a very short time-frame as the average time for analysis of each sample is in the order of milliseconds. The assay involves annealing an extension (genotyping) primer to the PCR product and its extension by a single nucleotide. The nature of the nucleotide added differentiates species as does the site to which the primer anneals. Multiple extension (genotyping) primers can be used together in a single reaction for detection of multiple species. In this project four genotyping primers (GPs) were designed from the ITS regions of Phytophthora palmivora, Phytophthora cinnamomi, Phytophthora citricola, and Phytophthora cambivora. The extension primers were tested for their specificity on the DNA of the target species. The four primers designed were specific for their intended targets except for GPpalm3 which in addition to being extended by ddT when tested with DNA from P. palmivora, was also extended by ddC when tested with DNA from other species of Phytophthora or Pythium. These primers were also tested for their ability to detect multiple Phytophthora species in a single reaction (multiplexing). Mixtures of primers were added to mixed DNA templates and the primer extension reaction carried out. The primers were designed so that their masses were sufficiently different for them to be identified from a mixture. Six replicates were analysed for each reaction. In general only about 1-3 of the six replicates gave a positive reaction. This indicates that there may be some interference between primers, or that the presence of all four nucleotides interfered with the primer extension reaction. Increasing either the amount of enzyme, the amount of nucleotides or both did not improve the results. The sensitivity of detection was tested by the addition of different amounts of mycelium to soil. The detection sensitivity depended on the primer pair used for PCR amplification. The ITS1/2 primer pair was more sensitive than the ITS1/4 pair. The limit of detection was 1 mcg mycelium g soil-1. However using nested PCR, levels of sensitivity comparable to those obtained using the ITS1/2 primer pair could be achieved. Primers to other regions of the genome such as the beta cinnamomin elicitin gene gave very low levels of sensitivity compared to the ITS primers. In comparison with DNA detection we found that the limit of detection using baiting was 4 mcg mycelium g soil-1. Results below this limit were unreliable. The method suffered from the additional disadvantage that it took a long time in comparison to DNA detection. DNA detection methods do not distinguish between living and dead organisms in the soil. However it can be hypothesised that DNA is unlikely to persist for any significant length of time in soil. To test this, we added plasmid DNA to soil and tested the persistence of this DNA using a variety of methods such as precipitation of labelled DNA, southern blotting and PCR amplification. It was found that in general, in soils from different ecosystems, the bulk of the DNA was undetectable after 24 hours. The rate of DNA breakdown differed with the soil type. In some soils, the added DNA was not detected even after 2 hours, whereas in others it could be observed after 10 hours. The detection depended on the method. Southern blotting showed that although DNA could be observed at 10 hours, by 24 hours it was completely degraded. In contrast a PCR product could be obtained from the soil extracts up to 24 hours. In a separate experiment, plasmid DNA was detectable over a 24 hour incubation period in 5 soil samples from 5 different sites. The results suggest that DNA is degraded rapidly in soil and is unlikely to persist longer than 24 hours. The results in this thesis demonstrate that MALDI-TOF MS is a suitable alternative to agarose gel electrophoresis for analysis of PCR products. The technique is rapid, differentiates species from mixtures, is high-throughput and amenable to automation. Implementation will require further research to automate the primer extension assay to reduce the sensitivity to impurities in the DNA and to design parameters for sampling asymptomatic material.
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10

Siricord, Cornelia Charito. "Detection of Phytophthora species by MALDI-TOF mass spectrometry." Siricord, Cornelia Charito (2005) Detection of Phytophthora species by MALDI-TOF mass spectrometry. PhD thesis, Murdoch University, 2005. http://researchrepository.murdoch.edu.au/314/.

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Phytophthora diseases have caused worldwide economic, social and environmental impacts for decades. Once their presence is confirmed, they are difficult to eradicate. To reduce and manage the damage inflicted by the pathogen, fast and reliable disease management protocols are required. Tests that enable the rapid and reliable identification of the pathogen assist greatly in disease management. Phytophthora species are traditionally not only detected by baiting but also by plating of symptomatic tissue on selective media. Species can be identified by the characteristics of the mycelium growing out of the bait. However, the method is low throughput, labour intensive, and prone to false negatives. An alternative approach would be to detect the pathogen by the presence of its DNA. This involves amplification of the pathogen DNA using Polymerase Chain Reaction (PCR) and detection of the amplification product. Detection is usually by agarose gel electrophoresis. However, this is also a labour intensive process involving pouring, loading, running, and staining of the gels. The aim of this thesis is to explore the use of Matrix Assisted Laser Desorption/ Ionisation Time-of-Flight (MALDI-TOF) mass spectrometry for detection of PCR products. This procedure enables the analysis of large numbers of samples within a very short time-frame as the average time for analysis of each sample is in the order of milliseconds. The assay involves annealing an extension (genotyping) primer to the PCR product and its extension by a single nucleotide. The nature of the nucleotide added differentiates species as does the site to which the primer anneals. Multiple extension (genotyping) primers can be used together in a single reaction for detection of multiple species. In this project four genotyping primers (GPs) were designed from the ITS regions of Phytophthora palmivora, Phytophthora cinnamomi, Phytophthora citricola, and Phytophthora cambivora. The extension primers were tested for their specificity on the DNA of the target species. The four primers designed were specific for their intended targets except for GPpalm3 which in addition to being extended by ddT when tested with DNA from P. palmivora, was also extended by ddC when tested with DNA from other species of Phytophthora or Pythium. These primers were also tested for their ability to detect multiple Phytophthora species in a single reaction (multiplexing). Mixtures of primers were added to mixed DNA templates and the primer extension reaction carried out. The primers were designed so that their masses were sufficiently different for them to be identified from a mixture. Six replicates were analysed for each reaction. In general only about 1-3 of the six replicates gave a positive reaction. This indicates that there may be some interference between primers, or that the presence of all four nucleotides interfered with the primer extension reaction. Increasing either the amount of enzyme, the amount of nucleotides or both did not improve the results. The sensitivity of detection was tested by the addition of different amounts of mycelium to soil. The detection sensitivity depended on the primer pair used for PCR amplification. The ITS1/2 primer pair was more sensitive than the ITS1/4 pair. The limit of detection was 1 mcg mycelium g soil-1. However using nested PCR, levels of sensitivity comparable to those obtained using the ITS1/2 primer pair could be achieved. Primers to other regions of the genome such as the beta cinnamomin elicitin gene gave very low levels of sensitivity compared to the ITS primers. In comparison with DNA detection we found that the limit of detection using baiting was 4 mcg mycelium g soil-1. Results below this limit were unreliable. The method suffered from the additional disadvantage that it took a long time in comparison to DNA detection. DNA detection methods do not distinguish between living and dead organisms in the soil. However it can be hypothesised that DNA is unlikely to persist for any significant length of time in soil. To test this, we added plasmid DNA to soil and tested the persistence of this DNA using a variety of methods such as precipitation of labelled DNA, southern blotting and PCR amplification. It was found that in general, in soils from different ecosystems, the bulk of the DNA was undetectable after 24 hours. The rate of DNA breakdown differed with the soil type. In some soils, the added DNA was not detected even after 2 hours, whereas in others it could be observed after 10 hours. The detection depended on the method. Southern blotting showed that although DNA could be observed at 10 hours, by 24 hours it was completely degraded. In contrast a PCR product could be obtained from the soil extracts up to 24 hours. In a separate experiment, plasmid DNA was detectable over a 24 hour incubation period in 5 soil samples from 5 different sites. The results suggest that DNA is degraded rapidly in soil and is unlikely to persist longer than 24 hours. The results in this thesis demonstrate that MALDI-TOF MS is a suitable alternative to agarose gel electrophoresis for analysis of PCR products. The technique is rapid, differentiates species from mixtures, is high-throughput and amenable to automation. Implementation will require further research to automate the primer extension assay to reduce the sensitivity to impurities in the DNA and to design parameters for sampling asymptomatic material.
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11

Segu, Mohideen Mohamed Zaneer. "TARGET MODIFICATION FOR ENHANCED PERFORMANCE MATRIX ASSISTED LASER DESORPTION IONIZATION (MALDI) MASS SPECTROMETRY." Available to subscribers only, 2008. http://proquest.umi.com/pqdweb?did=1674093101&sid=1&Fmt=2&clientId=1509&RQT=309&VName=PQD.

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Thesis (Ph. D.)--Southern Illinois University Carbondale, 2008.
"Department of Chemistry." Keywords: Enhanced MALDI, MALDI-MS, On-probe separation, Protein-surface interactions, Sublayers, Surface binding capacity. Includes bibliographical references (p. 130-148). Also available online.
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12

Jaber, Ali. "Matrices MALDI bithiophéniques spécifiques aux alcaloïdes : étude des mécanismes fondamentaux et applications." Thesis, Angers, 2017. http://www.theses.fr/2017ANGE0042/document.

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Mon travail de thèse a consisté à poursuivre le développement et l’application des matrices bithiophéniques spécifique aux alcaloïdes. Après l’optimisation d’un protocole efficace d’analyse, adapté à l’objectif de l’étude, la mise au point d’une méthode de dosage des alcaloïdes par MALDI dans des extraits végétaux et sans prétraitement préalable a été étudiée. Cette méthode a pu être validée en étudiant des alcaloïdes existant dans différents extraits des plantes toxiques. Ensuite, la synthèse et l’évaluation de nouveaux composés bithiophéniques ont été présentés de manière à évaluer les facteurs favorisant l’interaction avec les alcaloïdes. Ultérieurement, cinq nouvelles matrices intéressantes furent l’objet d’une étude plus détaillée. Sur la base des résultats obtenus, le dérivé fluoré F T3 s’avère le plus efficace. ll présente une meilleure sélectivité que la matrice courante CHCA vis-à-vis des alcaloïdes et plus performant pour analyser les alcaloïdes dans différents mélanges complexes tels que des extraits bruts de plantes, des insectes, et des solutions bio-actives commerciales (médicament et répulsif). À la fin, ces sont regroupés les résultats de l’étude des paramètres thermodynamiques de la matrice MT3P, ce qui permettra de proposer des hypothèses expliquant la sélectivité de la matrice bithiophéniques fonctionnalisée pour les alcaloïdes
My thesis work consisted of pursuing the development and application of bithiophenic maldi matrices specific for alkaloids. After optimization of an efficient analysis protocol adapted to the objective of the study, a method for the determination of alkaloids in vegetable extracts by MALDI was developed. This method was validated by studying many alkaloids existing in extracts of different toxic plants. Subsequently, synthesis and evaluation of novel bithiophenic compounds were presented in order to evaluate the factors favoring the interaction with alkaloids. Then, five matrices among the molecules tested and having produced interesting results are chosen and were the subject of a more detailed study. On the basis of the results obtained, the fluorinated derivative PFPT3P proves to be the most effective molecules. It has a better selectivity with respect to alkaloids than the current matrix HCCA and performs better to analyze these metabolites in different complex mixtures such as crude extracts of plants,insects and commercial bioactive solutions (drug and repellent). At the end, the results of the study of the thermodynamic parameters of MT3P matrix are grouped. This will make possible to propose hypotheses explaining the selectivity of the functionalized bithiophene matrices for alkaloids
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13

Mazarin, Michaël. "L'ionisation MALDI [Matrix assisted laser desorption/ionization] de polymères synthétiques en spectrométrie de masse." Aix-Marseille 1, 2008. http://theses.univ-amu.fr.lama.univ-amu.fr/2008AIX11034.pdf.

