In the assessment of the environment pollution level, bio indicators of vegetable or animal origin are often used. Bio indicators include also needles and moss. The samples of moss and needles taken in different locations in the Czech Republic were examined to find out the presence of xenobiotics of polychlorine biphenyls and polybromide diphenylethers types. Selected analytes have been extracted from the matrix by hexan. Extracts have been refined using column chromatography on mixed florisil/silicagel sorbent. To analysis of selected compounds, GC/ECD method has been chosen. Based on our results a comparison of the contamination level in individual locations was enabled.

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In dieser Arbeit werden hochgeladene, mit einer Electron Beam Ion Trap produzierte Ionen für die Erforschung des Elektroneneinfangs von Oberflächen und Gasen eingesetzt. Die Untersuchungen mit Gastargets konzentrieren sich auf die Energieabhängigkeit der Verteilung der K-Schalen-Röntgenstrahlen, die nach Elektroneneinfang in Rydberg-Zustände von Ar-17+ und Ar-18+ Ionen am Ende einer Kaskade von Elektronenübergängen entstehen. Die Ionen werden von der Ionenquelle mit einer Energie von 2 keV/u extrahiert, ladungsselektiert und anschließend bis auf 5 eV/u abgebremst, um dann mit einem Argon Gastarget zu interagieren. Für abnehmende Stoßenergien wird eine Verschiebung des Elektroneneinfangs in Zustände mit niedrigen Drehumpulsquantenzahlen beobachtet. Zum Vergleich wird auch die K-Schalen-Röntgenstrahlung auf Grund des Elektroneneinfangs bei Ar-17+ und Ar-18+ von dem Restgas in der Falle gemessen. Dabei wird eine Diskrepanz zu den Resultaten der Extraktionsversuche festgestellt. Mögliche Erklärungen werden diskutiert. In den Untersuchungen zum Elektroneneinfang von Oberflächen werden hochgeladene Ionen von der Ionenquelle mit Energien von 2 bis 3 keV/u extrahiert, ladungsselektiert und auf Targets gelenkt. Diese bestehen aus Siliziumnitridmembranen mit einer Vielzahl nanometergroßer Löcher, welche mittels eines fokussierten Ionenstrahls in Kombination mit ionenstrahlinduzierter Abscheidung dünner Filme erstellt werden. Es werden hierbei Lochdurchmesser von 50 bis 300 nm mit Formfaktoren von 1:5 bis 3:2 erreicht. Bei den hochgeladenen Ionen handelt es sich um Ar-16+ und Xe-44+. Nach dem Transport durch die Kapillare passieren die Ionen einen elektrostatischen Ladungstrenner und werden detektiert. Der Anteil des Elektroneneinfangs von den Wänden der Löcher ist weitaus geringer als Modellberechnungen vorhersagen. Die Resultate werden an Hand eines Kapillareffekts zur Ionenleitung diskutiert. / In this study highly charged ions produced in Electron Beam Ion Traps are used to investigate electron capture from surfaces and gases. The experiments with gas targets focus on spectroscopic measurements of the K-shell x-rays emitted at the end of radiative cascades following electron capture into Rydberg states of Ar-17+ and Ar-18+ ions as a function of collision energy. The ions are extracted from an Electron Beam Ion Trap at an energy of 2 keV/u, charge-selected and then decelerated down to 5 eV/u for interaction with an argon gas target. For decreasing collision energies a shift to electron capture into low orbital angular momentum capture states is observed. Comparative measurements of the K-shell x-ray emission following electron capture by Ar-17+ and Ar-18+ ions from background gas in the trap are made and a discrepancy in the results compared with those from the extraction experiments is found. Possible explanations are discussed. For the investigation of electron capture from surfaces, highly charged ions are extracted from an Electron Beam Ion Trap at energies of 2 to 3 keV/u, charge-selected and directed onto targets comprising arrays of nanoscale apertures in silicon nitride membranes. The highly charged ions implemented are Ar-16+ and Xe-44+ and the aperture targets are formed by focused ion beam drilling in combination with ion beam assisted thin film deposition, achieving hole diameters of 50 to 300 nm and aspect ratios of 1:5 to 3:2. After transport through the nanoscale apertures the ions pass through an electrostatic charge state analyzer and are detected. The percentage of electron capture from the aperture walls is found to be much lower than model predictions and the results are discussed in terms of a capillary guiding mechanism.