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La spectrométrie de masse après ionisation/désorption laser assistée par matrice (MALDI) apparaît comme une technique de choix pour la caractérisation structurale des polymères synthétiques. Néanmoins, parce que les processus fondamentaux qui régissent la technique MALDI sont encore mal connus, l’optimisation des conditions expérimentales reste empirique. L’objectif de ces travaux de thèse est d’utiliser conjointement des techniques de spectrométrie de masse et de résonance magnétique nucléaire (RMN) pour rationaliser les méthodologies d'analyse des polymères synthétiques par MALDI. Une première approche consiste à utiliser la RMN diffusionnelle pour pré-évaluer la masse moyenne des polymères, valeur qui sert ensuite de guide pour la préparation des dépôts MALDI et l’interprétation des données spectrales obtenues. Un deuxième axe de recherche s’intéresse à la fragilité des groupements terminaux des macromolécules synthétisées par polymérisation radicalaire contrôlée. Les mécanismes de rupture de ces groupements pendant l’ionisation MALDI ont été élucidés en combinant des expériences de dissociation induite par collision après ionisation electrospray, des expériences de RMN en phase liquide et des calculs théoriques. Il ressort de cette étude que seule la protonation du groupement fragile permet la production d’ions oligomères intacts. A cet effet, une préparation sans solvant des dépôts MALDI a été développée pour promouvoir la protonation des macromolécules étudiées. Son efficacité reste néanmoins limitée aux polymères de faible taille. Enfin, le potentiel de la RMN du solide pour caractériser la microstructure des dépôts MALDI a été évalué
Matrix assisted laser desorption/ionization (MALDI) mass spectrometry is a key technique for synthetic polymer structural characterization. Nevertheless, because fundamental process of MALDI is still not fully understood, no standard protocol is available and experimental conditions are empirically optimized. The aim of this PhD work is to combine mass spectrometric techniques with nuclear magnetic resonance (NMR) spectroscopies to develop rationalized MALDI methodologies for structural studies of synthetic polymers. A first approach consists of using diffusion NMR for a rapid evaluation of polymer average mass, to be further used as a guideline in MALDI sample preparation and spectral data interpretation. A second axis deals with fragile end-groups of macromolecules synthesized via controlled radical polymerization reactions. Combining collision-induced dissociation of electrosprayed oligomers with liquid state NMR and theoretical calculations allowed the elucidation of mechanisms involved in the bond cleavage which is observed to occur within such end-groups during the MALDI process. This study shows that protonation of the fragile termination is the main way to allow intact oligomer ions to be produced. A solvent-free MALDI sample preparation was thus developed to promote macromolecule protonation but its efficiency was shown to be limited to the case of small polymers. Finally, the potential of solid state NMR to characterize the microstructure of MALDI sample was evaluated
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14

Hongming, Guo. "IMPROVING MATRIX DEPOSITION FOR SURFACE LAYER MATRIX-ASSISTED LASER DESORPTION/IONIZATION TIME-OF-FLIGHT MASS SPECTROMETRY IMAGING (SL-MALDI-TOF MSI)." University of Akron / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=akron155654549756264.

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15

Schibur, Stephanie. "Qualitativer und quantitativer Nachweis von Bestandteilen der extrazellulären Matrix des Knorpels mittels MALDI-TOF MS." Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-134850.

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Eine traumatische Läsion am artikulären Knorpel stellt eine noch ungelöste Herausforderung für den behandelnden Arzt dar. Bei den betroffenen Patienten handelt es sich häufig um junge, sportlich aktive Menschen im Arbeitsprozess {Hjelle et al. 2002}, bei denen eine längerfristige Belastungs- und Bewegungseinschränkung oder sogar eine Verminderung der Erwerbsfähigkeit zwingend vermieden werden muss. Jedoch existiert für den traumatischen Gelenkknorpelschaden derzeit noch keine Therapie mit sehr gutem, funktionellem Langzeitergebnis {Richter 2005}. Die konservativen Therapieformen haben immer eine narbige Ausheilung zur Folge. Aber auch mit der chirurgischen Basisversorgung, bestehend aus Debridement und Lavage des betroffenen Gelenks, kann keine Ausheilung erreicht werden. Regenerierende Verfahren, die auf der Grundlage der Penetration des subchondralen Knochens basieren, sollen durch das Einspülen von körpereigenen Stammzellen in den Defekt eine autologe Regeneration induzieren. Langzeitstudien zeigen, dass trotz der oft erreichten, guten funktionellen Ergebnisse histomorphologisch keine Wiederherstellung von intaktem, hyalinem Gelenkknorpel erreicht werden kann {Gaissmaier et al. 2003, Bernholt/Höher 2003}. Vielversprechende neue Therapiekonzepte liefert derzeit das „Tissue Engineering“ am Gelenkknorpel. Vor allem die Autologe Chondrozytentransplantation (ACT) eröffnet vollkommen neue Behandlungsstrategien. Bei der ACT werden arthroskopisch patienteneigene Chondrozyten gewonnen, die in dreidimensionale Gele eingesät und in Zellkultur gebracht werden. Durch verschiedene Stimulationstechniken werden die Zellen zur Proliferation und Produktion von Extrazellulärer Matrix (ECM), insbesondere Kollagen und Proteoglykan, angeregt. Nach drei bis sechs Wochen Kultivierung erfolgt die Implantation in den aufbereiteten Knorpeldefekt des Patienten. Aktuelle Studien konnten zeigen, dass das Transplantat mittelfristig ohne Narbenbildung in den bestehenden Gelenkknorpel einwächst und so die Inkongruenz des Gelenks, welche präarthrotisch wirkt, aufhebt {Brittberg et al. 1996, Peterson et al. 2000, Horas et al. 2000}. Um dieses neuartige Verfahren schnell im klinischen Alltag zu etablieren, bedarf es ausgereifter analytischer Methoden, die eine Qualitätsprüfung des biotechnologisch hergestellten Knorpels ermöglichen. MALDI-TOF MS (matrix-assisted laser desorption and ionization time-of-flight mass spectrometry) ist eine schnelle und sehr sensitive Methode, um die molaren Massen von Stoffen genau zu bestimmen und komplex zusammengesetzte Proben zu analysieren. Ziel dieser Arbeit war es, MALDI-TOF Massenspektrometrie als Analyseverfahren zu nutzen, um die Zusammensetzung des natürlichen Knorpels zu bestimmen und die hier gewonnenen Erkenntnisse auf biotechnologisch hergestellten Knorpel anzuwenden. Somit war die Überprüfung der Anwendbarkeit dieser massenspektrometrischen Untersuchungsmethode auf das komplexe biologische System Knorpel die erste Fragestellung in dieser Arbeit. Es erfolgte daher zunächst die Anpassung und Optimierung der Präparations- und Messmethoden mit dem Ziel, standardisierte Protokolle festzulegen, welche zu reproduzierbaren Spektren führen. Es schloss sich die Analyse der kommerziell verfügbaren Hauptbestandteile der ECM - Proteoglykane und Kollagene – mittels MADI-TOF MS an. Hierzu wurden Chondroitinsulfat und Kollagen verschiedener Typen enzymatisch verdaut und analysiert. So konnten Referenzspektren erstellt werden, welche die Grundlage für die Analyse des wesentlich komplexeren Systems des natürlichen Knorpels bildeten. Durch den Einsatz von Trypsin zur Hydrolyse nach thermischer Denaturierung des Kollagens wurde die Differenzierung zwischen den verschiedenen Kollagentypen ermöglicht. Es schlossen sich Studien zur Quantifizierung der enzymatischen Verdauungsprodukte der ECM an, welche das Ziel verfolgten, neben der stofflichen Zusammensetzung Aussagen zu den relativen Anteilen der einzelnen Bestandteile zu erlauben. Nachdem die grundsätzliche Eignung der Methode gezeigt werden konnte, diente der zweite Teil der hier dargelegten Forschungsarbeit der Beantwortung der Frage, ob die Erkenntnisse, welche bei der Analyse der Einzelbestandteile gewonnen wurden, auf natürliches Knorpelgewebe anwendbar sind. Der artikuläre Schweineknorpel ähnelt im Aufbau und den biomechanischen Eigenschaften dem menschlichen Knorpel. Da er zudem noch günstig und in adäquaten Mengen zur Verfügung gestellt werden kann, wurde der Gelenkknorpel des Schweins als Modellgewebe für die Anwendbarkeit der Methode auf natürlichen Knorpel genutzt. Ziel war es, die Hauptbestandteile der ECM einwandfrei zu identifizieren, Untersuchungen zur Quantifizierung anzustellen und Unterschiede zwischen den Knorpeltypen verschiedener Spezies nachzuweisen. Im letzten Abschnitt dieser Arbeit erfolgte die Analyse von biotechnologisch hergestelltem Knorpel und somit die Anwendung der bisher erworbenen, vor allem einem theoretisch-wissenschaftlichem Interesse folgenden Erkenntnisse auf eine praktisch-klinische Fragestellung nach der tatsächlichen Beschaffenheit des zu transplantierenden Konstrukts. Dazu wurden Konstrukte, welche zum einem aus dreidimensionalen Agarosegele bestückt mit Chondrozyten, zum anderen aus Kollagengel mit eingesäten Stammzellen oder Chondrozyten bestanden, untersucht. Dieser Schritt erfolgte in Zusammenarbeit mit dem Biotechnologisch-Biomedizinischen Zentrum Leipzig. Ziel war es, die bis dahin etablierten Probenpräparations- und Messbedingungen auf den künstlichen Knorpel anzuwenden und mit Referenzspektren von Bestandteilen der ECM sowie des natürlichen Schweineknorpels zu vergleichen. Durch die Analyse des Materials zu verschiedenen Kultivierungszeitpunkten sollte eine Aussage über die Qualität und die Menge der de novo synthetisierten ECM erreicht werden. Mit dieser Arbeit wurde die Grundlage geschaffen, die MALDI-TOF MS als geeignetes analytisches Verfahren zur Bestimmung der Konstruktqualität einzuführen. Perspektivisch sollte es so möglich sein, die Qualität der Konstrukte, welche für die Autologe Chondrozytentransplantation bestimmt sind, zu bewerten und zu überwachen.
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16

Olafsson, Jonas. "Antimicrobial Susceptibility Testing Directly from Urine Samples : a Comparison between Standardised and Direct Disk Diffusion Testing together with Direct Species Identification using Matrix Assisted Laser Desorption/Ionisation Time of Flight." Thesis, Linnéuniversitetet, Institutionen för naturvetenskap, NV, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-27645.

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Urinary tract infection (UTI) is a very common infection in humans and a majority is caused by Escherichia coli. UTI are commonly treated empirically. However, empiric treatment has become more problematic due to increased antibiotic resistance to commonly used antibiotic agents. It is therefore desirable with short turnover times for antimicrobial susceptibility testing and species identification to improve antibiotic treatment at an early stage. Matrix Assisted Laser Desorption/Ionisation Time of Flight (MALDI-TOF) can provide species identification faster than former routine methods. This study compared direct and standard susceptibility testing using disk diffusion on Enterobacteriaceae (EB) from urine samples. The possibility to standardise the inoculum for direct susceptibility testing via a pellet obtained by a series of centrifugations was also evaluated, as well as direct species identification with MALDI-TOF from the pellet. Results from direct susceptibility testing from urine samples with EB, performed either directly from the urine or with a standardised inoculum, correlated well to those obtained with standardised susceptibility testing using EUCAST disk diffusion methodology with few errors, of which most were associated with Proteus mirabilis. The concept of standardising the inoculum for direct susceptibility testing to 0.5 McFarland was labour intensive and did not improve the results further. However, direct species identification from the urine pellet using MALDI-TOF showed good correlation to routine identification. Of 238 samples, an EB was correctly identified in 148 samples using MALDI-TOF.
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17

Djidja, M.-C., V. A. Carolan, Paul M. Loadman, and M. R. Clench. "Method development for protein profiling in biological tissues by matrix-assisted laser desorption/ionisation mass spectrometry imaging." Wiley, 2008. http://hdl.handle.net/10454/4568.

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18

Xu, Zeyuan. "PTMomics : Microfluidics for post-translational modifications studies : application to glycoproteomics." Electronic Thesis or Diss., Université Paris sciences et lettres, 2023. http://www.theses.fr/2023UPSLS029.

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Les glycoprotéines jouent un rôle fondamental dans la vie. Des études récentes montrent qu'elle est largement présente dans les activités biologiques, telles que la liaison des récepteurs, la signalisation cellulaire, la réponse immunitaire, le repliement des protéines et l'action des hormones. Parallèlement, la glycosylation des protéines a été associée au pronostic et à l'évolution de maladies comme les cancers. Ainsi, elle devient un biomarqueur important, et est également significative pour le développement thérapeutique. La glycosylation mérite donc d'être étudiée en détail. La glycoprotéine acquiert sa fraction d'hydrate de carbone par un processus appelé modification post-traductionnelle (PTM). Ce qui est différent de la plupart des PTM, c'est qu'il existe plusieurs formes de glycosylation. Les glycosylations N- et O-liées sont parmi les types les plus courants. D'autres comme la C-mannosylation et la phosphosérine sont rares. Si l'on considère simplement la glycosylation liée à l'azote, on peut la diviser en types complexes, hybrides et à haute teneur en mannose, qui résultent d'une synthèse non dirigée par un modèle. Sur la membrane du RE, un oligosaccharide sur Dol-PP est transféré à Asn dans la séquence Asn-X-Thr/Ser (X n'est pas la proline). Ensuite, les glycosidases et les glycosyltransférases agissent pour éliminer le glucose et ajouter une fraction de sucre dans le RE et le Golgi. Leurs activités dépendent des espèces, des types de cellules, des protéines, des sites et de l'état physiologique de la cellule, ce qui donne lieu à divers glycanes N-liés. Et l'hétérogénéité sera un obstacle majeur à l'étude des glycoprotéines. Les informations sur l'occupation de plusieurs sites peuvent être compliquées par le faible rendement d'ionisation et la fragmentation (macro-hétérogène). Sur chaque site, de multiples glycoformes existent, ce qui entraîne une diminution du signal (micro-hétérogène). De nombreux efforts ont été investis pour résoudre ce problème. La spectrométrie de masse (MS) est maintenant progressivement appliquée à l'étude de la glycosylation des protéines pour sa sensibilité, sa vitesse et son haut débit. Le couplage avec un système de chromatographie liquide à haute performance (HPLC) est une combinaison largement adoptée. Dans le même temps, des glycosidases, par exemple l'endo H et la PNGase F, sont découvertes et utilisées pour la libération des glycanes. La microfluidique est apparue pour le traitement des échantillons, et les approches hybrides sont de plus en plus populaires et devraient être la solution. En conclusion, pour une étude approfondie de sa fonction, l'occupation du site, la composition, la quantité et d'autres informations sont essentielles. Un protocole d'analyse amélioré doit être mis en œuvre pour acquérir spécifiquement ces informations à haute sensibilité, ce qui constitue le point d'ancrage de l'étude glycoprotéomique
Glycoprotein acts as a fundamental undertaker of life. Recent studies show that it is widely found in biological activities, such as in receptor binding, cell signaling, immune response, protein folding, and hormone action. Meanwhile, protein glycosylation has been associated to prognosis and progress of diseases like cancers. Thus, it becomes an important biomarker, and as well as is significant to therapeutics development. Thus, glycosylation worth to be studied in detail. Glycoprotein gains its carbon hydrate moiety through a process so called post translational modification (PTM). What is different from most of the PTMs is that there are various forms of glycosylation. N- and O-linked glycosylation are among the most common types. Others like C-mannosylation and phosphoserine are rare. Merely looking at the N-linked glycosylation, it can be further divided into complex, hybrid, and high mannose types, which is a result of the non-template-driven synthesis. On the ER membrane, an oligosaccharide on Dol-PP is transferred to Asn in the sequence Asn-X-Thr/Ser (X is not proline). Then, glycosidases and glycosyltransferases act in to remove glucose and adding sugar moiety in ER and Golgi. Their activities depend on the species, cell types, protein, sites, and physiological state of the cell resulting in various N-linked glycans. And heterogeneity will be a major hurdle to study glycoprotein. Multiple sites occupancies information can be complicated by the poor ionization yield and fragmentation (macro-heterogenous). On each site, multiple glycoforms existed leading to even diminished signal(micro-heterogenous). Many efforts have been invested in to solve it. Mass spectrometry (MS) is now progressively applied to protein glycosylation study for its sensitivity, speed, and high throughput. The coupling with a high-performance liquid chromatography system (HPLC) is a widely adopted combination. In the meantime, glycosidase, for example, endo H and PNGase F are discovered and used for glycan release. Microfluidics emerged for sample treatment, and hybrid approaches are becoming increasingly popular and expected to be the solution. To conclude, for an in-depth study of its function, site occupancy, composition, quantity, and other information are essential. An improved analysis protocol should implemented to specifically acquire this information at high sensitivity, which is the anchor for glycoproteomic study
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19

Walton, Barbara Lynn. "A Study of Silver: an Alternative Maldi Matrix for Low Weight Compounds and Mass Spectrometry Imaging." Thesis, University of North Texas, 2014. https://digital.library.unt.edu/ark:/67531/metadc499981/.

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Soft-landing ion mobility has applicability in a variety of areas. The ability to produce material and collect a sufficient amount for further analysis and applications is the key goal of this technique. Soft-landing ion mobility has provided a way to deposit material in a controllable fashion, and can be tailored to specific applications. Changing the conditions at which soft-landing ion mobility occurs effects the characteristics of the resulting particles (size, distribution/coverage on the surface). Longer deposition times generated more material on the surface; however, higher pressures increased material loss due to diffusion. Larger particles were landed when using higher pressures, and increased laser energy at ablation. The utilization of this technique for the deposition of silver clusters has provided a solvent free matrix application technique for MALDI-MS. The low kinetic energy of incident ions along with the solvent free nature of soft-landing ion mobility lead to a technique capable of imaging sensitive samples and low mass analysis. The lack of significant interference as seen by traditional organic matrices is avoided with the use of metallic particles, providing a major enhancement in the ability to analyze low mass compounds by MALDI.
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20

Akinapalli, Srikanth. "MICROFLUIDIC DYNAMIC ISOELECTRIC FOCUSING COUPLED TO MATRIX ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY." OpenSIUC, 2016. https://opensiuc.lib.siu.edu/dissertations/1289.

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Proteomics is an increasingly important area of biological research and has gathered much attention over recent years. Major challenges that make a proteomic analysis difficult are sample complexity, diversity and dynamic range. Progress in the area of proteomics relies heavily on new analytical tools for the sensitive, selective, and high-throughput studies of target analytes. It is estimated that there are several hundred thousand proteins in a human cell. In order to be able to analyze such a complex sample, an analytical method must be capable of separating and detecting many different sample peaks. The complexity of such samples indicates that a single separation method will not be able to provide the needed resolution. If two methods that are orthogonal are combined, then the peak capacity of the combined system is the product of the two individual peak capacities. Development of such systems would cater to the current demands of proteomics studies. Matrix assisted laser desorption/ionization (MALDI) mass spectrometry has evolved into a primary analytical tool for proteomics research. MALDI is fast and efficient and has a high tolerance to non-volatile buffers and impurities. The samples for MALDI are typically applied to solid supports after having been subjected to off-line liquid or gel separations. Several methods have been reported involving various chromatographic or electrophoretic separation methods. However, the current methods often require highly sophisticated sample handling systems, which are often expensive and in need of skilled human resources. The current demands of proteomic analyses require fast, efficient and inexpensive methods for separation to fully harness the capability of MALDI mass spectrometry. In this work a microfluidic device has been designed to perform dynamic isoelectric focusing (DIEF) based protein separation with digital sample deposition directly on a MALDI target for offline analysis. DIEF is related to capillary isoelectric focusing which and can facilitate the interface without the loss of the separation resolution. Compared to traditional capillary isoelectric focusing (cIEF) DIEF uses additional high-voltage power supplies to control the pH gradient by manipulating the electric field. The proteins can be focused at a desired sampling position according to their isoelectric point, to be collected for further analysis by MALDI mass spectrometry. DIEF has a peak capacity of over a thousand and offers an ease of interfacing to other techniques making it a preferred separation method for the interface with mass spectrometric techniques such as MALDI. The design of the microfluidic device is based on a digital droplet fractionation. Multiple fractions of the sample solution from DIEF are generated to retain the resolution and to act as an additional separation mode. The microfluidic device is controlled by actuating pneumatic valves built into the device. The DIEF operational parameters were optimized according to the surface functionality and the design of the microfluidic device. A suitable MALDI sample preparation method was found by studying different existing methods. The methods were studied using test proteins prepared in solutions having the additives used in the experiment. A simple mixture of three proteins was used to demonstrate the application of the developed method. The separation between the proteins insulin, hemoglobin and the myoglobin was demonstrated by varying the separation resolution in three experiments.
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21

Crumpton, Jason. "Click Chemistry on DNA and Targeting RNA structure with Peptide Boronic Acids." Diss., Virginia Tech, 2004. http://hdl.handle.net/10919/77076.

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The utilization of click chemistry to perform inter- and intramolecular ligation on DNA has become ubiquitous in the literature. Advances in copper (I) stabilizing ligands that prevent DNA degradation via redox pathways have provided nucleic acid researchers access to the efficiency and quantitative nature of the click reaction. The majority of ligation procedures in the literature are performed in solution after DNA assembly and modification with alkyne reporter groups. However, without specialty alkyne reagents that can be sequentially and selectively deprotected, the solution phase method requires that the click reaction be performed on all DNA-attached alkynes simultaneously. Therefore, the variability of the azide reagent is limited to a singular R group. However, performing the click reaction on DNA during synthetic elongation (immediately after each alkyne installation) allows for the possibility of performing multiple click reactions with variable azide reagents. Unfortunately, most solid phase click procedures require long reaction times or the utilization of microwave irradiation to accelerate the reaction. The development of methods for the ligation of azides to alkynes without the use of microwave irradiation on solid phase is potentially very useful. Herein, we report a simple, efficient, and robust solid phase synthetic method for the ligation of azido-diamondoids to the alkyne-modified phosphate backbone of DNA with click chemistry using [Cu(CH₃CN)₄]PF₆ without stabilizing ligand. Interestingly, it was found that as the size of diamondoid increased, a corresponding increase in melting temperature of hybridized duplexes was observed. The developed method has the potential to complement existing DNA ligation procedures for applications in biotechnology and diagnostics. Interest in peptides incorporating boronic acid moieties is increasing due to their potential as therapeutics/diagnostics for a variety of diseases such as cancer. The utility of peptide boronic acids may be expanded with access to vast libraries that can be deconvoluted rapidly and economically. Unfortunately, current detection protocols using mass spectrometry are laborious and confounded by boronic acid trimerization, which requires time consuming analysis of dehydration products. These issues are exacerbated when the peptide sequence is unknown, as with de novo sequencing, and especially when multiple boronic acid moieties are present. Thus, a rapid, reliable and simple method for peptide identification is of utmost importance. Herein, we report the identification and sequencing of linear and branched peptide boronic acids containing up to five boronic acid groups by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protocols for preparation of pinacol boronic esters were adapted for efficient MALDI analysis of peptides. Additionally, a novel peptide boronic acid detection strategy was developed in which 2,5-dihydroxybenzoic acid (DHB) served as both matrix and derivatizing agent in a convenient, in situ, on-plate esterification. Finally, we demonstrate that DHB-modified peptide boronic acids from a single bead can be analyzed by MALDI-MSMS analysis, validating our approach for the identification and sequencing of branched peptide boronic acid libraries. It is well known that RNA ligands incorporating basic and intercalating moieties display high RNA affinity. Unfortunately, these ligands are also often plagued by promiscuous binding to off-target substrates. Due to the potential utility of RNA ligands in biology and medicine, it is imperative to elucidate RNA binders which display high specificity as well as affinity. Boronic acid peptides promise unique RNA binding motifs through the interaction between the empty p-orbital of boron and the 2'-hydroxyl group of RNA. Herein, we describe the incorporation of lysine and phenylalanine boronic acid analogues into a branched peptide combinatorial library in an effort to impart increased selectivity towards the HIV-1 Rev Response Element (RRE). We were able to easily select and deconvolute 6 resulting "hit" peptides from 65,536 unique library members by high throughput screening and de novo sequencing. Although we were unable to evaluate peptide selectivity towards RRE due to general insolubility in aqueous media, we demonstrated the efficient deconvolution of a branched peptide library that incorporates boronic acids.
Ph. D.
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22

Crumpton, Jason B. "Click Chemistry on DNA and Targeting RNA structure with Peptide Boronic Acids." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77076.

Full text
Abstract:
The utilization of click chemistry to perform inter- and intramolecular ligation on DNA has become ubiquitous in the literature. Advances in copper (I) stabilizing ligands that prevent DNA degradation via redox pathways have provided nucleic acid researchers access to the efficiency and quantitative nature of the click reaction. The majority of ligation procedures in the literature are performed in solution after DNA assembly and modification with alkyne reporter groups. However, without specialty alkyne reagents that can be sequentially and selectively deprotected, the solution phase method requires that the click reaction be performed on all DNA-attached alkynes simultaneously. Therefore, the variability of the azide reagent is limited to a singular R group. However, performing the click reaction on DNA during synthetic elongation (immediately after each alkyne installation) allows for the possibility of performing multiple click reactions with variable azide reagents. Unfortunately, most solid phase click procedures require long reaction times or the utilization of microwave irradiation to accelerate the reaction. The development of methods for the ligation of azides to alkynes without the use of microwave irradiation on solid phase is potentially very useful. Herein, we report a simple, efficient, and robust solid phase synthetic method for the ligation of azido-diamondoids to the alkyne-modified phosphate backbone of DNA with click chemistry using [Cu(CH₃CN)₄]PF₆ without stabilizing ligand. Interestingly, it was found that as the size of diamondoid increased, a corresponding increase in melting temperature of hybridized duplexes was observed. The developed method has the potential to complement existing DNA ligation procedures for applications in biotechnology and diagnostics. Interest in peptides incorporating boronic acid moieties is increasing due to their potential as therapeutics/diagnostics for a variety of diseases such as cancer. The utility of peptide boronic acids may be expanded with access to vast libraries that can be deconvoluted rapidly and economically. Unfortunately, current detection protocols using mass spectrometry are laborious and confounded by boronic acid trimerization, which requires time consuming analysis of dehydration products. These issues are exacerbated when the peptide sequence is unknown, as with de novo sequencing, and especially when multiple boronic acid moieties are present. Thus, a rapid, reliable and simple method for peptide identification is of utmost importance. Herein, we report the identification and sequencing of linear and branched peptide boronic acids containing up to five boronic acid groups by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protocols for preparation of pinacol boronic esters were adapted for efficient MALDI analysis of peptides. Additionally, a novel peptide boronic acid detection strategy was developed in which 2,5-dihydroxybenzoic acid (DHB) served as both matrix and derivatizing agent in a convenient, in situ, on-plate esterification. Finally, we demonstrate that DHB-modified peptide boronic acids from a single bead can be analyzed by MALDI-MSMS analysis, validating our approach for the identification and sequencing of branched peptide boronic acid libraries. It is well known that RNA ligands incorporating basic and intercalating moieties display high RNA affinity. Unfortunately, these ligands are also often plagued by promiscuous binding to off-target substrates. Due to the potential utility of RNA ligands in biology and medicine, it is imperative to elucidate RNA binders which display high specificity as well as affinity. Boronic acid peptides promise unique RNA binding motifs through the interaction between the empty p-orbital of boron and the 2'-hydroxyl group of RNA. Herein, we describe the incorporation of lysine and phenylalanine boronic acid analogues into a branched peptide combinatorial library in an effort to impart increased selectivity towards the HIV-1 Rev Response Element (RRE). We were able to easily select and deconvolute 6 resulting "hit" peptides from 65,536 unique library members by high throughput screening and de novo sequencing. Although we were unable to evaluate peptide selectivity towards RRE due to general insolubility in aqueous media, we demonstrated the efficient deconvolution of a branched peptide library that incorporates boronic acids.
Ph. D.
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23

Huang, Huan. "Optimizing Deposition of Matrix and Ionization Salt via Two-Step Sublimation in Sample Preparation for Surface-Layer Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Imaging (SL-MALDI-TOF MSI)." University of Akron / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=akron1619183035472425.

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24

Ratcliffe, Lucy Vivien. "Proteomic strategies for protein and biomarker identification by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)." Thesis, Nottingham Trent University, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.431885.

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This thesis describes the development of novel strategies for the analysis of peptides by MALDI mass spectrometry. The developed techniques are applied to the identification of protein and proteomic biomarkers for melanoma. A commercial atmospheric pressure (APMALDI) source (MassTechnologies, Burtonsville, MD, USA) was modified to allow operation with a high powered nitrogen laser and independent PC control of the sample stage. A software interface was developed using LabVIEW 6.1 that allows full control of the target position with respect to the laser fibre optic interface, allowing the target to be adjusted within any point within a particular sample spot to enhance signal quality. The modified AP-MALDI-QIT interface was evaluated for the analysis of standard peptide mixtures and tryptic digests of proteins. AP-MALDI-QIT analysis of tryptic peptides following capillary liquid chromatographic (LC) separation and direct analysis of a protein digest is reported. Peptide fragments were identified by peptide mass fingerprinting from mass spectrometric data and sequence analysis obtained by tandem mass spectrometry of the principal mass spectral peaks using a data-dependent scanning protocol. These data were compared with those from mass spectrometric analysis using capillary LC/MALDI-time-of-flight (TOF) and capillary LC/electrospray ionisation (ESI)-quadrupole TOF. For all three configurations the resulting data were searched against the MSDB database, using MASCOT and the sequence coverage compared for each technique. Complementary data were obtained using the three techniques. A bottom-up proteomic methodology for the peptide profiling of human serum samples using MALDI mass spectrometry was developed. Reproducibility studies were carried out to define the MALDI measurement precision. Pre-analytical sample handling factors, such as room temperature incubation and freeze thaw cycles have also been investigated. The methodology developed was applied to the analysis of serum peptides from stage IV melanoma patients and healthy control subjects. Prediction of human melanoma metastatic cancer from peptide profiling using artificial neural networks (ANNs) model classified 98 % of samples correctly. The identification of three out of six ions predicted by the ANNs model to be indicative biomarkers that have good predictive performance were identified using MALDI PSD, AP-MALDI MSIMS and LC-ESI-MS/MS. Two of the ions were shown to belong to the same identified peptide, u-l-acid glycoprotein precursor (l, 2) which correctly predicted 95 % (i.e. 45/50) of metastatic melanoma patients.
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25

Jiang, Yanjie. "Oligosaccharide analysis via anion attachment using negative mode electrospray (ES) and matrix assisted laser desorption/ionization (MALDI) mass spectrometry." ScholarWorks@UNO, 2004. http://louisdl.louislibraries.org/u?/NOD,27.

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Thesis (M.S.)--University of New Orleans, 2004.
Title from electronic submission form. "A thesis ... in partial fulfillment of the requirements for the degree of Master of Science in the Department of Chemistry."--Thesis t.p. Vita. Includes bibliographical references.
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26

Lu, Kuan. "Optimization Of Sublimation Conditions for Surface Layer Matrix-assisted Laser Desorption Ionization Time of Flight Mass Spectrometry Imaging (SL-MALDI- Tof MSI) of Polymer Surfaces." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1524846943404769.

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27

Liu, Xi [Verfasser]. "Charakterisierung der Glykosylierungsstelle von Glykoproteinen mittels Matrix-unterstützter Laserdesorption / Ionisations- (MALDI) und Elektrosprayionisations-Massenspektrometrie (ESI-MS) / Xi Liu." Berlin : Medizinische Fakultät Charité - Universitätsmedizin Berlin, 2015. http://d-nb.info/1075493307/34.

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28

Sorensen, Christina M. "ESI-MS and MALDI-TOF-MS for the characterization and analysis of metallo-oligomers and proteins." Laramie, Wyo. : University of Wyoming, 2005. http://proquest.umi.com/pqdweb?did=1031044031&sid=4&Fmt=2&clientId=18949&RQT=309&VName=PQD.

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29

Jacksén, Johan. "Improved techniques for CE and MALDI-MS including microfluidic hyphenations foranalysis of biomolecules." Doctoral thesis, KTH, Analytisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-27342.

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In this thesis, improved techniques for biomolecule analysis using capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) and hyphenations between those have been presented.A pre-concentration method which is possible to apply in both techniques, has also been investigated. In this work the off-line MS mode has been used either in the form of fractionation (Paper I) or by incorporating the MALDI target in the CE separation system (Paper II).In Paper I, a protocol for CE-MALDI analysis of cyanogen bromide digested bacteriorhodopsin (BR) peptides as model integral membrane protein peptides were established. Also, an improved protocol for partially automated manufacturing of a concentration MALDI-target plate is presented. The design of the targets was suitable for the fractions from the CE. A novel technique for the integration of CE to MALDI-MS using a closed-open-closed system is presented in Paper II, where the open part is a micro canal functioning as a MALDI target window. A protein separation was obtained and detected with MALDI-MS analysis in the micro canal. A method has been developed for detection of monosaccharides originating from hydrolysis of a single wood fiber performed in a micro channel, with an incorporated electromigration pre-concentration step preceding CE analysis in Paper III. The pre-concentration showed to be highly complex due to the fact that several parameters are included that affecting each other. In Paper IV a protocol using enzymatic digestion, MALDI-TOF-MS and CE with laser induced fluorescence (LIF) detection for the investigation of the degree of substitution of fluorescein isothiocyanate (FITC) to bovine serum albumin (BSA), as a contact allergen model system for protein-hapten binding in the skin, is presented. The intention of a further CE-MALDI hyphenation has been considered during the work. In Paper V 2,6-dihydroxyacetophenone (DHAP) was investigated, showing promising MALDI-MS matrix properties for hydrophobic proteins and peptides. 2,5-dihydroxybenzoic acid (DHB) was undoubtedly the better matrix for the hydrophilic proteins, but its performance for the larger and hydrophobic peptides was not optimal. Consequently, DHAP can be used as a compliment matrix for improved analysis of hydrophobic analytes.
QC 20101214
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30

Saad, Bessem. "Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry som verktyg för att detektera nedbrytning av Ceftolozan/Tazobaktam orsakad av karbapenemaser." Thesis, Örebro universitet, Institutionen för hälsovetenskaper, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-84598.

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Under senare år har en särskilt hög resistensutveckling observerats hos gramnegativa bakterier inom familjen Enterobacteriaceae. Den främsta resistensmekanismen utgör produktion av så kallade "extended-spectrum β-lactamases" (ESBL) och särskilt oroväckande är karbapenemaser (ESBLCARBA) som har förmåga att bryta ner ett flertal olika grupper av β-laktamantibiotika. Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) har utforskats som metod för snabb detektion av karbapenemasaktivitet genom analys av nedbrytning av antibiotika. Syftet med denna studie var att utvärdera om MALDI-TOF MS kan användas som metod för att detektera enzymatisk nedbrytning av Ceftolozan/Tazobaktam samt att undersöka vilka enzymer som uppvisar nedbrytning av antibiotikan. Sju karbapenemasproducerande isolat och en β-laktamasnegativ kontrollstam användes i studien. Isolaten inkuberades 120 min respektive 270 min med antibiotika (1mg/ml) i en buffertlösning (0,08% ammoniumbikarbonat, pH 8). Efter centrifugering analyserades supernatanten med MALDI-TOF MS. Nedbrytning av Ceftolozan detekterades hos samtliga karbapenemasproducerande stammar, utom hos E. coli med NDM-1 produktion. Nedbrytningstoppar av Tazobaktam detekterades emellertid enbart hos stammar med OXA-48 och NDM-7 produktion. Tydligast nedbrytning sågs efter 120 min. För tydligare visualisering av nedbrytningstoppar bör metoden dock optimeras med avseende på matrix, buffert och antibiotikakoncentration.
In recent years, an alarming increase of antibiotic resistance has been observed in Gram-negative bacteria, classified in the family Enterobacteriaceae. The main resistance mechanism is the production of extended-spectrum β-lactamases (ESBL). Particularly worrisome is the production of carbapenemases (ESBLCARBA) due to their ability to hydrolyze a broad range of β-lactams. Recently, Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) has been investigated as a method for rapid detection of carbapenemase activity through observation of antibiotic degradation. The aim of this study was to investigate whether MALDI-TOF MS can be used as a method to detect degradation of Ceftolozane/Tazobactam as well as to examine which enzymes that possess the ability to hydrolyze the antibiotic. A total of seven carbapenemase-producing strains were used in the study. The experiment also included a β-lactamase-negative isolate as a negative control. The strains were incubated with antibiotic (1mg/ml) in a buffered solution (0,08% ammonium bicarbonate, pH 8) for 120 min and 270 min. The supernatant, after centrifugation, was analyzed by MALDI-TOF MS. All the carbapenemase-producing strains demonstrated hydrolysis of Ceftolozane, except for NDM-1 producing E. coli. However, mass peaks corresponding to the degradation of Tazobactam were only detected in strains producing OXA-48 and NDM-7. The degradation of Ceftolozane/Tazobactam was most apparent after 120 minutes. However, to better enable detection of mass peaks, further optimization is needed in regard to appropriate matrix, buffer and antibiotic concentration.
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31

Saleem, Saira. "Proteomic profiling of pro and active matrix metalloproteinases using tandem mass spectrometry. optimization of affinity chromatography and nHPLC-MALDI-MS/MS for proteomic discrimination of matrix metalloproteinases in pre-clinical cancer model." Thesis, University of Bradford, 2012. http://hdl.handle.net/10454/5752.

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Matrix metalloproteinases (MMPs) network with other biological molecules to maintain the extracellular matrix (ECM) in normal physiology and perform different roles. Understanding and assigning specific role to each of 24 members of these endoproteinases is impeded because of lack of specific and efficient detection methods in biological samples. Moreover, MMP-based anti-cancer drug development has also been challenged because, currently, there is no robust methodology to distinguish the inactive pro-enzymes, active enzymes or those complexed with endogenous inhibitors in biological specimens. The objective of this project is to develop a chemical proteomics strategy based on Matrix assisted laser desorption ionization tandem mass spectrometry (MALDI-MS/MS) to help identify and discriminate the various MMP forms. Firstly, a triazine dye-based ligand immobilized on chromatography beads was utilized to assess whether it binds to recombinant human MMPs (rhMMPs). The results highlighted that the ligand interacts with latent forms of MMPs in agreement with the literature. Secondly, the potential of the ligand was assessed using MALDI-MS/MS based methodology in in vitro cancer models. Cell line culture supernatants were used in amounts to emulate the availability of tumour biopsies in clinical settings. The MS/MS spectral peaks specific to MMPs (MMP-2 and MMP- 14), and two endogenous inhibitors TIMP-1 and TIMP-2 were found in affinity chromatography eluates of cell culture supernatants with higher Mascot scores for the latter. While western blot detected MMP-2 in cell extracts, MALDI-MS/MS did not detect MMPs because of amounts below the limit of detection (LOD) of the instrument. Although the ligand was found to be interacting with MMPs and detergent-free salt elution buffers improved MALDI analysis, recovery of MMPs from biological samples was sub-optimal. The dye ligand was observed to bind other enzymes and despite various strategies to reduce non-specific binding of proteins or enable selective elution did not improve MMP enrichment. Further work using methodology described in this study is required after scaling up the MMP amounts in biological specimen and to resolve the issue of non-specific binding of proteins to the ligand by understanding its structure.
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32

Barandas, Guilherme Mayrink. "Caracterização de Bacilos Gram-Negativos Não Fermentadores não usuais em bacteremias pelas técnicas de Matrix-Assisted Laser Desorption IonizationTime of Flight Mass Spectrometry, sequenciamento de DNA e método fenotípico convencional." Universidade do Estado do Rio de Janeiro, 2013. http://www.bdtd.uerj.br/tde_busca/arquivo.php?codArquivo=9548.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico
Alguns Bastonetes Gram-negativos não fermentadores (BGNNF) costumam ser considerados clinicamente pouco significantes e a sua implicação em infecções é subestimada. Devido à similaridade fenotípica, mudanças taxonômicas, baixa reatividade bioquímica e limitações nos bancos de dados em sistemas comerciais, a identificação de BGNNF é frequentemente equivocada, culminando com a denominação de diferentes micro-organismos apenas como BGNNF, por falta de melhor diferenciação. O objetivo desse estudo foi avaliar, por métodos fenotípico convencional, proteômico e molecular, a identificação de BGNNF incomuns isolados em hemoculturas de pacientes atendidos em um hospital universitário no Rio de Janeiro. Foram selecionadas 78 amostras isoladas de hemoculturas caracterizadas no laboratório clinico como BGNNF para a identificação por sequenciamento dos genes 16S RNA e recA, por um conjunto amplo de testes fenotípicos manuais e por MALDI-TOF MS. Os micro-organismos predominantes na amostragem foram genotipados pela técnica de eletroforese em gel de campo pulsado (PFGE). Pelo sequenciamento do gene 16S rRNA, a maioria das amostras (n=31; 40%) foi incluída no gênero Burkholderia, seguido de Pseudomonas stutzeri (10%) e Delftia acidovorans (4%). Os demais isolados foram agrupados em 27 diferentes espécies. O sequencimento do gene recA identificou a maioria das espécies de Burkholderia como Burkholderia contaminans (n=19; 24%). Os testes fenotípicos incluíram as 31 amostras apenas no CBc e para as outras 47 amostras, a concordância com o sequenciamento do gene 16S rRNA em nível de espécie foi de 64% (n=30) e apenas em gênero a concordância foi de 17% (n=8). A análise comparativa geral da identificação por MALDI-TOF MS com o sequenciamento do gene16S rRNA mostrou que 42% (n=33) das 78 amostras foram concordantes em nível de espécie e 45% (n=35) apenas em gênero. Excluindo as amostras do CBc, houve um aumento da concordância em nível de espécie para 60%. As discordâncias parecem ser devido às diferenças nos perfis proteicos das amostras em relação às amostras-referência do banco de dados do equipamento e podem ser aprimorados com a atualização de perfis no sistema. A análise do polimorfismo genético de B. contaminans mostrou a ausência de um clone disseminado causando surto, além da provável origem ambiental das infecções. Os setores de nefrologia e hemodiálise contribuíram com maior número de pacientes com amostras positivas (5 pacientes e 9 amostras). Os grupos clonais BcoD e BcoE foram encontrados em pacientes assistidos no mesmo setor com diferença de quatro meses (BcoD, nefrologia) e 1,5 ano (BcoE, hemodilálise), entre as culturas, respectivamente. As discordâncias entre as técnicas ocorreram principalmente devido a dificuldade de identificação das espécies do CBc. Os BGNNF incomuns são de difícil caracterização independente da metodologia usada e nenhum método por si só foi capaz de identificar todas as amostras.
Some nonfermenting Gram-negative Bacilli (NFGNB) are considered of low clinical significance, and their implication in infections is usually underestimated. Due to their phenotypic similarities, frequent taxonomic changes and low biochemical reactivity, as well as to limitations of bacterial identification commercial system databases, these NFGNB are frequently misidentified and are collectively referred to as NFGNB group, in the lack of a better differentiation. The aim of the present study was to evaluate the performance of the conventional phenotypic method, the proteomic matrix-assisted laser desorption ionization time of flight mass spectometry method (MALDI-TOF MS) and of molecular methods (16S RNA and recA gene sequencing) in the identification of 78 unusual NFGNB isolated from blood cultures of pacients treated at an university hospital in Rio de Janeiro. Clonality of the predominant species identified within these isolates was determined by pulsed-field gel electrophoresis (PFGE). By the 16S rRNA gene sequence analysis, most strains (n = 31; 40%) were included in the Burkholderia spp. followed by Pseudomonas stutzeri (n = 8; 10%), Delftia acidovorans (n = 3; 4%) and Stenotrophomonas maltophilia (n = 3; 4%). The remaining bacterial isolates were included in 27 different species. By the recA gene sequencing technique, most bacteria from the Burkholderia cepacia complex (BCC), samples were classified as Burkholderia contaminans (n=19; 24%). Phenotypic tests provided accurate identification of all 31 isolates included in the BCC by the 16S rRNA gene sequence analysis. For the other 47 samples, agreement of the results obtained with these two techniques in species and genus level identifications occurred in 30 (63,8%) and 17 samples (36,2%), respectively. The results obtained by the MALDI-TOF MS and 16S rRNA gene sequencing methods agreed at species and genus levels in 33 (42%) and 35 isolates (45%), respectively. When bacteria from the BCC were excluded from the analysis, the agreement between the two techniques at species level increased to 60%. Misidentification by the MALDI-TOF MS method may be due to differences in protein spectra between the samples and the reference strains in the equipment database. PFGE analysis of B. contaminans isolates revealed the absence of a disseminate clone causing an outbreak, and the probable environmental source of infections. The nefrology ang dialisis sectors contributed to the greatest number of patients with positive cultures (5 pacients and 9 isolates). Clones BcoD and BcoE were found in blood cultures of pacientes treated in a same sector with differences of 4 months (BcoD, nefrology) and 1.5 year (BcoE, dialisis). The misidentifications occurred mainly due to the hard differentiation of BCC species. Unusual NFGNB are of difficult characterization whatever the methodology used and no method alone was able to identify all the isolates.
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33

Robins, Chad LaJuan. "Nonpolar matrices for matrix assisted laser desportion ionization - time of flight - mass spectrometry." Cincinnati, Ohio : University of Cincinnati, 2005. http://www.ohiolink.edu/etd/view.cgi?acc%5Fnum=ucin1115293526.

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Thesis (Ph. D.)--University of Cincinnati, 2005.
Title from electronic thesis title page (viewed May 18, 2006). Includes abstract. Keywords: Matrix Assisted Laser Desorption/Ionization Mass Spectrometry; MALDI; Nonpolar Matrices; Charge-Transfer Ionization; Crude Oil; Mass Spectrometry. Includes bibliographical references.
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34

Yao, Mengmeng. "Determining Polymer Blend Surface Concentration Using Surface Layer Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (SL-MALDI-TOF MS)." University of Akron / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=akron1407941345.

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Hill, Jacob A. Hill. "SURFACE LAYER MATRIX-ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY (SL-MALDI-TOF MS) ANALYSIS OF POLYMER BLEND SURFACE COMPOSITION." University of Akron / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=akron1514479406062149.

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36

Hall, Bradley John. "Development of solid phase microextraction (SPME) and matrix assisted laser desorption ionization (MALDI) with quadrupole ion trap mass spectrometry for analytical applications /." Digital version accessible at:, 1998. http://wwwlib.umi.com/cr/utexas/main.

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37

Navare, Arti T. "Development of high-sensitivity atmospheric pressure (ap) matrix-assisted laser desorption/ionization (maldi) and open air ionization techniques for the analysis of biomolecules by mass spectrometry." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/33942.

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Matrix-assisted laser desorption/ionization (MALDI) has been celebrated as a soft ionization method for analyzing very diverse biological species including large proteins, peptides, carbohydrates, lipids and metabolites. The fact that MALDI is tolerant to salts and buffers and that it mostly produces singly charged ions from intact biomolecules is considered highly advantageous over electrospray ionization (ESI). Almost two decades after the introduction of vacuum MALDI, the technique was successfully implemented under atmospheric pressure (AP) conditions by Laiko and co-workers. Some of the most salient advantages of AP-MALDI over vacuum MALDI are its ability to generate intact ions from labile species with minimal fragmentation due to collisional cooling under AP, the ability of performing MSn experiments, and its exchangeability with other ion sources. However, AP-MALDI suffers from limited sensitivity due to low ion transmission efficiency under AP conditions. Because sensitivity is a function of the sample pretreatment method of choice, both preconcentration and selective sample fractionation can be used during the initial stages of the analytical pipeline to improve detectability. To that end, the first part of the work presented in this thesis is aimed at investigating various approaches to improve the sensitivity of AP-MALDI for mass spectrometric analysis of biomolecules. Chapter 1 reviews the history of laser desorption ionization (LDI), presenting salient features of vacuum MALDI and AP-MALDI, and concludes with a brief overview of leading ambient ionization techniques, such as Direct Analysis in Real Time (DART) ionization. Chapter 2 presents an investigation of an on chip sample preconcentration approach coupled to AP-MALDI for high-sensitivity analysis of neuropeptides extracted from Aedes aegypti mosquito heads. The theme of exploring efficient and reproducible purification methods for complex biosamples is continued in Chapter 3, where an evaluation of new on-tip solid-phase extraction (SPE) micro columns with various functional groups is presented. A second approach for enhancing AP-MALDI sensitivity by constructing a new pneumatically-assisted (PA) AP-MALDI ion source is presented in Chapter 4, where various factors affecting the performance of this device are investigated. Chapter 5 describes work involving the evaluation of DART ionization as a high-throughput method for the detection and identification of small terpene molecules central to the Aedes aegypti mosquito lifecycle.
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38

Schibur, Stephanie [Verfasser], Daniel [Akademischer Betreuer] Huster, and Klaus [Gutachter] Eschrich. "Qualitativer und quantitativer Nachweis von Bestandteilen der extrazellulären Matrix des Knorpels mittels MALDI-TOF MS / Stephanie Schibur ; Gutachter: Klaus Eschrich ; Betreuer: Daniel Huster." Leipzig : Universitätsbibliothek Leipzig, 2014. http://d-nb.info/1238600212/34.

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39

Kilburg, Arnaud. "Cristallisation du transporteur ABC BmrA de Bacillus subtilis : développement d’une nouvelle méthode de dosage des détergents par Matrix-Assisted Laser Desorption Ionization (MALDI)." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10116/document.

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Notre projet vise à déterminer la structure 3D du transporteur BmrA de Bacillus subtilis. La protéine a été purifiée dans six détergents différents. L'utilisation de foscholine 12, a conduit à cristalliser OmpF, une porine de la membrane externe d'E. coli. Nous montrons que les conditions de cristallisation influencent directement l'empilement cristallin d'OmpF. Le protocole de purification de BmrA, optimisé en utilisant du triton X100 à l'extraction puis un mélange β-D-dodecyl maltoside-cholate pour les étapes chromatographiques nous a permis d'obtenir à 4°C des cristaux, pour lesquels nous avons vérifié qu'ils sont constitués de BmrA. Ces cristaux ont permis d'obtenir un jeu complet jusqu'à 7 Å. Ces données de diffraction constituent une avancée significative pour résoudre à court terme la structure 3D de BmrA. Nous avons développé une nouvelle méthode de dosage des détergents qui est basée sur la détermination par spectrométrie de masse de type MALDI du ratio d'isotopes deutérés/ protonés. La méthode a été validée avec la FC12, le DDM, le β-OG, le LMNG, le CHAPS, le cholate et des détergents calix[4]aréniques, en mesurant la concentration de ces détergents dans différentes conditions d'extraction/purification, de concentration, dialyse et gel filtration, de différentes protéines membranaires. Cette méthode nous a permis (i) d'estimer la taille de la ceinture de détergent associée à BmrA et d'autres protéines membranaires (ii) de moduler cette taille en fonction de mélange de détergents et (iii) d'apporter des informations sur le comportement des complexes protéine-détergent
Our project aims to determine the 3D structure of BmrA from Bacillus subtilis. The protein was purified in six different detergents. Using foscholine 12, led to crystallize OmpF, an outer membrane porin of E. coli. We show that the crystallization conditions directly influence the crystal packing of OmpF. The BmrA purification protocol optimized by using Triton X100 at the extraction and a mixture β-D-dodecyl-maltoside cholate for chromatographic steps allowed us to get to 4°C crystals, for which we verified they consist of BmrA. These crystals have yielded full data to 7 Å. These diffraction data are a significant advance in the short term to resolve the 3D structure of BmrA. We have developed a new detergents dosage assay which is based on the determination by MALDI-type mass ratio of deuterated isotopes / protonated. The method was validated with the FC12, the DDM, the β-OG, the LMNG, CHAPS, cholate detergents and calix [4] aréniques by measuring the concentration of these detergents in different conditions of extraction/ purification, concentration, dialysis and gel filtration, of different membrane proteins. This method allowed us (i) to estimate the size of the detergent belt associated to BmrA and other membrane proteins (ii) to modulate this size in terms of the detergent mixture and (iii) to provide information on the behavior of complex protein-detergent
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40

Holcomb, April M. Owens Kevin G. "Investigation into the ionization mechanism occurring in matrix assisted laser desorption ionization and factors affecting ion flight time in MALDI time-of-flight mass spectrometry /." Philadelphia, Pa. : Drexel University, 2009. http://hdl.handle.net/1860/3161.

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41

Åminne, Ann. "Evaluation of preanalytic methods in order to shorten the processing time before identification of fungal microorganisms by the MALDI-TOF MS." Thesis, Uppsala universitet, Institutionen för kvinnors och barns hälsa, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-255132.

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Identification of fungi is based on macroscopic observations of morphology and microscopic characteristics. These conventional methods are time-consuming and requires expert knowledge. For the past years Matrix-assisted laser desorption ionization-time of flight mass spectrometry has been used for routine bacterial identification in clinical laboratories but not yet in the same extension for fungi. In this study three preanalytic preparation methods for fungi were evaluated in order to shorten the processing time in routine laboratory performance. Clinically relevant strains (n=18) of molds and dermatophytes were cultivated on agar plates and prepared according to the different preparation methods for protein extraction. Each strain was analyzed in quadruplicate by the MALDI Biotyper and the database Filamentous Fungi Library 1.0. The results showed that the genus and species identification rates of the least time-consuming direct extraction method were 33% and 11% respectively. Using the formic acid extraction method, the genus and species identification rates were 83% and 44%, respectively. For the longest sample preparation method, liquid media culturing before formic acid extraction, successfully identified all strains except one, which resulted in an identification rate of 94% and 78% respectively. This study shows that preparing samples in cultured liquid media MADLI-TOF MS effectively identified fungal strains to both genus- and species-level. This method was however too time-consuming and cumbersome to be recommended as a replacement to the conventional method. Future studies should be aimed at expanding the reference library and making the direct extraction method more reproducible in terms of obtaining more reliable identification rates.
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42

Júnior, João Nobrega de Almeida. "Padronização da espectrometria de massa MALDI-TOF para identificação de cepas de Trichosporon spp. de importância médica." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/5/5144/tde-05052014-110905/.

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O gênero Trichosporon é composto por leveduras artrosporadas do Filo Basidiomycota e é conhecido agente de infecção fúngica invasiva (IFI) em pacientes imunodeprimidos ou com outros fatores de risco. Em pacientes onco-hematológicos é a principal levedura responsável por IFI depois do gênero Candida. Entre as espécies responsáveis por infecções no homem encontram-se: T. asahii, T. inkin, T. mucoides, T. dermatis, T. jirovecii, T. ovoides, T. cutaneum, T. montevideense, T. domesticum, T. asteroides, T. coremiiforme, T. faecale, T. dohaense, T. lactis, T. japonicum. A tecnologia de identificação de fungos por espectrometria de massa (SM) MALDI-TOF ainda carece de padronização para identificação de fungos do gênero Trichosporon, mas a literatura mostra resultados encorajadores. O objetivo deste estudo é padronizar a técnica de espectrometria de massa MALDI-TOF para a identificação das espécies do gênero Trichosporon de importância médica. O estudo foi realizado em cooperação entre a Divisão de Laboratório Central do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (DLC, HC-FMUSP), Instituto de Medicina Tropical da USP (IMT-USP), Instituto Adolfo Lutz (IAL) e Laboratoire de Parasitologie-Mycologie do Hospital Saint Antoine de Paris, vinculado ao grupo de pesquisa INSERM/UPMC UMR S945 \"Immunité et Infection\" Faculté de Medecine et Université Pierre et Marie Curie de Paris. Noventa e três cepas/isolados foram analisado(a)s, sendo dezenove cepas de referência adquiridas junto à coleção holandesa Centraalbureau Schimmelcultures (CBS), 19 isolados do HC-FMUSP e IAL, e 55 isolados de diferentes hospitais franceses. A identificação molecular foi realizada através do sequenciamento da região IGS1 do rDNA e foi considerada como método de referência. O protocolo de extração de proteínas foi estabelecido através da comparação do desempenho de três metodologias (Bruker®, Cassagne et al., Sendid et al.). Os espectros de massa foram obtidos no laboratório de bacteriologia do Hospital Saint Antoine de Paris através do aparelho Microflex LT®. A interpretação dos resultados qualitativos e quantitativos (logscore) foi realizada através do Software Biotyper 3.0®. O desempenho de identificação do banco de espectros de referência Biotyper 3.0® foi comparado a outros cinco bancos criados a partir de espectros de referência (ERs) derivados de 18 cepas de referência CBS, sete isolados clínicos e 11 ERs do banco Biotyper 3.0. O protocolo de extração de proteínas descrito por Sendid et al. foi escolhido como protocolo de referência pois os espectros produzidos tiveram logscore superiores àqueles obtidos através do método do fabricante. O banco de ERs Biotyper 3.0® apresentou 32,3% de identificações corretas das espécies, sendo que o banco de ERs in house (número 5, constituído cepas CBS e isolados clínicos) apresentou 98,5% de identificações de espécies. Espectros de referência do banco de dados Biotyper 3.0® foram submetidos à identificação com a utilização dos ERs criados a partir de cepas CBS e isolados clínicos e foram evidenciados com erros de identificação: T. mucoides (2), T. ovoides (1) e T. cutaneum (2). Após padronização do protocolo de extração e criação de banco de ERs com cepas CBS e isolados clínicos caracterizados pelo sequenciamento da região IGS, a SM por MALDI-TOF apresentou-se como potente uma ferramenta para a identificação de fungos do gênero Trichosporon. O banco de ERs Biotyper 3.0® apresentou um fraco desempenho, relacionado a ERs que foram criados a partir de cepas mal identificadas
Trichosporon spp. are arthrospored yeasts from the Filum Basidiomycota that are known to produce invasive fungal infection (IFI) in patients with immunosupression or other risk factors. After Candida, Trichosporon is the second genus of yeasts responsible for IFI in patients with onco-hematological diseases. The most important species related to human infection are: T. asahii, T. inkin, T. mucoides, T. dermatis, T. jirovecii, T. ovoides, T. cutaneum, T. montevideense, T. domesticum, T. asteroides, T. coremiiforme, T. faecale, T. dohaense, T. lactis, T. japonicum. The technology of mass spectrometry (MS) for identification of Trichosporon species has not yet been standardized. However, preliminary promising results can be found in the literature. The objective of this study is to analyse and validate MS MALDI-TOF for the identification of Trichosporon species of medical relevance. This was a multicentric study with collaboration from the Central Laboratory Section from Clinics Hospital of the Medical School from the University of São Paulo (DLC-HCFMUSP), Tropical Medicine Institute from the University of São Paulo (IMT-USP), Instituto Adolfo Lutz (IAL) and Laboratoire de Parasitologie-Mycologie from the Hospital Saint Antoine of Paris and INSERM/UPMC UMR S945 \"Immunité et Infection\", Faculté de Medecine et Université Pierre et Marie Curie of Paris. Ninety three strains/isolates belonging to sixteen Trichosporon species were analysed. Nineteen were purchased from Centraalbureau Schimmelcultures (CBS) yeast collection, 19 belonged to HC-FMUSP and IAL collections, 55 belonged to different French collections. The reference identification method was the IGS1 rDNA sequencing. A protein extraction protocol was first established after comparing the performance of three different methodologies (Bruker(TM), Cassagne et al., Sendid et al.). The mass spectra were obtained through a Microflex LT(TM) mass spectrometer located at the bacteriology laboratory from Saint Antoine Hospital, Paris. Mass spectra, qualitative and quantitative results were produced through the software Biotyper 3.0(TM). The performance of the original main spectrum (MSP) library was compared to other 5 in house libraries built with the combination of MSPs derived from CBS strains (18), clinical strains (7) or (Bruker Daltonics/BD, Germany/USA) (11). The extraction protocol described by Sendid et al. showed better performance when compared to the manufacturer\'s one and was chosen for the subsequent extractions. Among the 6 different reference spectra databases tested, a specific one composed of 18 reference strains plus 7 clinical isolates (database 5) allowed the correct identification of 66 amongst 67 clinical isolates (98,5%). Biotyper 3.0 library produced only 32,3% of correct identifications. Biotyper\'s MSPs were submitted to cross-identification with MSPs derived from CBS strains and clinical isolates and misidentified original MSPs were identified: T. mucoides (2), T. ovoides (1) e T. cutaneum (2). While until now less widely applied to basidiomycetous fungi, MALDI-TOF appears to be a valuable tool for identifying clinical Trichosporon isolates at the species level. The MSP library Biotyper 3.0 showed a poorer performance which was due to misidentified strains utilized as reference for the MSPs
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43

Rashed, Alia [Verfasser], and Guido [Akademischer Betreuer] Sauter. "Anwendung von MALDI (matrix-assisted laser desorption/ionization) Imaging zur Identifikation von relevanten biologischen Veränderungen auf TMA (Tissue Microarrays) und Großschnitten / Alia Rashed. Betreuer: Guido Sauter." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2014. http://d-nb.info/1054422710/34.

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44

Chen, Ping. "Applications of Chemometric Algorithms to Ion Mobility Spectrometry and Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry." Ohio University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1206019463.

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45

Thenstedt, Niklas. "Detektion av hydrolyserad β-laktamantibiotika i plasma med Matrix-Assisted Laser Desorption Ionization – Time of Flight Mass Spectrometry och Liquid Chromatography tandem Mass Spectrometry." Thesis, Örebro universitet, Institutionen för hälsovetenskaper, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-84594.

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Introduktion Antibiotikaresistens är ett globalt växande problem. Till gruppen β-laktamantibiotika hör piperacillin-tazobaktam och cefotaxim som båda verkar genom att försvaga cellväggen med kovalenta bindningar till peptidoglykanlagret som lyserar cellen. E. coli och K. pneumoniae tillhör gruppen Enterobacteriaceae, som är en del av den humana tarmfloran och ofta förekommande vid urinvägsinfektion och sepsis. Utvidgat Spektrum β-Laktamas (ESBL) är ett enzym som finns hos Enterobacteriaceae och som hydrolyserar β-laktamantibiotika. Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) är en kvalitativ analysteknik för detektion av kemiska föreningar i avseende på massa och laddning. Kännedom om antibiotikametaboliters molekylvikt vid hydrolys möjliggör detektion. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) är en högsensitiv kvantifieringsmetod som separerar molekyler i avseende på polaritet för vidare detektion i avseende på massa och laddning. Syfte Syftet med denna studie var att vidareutveckla en snabb och effektiv metod för att påvisa nedbrytning av piperacillin-tazobaktam och cefotaxim i blodplasma med LC-MS/MS. Material och Metod Tiofaldigt sjunkande koncentrationer av piperacillin-tazobaktam från 2000 till 2 µg/ml, och cefotaxim med koncentrationerna 500 till 0,5 µg/ml analyserades med MALDI-TOF MS, dels intakt men även med bakterierna E. coli och K. pneumoniae med uttryck av olika resistensmekanismer. Vid optimerade koncentrationer spikades plasmaprover med nedbrutet antibiotika som sedan kvantifierades med LC-MS/MS. Resultat Lägsta detektionsgräns med MALDI-TOF MS för intakt och hydrolyserat piperacillin-tazobaktam var 20/2,5 µg/ml. För cefotaxim var lägsta gränsen 5 µg/ml. Med kliniskt relevanta blodkoncentrationer gick hydrolys inte att detektera för. Med tre bakteriekolonier/50 µl kunde dock hydrolys detekteras och kvantifieras med LC-MS/MS. Slutsats Detektion av β-laktamantibiotika är möjligt med både MALDI-TOF MS och LC-MS/MS. För att påvisa hydrolys krävdes större mängder bakterier än förväntat med LC-MS/MS.
Introduction Antibiotic resistance is a global growing problem. Piperacillin-tazobactam and cefotaxime are parts of the group β-lactam antibiotics. The common feature is to inhibit the cell wall synthesis by covalent bindings to the peptidoglycan layer and thereby causing lysis of the bacterial cell. E. coli and K. pneumoniae are members of the Enterobacteriaceae which is a part of the human normal flora but also are commonly associated with urinary tract infections which sometimes develops into to sepsis. Extended Spectrum β-Lactamases (ESBLs) are enzymes with hydrolytic abilities acting on β-lactam antibiotics, expressed by Enterobacteriaceae. The qualitative, Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) can be used to detect chemical compounds in the ratio of mass to charge in accordance to their molecular weight. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) is a highly sensitive two-step method of quantification which first separate molecules by their polarity attraction force and then by the ratio of mass to charge. Aim The aim of this study was to develop a fast and efficient method to determine degradation of piperacillin-tazobactam and cefotaxime in blood plasma by LC-MS/MS. Method Tenfold dilution of piperacillin-tazobactam in concentrations of 2000 to 2 µg/ml, and cefotaxime in concentrations of 500 to 0,5 µg/ml where analyzed by MALDI-TOF MS, intact and also with the bacteria E. coli and K. pneumoniae with different expression of antibiotic resistance. Optimized concentrations where fixed in blood plasma and then quantified by LC-MS/MS. Result The detection limit by using MALDI TOF MS of hydrolyzed as well as non-hydrolyzed piperacillin-tazobactam was 20/2,5 µg/ml. The detection limit in cefotaxime was 5 µg/ml. Hydrolysis could not be detected in clinically fixed blood concentrations. Detection and quantification of hydrolysis by LC-MS/MS was possible in a concentration of three bacteria colonies/50 µl. Conclusion It is possible to detect hydrolysis in both MALDI TOF MS and LC-MS/MS. A larger amount of bacteria than expected was needed to demonstrate hydrolysis In LC-MS/MS.
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46

Andrade, Laíse de Oliveira. "Métodos rápidos para identificação microbiana aplicados ao monitoramento ambiental de salas limpas: ênfase na tecnologia MALDI-TOF." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/9/9139/tde-26102017-114152/.

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A espectrometria de massas baseada na tecnologia MALDI-TOF (do inglês, matrix-assisted laser desorption ionization-time of flight) (MALDI-TOF MS) tem sido cada vez mais incorporada à rotina de identificações microbiológicas nos laboratórios farmacêuticos de controle de qualidade, principalmente para as atividades do Programa de Monitoramento Ambiental de Salas Limpas. Isso porque o longo tempo necessário para a obtenção dos resultados por meio de métodos convencionais tem incentivado a procura por técnicas que permitam métodos rápidos. O objetivo deste trabalho foi avaliar a adequação da técnica MALDI-TOF MS para a identificação de bactérias isoladas do ambiente de salas limpas utilizadas em algumas etapas da produção de uma vacina viral. Treze espécies bacterianas conhecidas, normalmente isoladas das salas limpas estudadas, e cinco cepas ATCC foram identificadas pela técnica MALDI-TOF MS e por uma técnica bioquímica (BBL Crystal®). O desempenho da técnica MALDI-TOF MS foi superior ao da técnica bioquímica na identificação correta das espécies bacterianas (88,89% e 38,89%, respectivamente) e produziu menos identificações não confiáveis (5,55% e 22,22%, respectivamente). Os resultados evidenciaram que a técnica MALDI-TOF MS pode ser implementada para identificação rotineira de bactérias em um laboratório de controle de qualidade farmacêutico. Entretanto, a dependência de bases de dados exige estudos adicionais de isolados não identificados e, se apropriado, a adição destes a uma base de dados interna. O aperfeiçoamento de métodos de identificação microbiana é muito relevante no contexto de salas limpas, pois permitem ações corretivas e proativas essenciais para garantir a segurança microbiológica do processamento asséptico.
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been increasingly introduced in routine microbiological identifications of pharmaceutical quality control laboratories, mainly for the activities of the Environmental Monitoring Program of Clean Rooms. The long time needed to obtain the results through conventional methods has stimulated the search for techniques that allow rapid methods, as MALDI-TOF MS. Thus, the objective of this work was to evaluate the suitability of the MALDI-TOF MS technique for the identification of bacteria isolated from the environment of clean rooms used in some stages of the production of a viral vaccine. Thirteen bacterial species commonly isolated from clean rooms studied and five strains ATCC were identified by MALDI-TOF MS technique and by a biochemical technique (BBL Crystal® System). Performance of MALDI-TOF MS was better than biochemical technique for correct species identifications (88.89% and 38.89%, respectively) and produced fewer unreliable identifications (5.55% and 22.22%, respectively). MALDI-TOF MS can be implemented for routine identification of bacteria in a pharmaceutical quality control laboratory. However, as a database-dependent system, maybe some isolated not identified by this technique must be additionally studied and, if appropriate, added to an in-house database.
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Emanuele, Vincent A. II. "Advancements in high throughput protein profiling using surface enhanced laser desorption/ionization time of flight mass spectrometry." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/37287.

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Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI)is one of several proteomics technologies that can be used in biomarker discovery studies. Such studies often have the goal of finding protein markers that predict early onset of cancers such as cervical cancer. The reproducibility of SELDI has been shown to be an issue in the literature. There are numerous sources of error in a SELDI experiment starting with sample collection from patients to the signal processing steps used to estimate the protein mass and abundance values present in a sample. This dissertation is concerned with all aspects of signal processing related to SELDI's use in biomarker discovery projects. In chapter 2, we perform a comprehensive study of the most popular preprocessing algorithms available. Next, in chapter 3, we study the basic statistics of SELDI data acquisition. From here, we propose a quadratic variance measurement model for buffer+matrix only spectra. This model leads us to develop a modified Antoniadis-Sapatinas wavelet denoising algorithm that demonstrates superior performance when compared to MassSpecWavelet, one of the leading techniques for preprocessing SELDI data. In chapter 4, we show that the quadratic variance model 1) extends to real pooled cervical mucus QC data from a clinical study, 2) predicts behavior and reproducibility of peak heights, and 3) finds four times as many reproducible peaks as the vendor-supplied preprocessing programs. The quadratic variance measurement model for SELDI data is fundamental and promises to lead to improved techniques for analyzing the data from clinical studies using this instrument.
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48

Watson, R. Craig Jr. "Laser-Ionization Time-of-Flight Mass Spectrometry of High Molecular Mass Inorganic Complexes." Thesis, Virginia Tech, 1997. http://hdl.handle.net/10919/35554.

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Laser-Ionization Time-of-Flight Mass Spectrometry (LI-TOF-MS) is a sophisticated tool for the molecular-weight determination and structural characterization of a variety of molecules. Advances in instrumentation and ionization methods have recently expanded its role in the analysis of high-mass analytes. Large multimetallic complexes, which are efficient solar-energy converters, rely heavily on their chemical structure for optimum operation. Molecular mass determinations of these multimetallic complexes have been problematic due to their lability and high molecular weights.

This thesis describes the characterization of a LI-TOF-MS instrument and confirmation of theoretical time-of-flight mass-separation principles. Several test cases demonstrate the instrument's proper operation and calibration for a wide mass range of analytes. Mass spectral results of three organometallic compounds: i. [Ir(dpp)2Cl2](PF6), ii. {[(bpy)2Ru(dpp)]2IrCl2}(PF6)5, and iii. {[(bpy)2Ru(dpp)]2RuCl2}(PF6)5 under a variety of laser ionization and sample preparation conditions are compared. A complete structural characterization of the monometallic complex, [Ir(dpp)2Cl2](PF6), is presented. The two trimetallic analytes fragmented easily, but significant components of the molecules are successfully identified. After optimizing the ionization and analytical procedure, LI-TOF-MS proved useful in the analysis of high molecular mass metal complexes.
Master of Science

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49

Liu, Jun. "Integration of microchip-capillary electrophoresis separation with matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) ; and, Quantitative determination of oligosaccharide expression levels in individual cells /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2002. http://uclibs.org/PID/11984.

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50

Gibb, Sebastian. "Entwicklung einer flexiblen bioinformatischen Plattform zur Analyse von Massenspektrometriedaten." Doctoral thesis, Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-178678.

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Sowohl in der Klinischen Labormedizin, der Klinischen Mikrobiologie als auch in der Pathologie ist die Massenspektrometrie (MS) ein bedeutender Bestandteil der Diagnostik geworden. Der Fortschritt in der Gerätetechnik ermöglicht in kurzer Zeit viele, hochaufgelöste Spektren zu generieren. Diese Informationsvielfalt macht die manuelle Auswertung durch den Anwender sehr kompliziert bis unmöglich. Aus diesem Grund ist die Unterstützung durch bioinformatische Programme notwendig. Für die Reproduzierbarkeit der Ergebnisse und die Qualitätskontrolle ist es essentiell, dass die verwendeten Algorithmen transparent und die Programme als Open Source Software (OSS) frei verfügbar sind (Aebersold and Mann, 2003). Das Ziel dieser Arbeit war die Entwicklung von MALDIquant, einer unter der GNU General Public License (GPL) stehenden, flexiblen OSS, die für die o.g. Anwendungsbereiche modernste Algorithmen für die komplette Analyse bietet und in der freien Programmiersprache R (R Core Team, 2014) geschrieben ist. Im Zusammenspiel mit dem dazugehörigen Paket MALDIquantForeign ist MALDIquant in der Lage die üblichen Dateiformate der verschiedenen MS-Geräte zu verarbeiten. Dadurch ist MALDIquant hersteller- und geräteunabhängig und eignet sich nicht nur für MALDI/TOF, sondern für alle zweidimensionalen MS-Daten. Angefangen vom Datenimport über die Prozessierung bis hin zur Analyse der Spektren bietet MALDIquant eine komplette Analyse-Pipeline und implementiert state-of-the-art Methoden. Neben weit verbreiteten Verfahren zur Baseline Correction und Peak Detection zeichnet sich MALDIquant besonders durch ein hervorragendes Peak Alignment aus. Dieses ist sehr genau und aufgrund des Fokus auf die Peaks schneller als die meisten anderen Verfahren und weitestgehend unabhängig von der Qualität der Intensitätenkalibrierung. Eine weitere Stärke von MALDIquant ist die Möglichkeit, eigene Algorithmen zu integrieren, sowie den Ablauf der Analyse den individuellen Bedürfnissen anzupassen. In der beispielhaften Analyse der Daten von Fiedler et al. (2009) konnten durch MALDIquant Peaks gefunden werden, die Patienten mit Pankreaskarzinom von nicht erkrankten Probanden unterscheiden. Einige dieser Peaks wurden bereits in anderen Publikationen beschrieben. Neben diesem Beispiel hat MALDIquant seine Nützlichkeit bereits in verschiedenen Anwendungsbereichen und Publikationen bewiesen, wie etwa in Ouedraogo et al. (2013) oder Jung et al. (2014).
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