<p>In the growing field of proteomics identification of proteins by tandem mass spectrometry (MS/MS) is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein database. One problem with this approach is the false-positive identifications. MS-based proteomics experiments are further affected by a rather poor efficiency typical in the range of 10-15%, implicating that only a low percentage of acquired mass spectrometric data is significantly identified and assigned a peptide sequence.</p><p>In this thesis improvement in spectrum specificity is accomplished by using a combination of high-accuracy mass spectrometry and techniques that will yield complementary sequence information. Performing collision-activated dissociation (CAD) and electron capture dissociation (ECD) upon the same peptide ion will yield such complementary sequence information. Implementing this into a proteomics approach and showing the advantages of using complementary fragmentation techniques for improving peptide identification is shown. Furthermore, a novel database-independent score is introduced (S-score) based upon the maximum length of the peptide sequence tag derived from complementary use of CAD and ECD. The S-score can be used to separate poor quality spectra from good quality spectra. An-other aspect of the S-score is the development of the ‘reliable sequence tag’ which can be used to recover below threshold identifications and for a reliable backbone for de novo sequencing of peptides.</p><p>A novel proteomics-grade de novo sequencing algorithm has also been developed based upon the RST, which can retrieve peptide identification with the highest reliability (>95%). Furthermore, a novel software tool for unbiased identifications of any post-translational modifications present in a peptide sample is introduced (ModifiComb). Combining all the tools described in this thesis increases the identification specificity (>30 times), recovers false-negative identifications and increases the overall efficiency of proteomics experiements to above 40%. Currently one of the highest achieved in large-scale proteomics.</p>

In the growing field of proteomics identification of proteins by tandem mass spectrometry (MS/MS) is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein database. One problem with this approach is the false-positive identifications. MS-based proteomics experiments are further affected by a rather poor efficiency typical in the range of 10-15%, implicating that only a low percentage of acquired mass spectrometric data is significantly identified and assigned a peptide sequence. In this thesis improvement in spectrum specificity is accomplished by using a combination of high-accuracy mass spectrometry and techniques that will yield complementary sequence information. Performing collision-activated dissociation (CAD) and electron capture dissociation (ECD) upon the same peptide ion will yield such complementary sequence information. Implementing this into a proteomics approach and showing the advantages of using complementary fragmentation techniques for improving peptide identification is shown. Furthermore, a novel database-independent score is introduced (S-score) based upon the maximum length of the peptide sequence tag derived from complementary use of CAD and ECD. The S-score can be used to separate poor quality spectra from good quality spectra. An-other aspect of the S-score is the development of the ‘reliable sequence tag’ which can be used to recover below threshold identifications and for a reliable backbone for de novo sequencing of peptides. A novel proteomics-grade de novo sequencing algorithm has also been developed based upon the RST, which can retrieve peptide identification with the highest reliability (&gt;95%). Furthermore, a novel software tool for unbiased identifications of any post-translational modifications present in a peptide sample is introduced (ModifiComb). Combining all the tools described in this thesis increases the identification specificity (&gt;30 times), recovers false-negative identifications and increases the overall efficiency of proteomics experiements to above 40%. Currently one of the highest achieved in large-scale proteomics.

Advances in science and technology during the past decade have greatly enhanced the level of the structural investigation of macromolecules – peptides and proteins. Biological mass spectrometry has become one of the most precise and sensitive techniques in peptide and protein analysis. However, increasing demands of biotechnological applications require further progress to be made. In the present thesis the development and improvement of peptide and protein characterization methods and techniques based on ion-electron and ion-photon reactions in electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry are described. The focus is on the development of the electron capture dissociation method, recently discovered by the group of professor McLafferty, into a high rate, efficient tandem mass spectrometrical technique. The rate and reliability of the electron capture dissociation technique were greatly increased by implementation of low-energy pencil electron beam injection systems based on indirectly heated dispenser cathodes. Further implementation of a hollow electron beam injection system combined, in a single experimental configuration, two rapid fragmentation techniques, high rate electron capture dissociation and infrared multiphoton dissociation. Simultaneous and consecutive irradiations of trapped ions with electrons and photons extended the possibilities for ion activation/dissociation reaction schemes and lead to improved peptide and protein characterization. Using these improvements, high rate electron capture dissociation was employed in time-limited experiments, such as liquid chromatography–tandem mass spectrometry and capillary electrophoresis-tandem mass spectrometry. The analytical applications of the developed techniques have been demonstrated in top-down sequencing of peptides and proteins up to 29 kDa, improved sequencing of peptides with multiple disulfide bridges and secondary fragmentation (w-ion formation), as well as extended characterization of peptide mixtures separated by liquid chromatography and capillary electrophoresis. For instance, the dissociation of peptides resulting from enzymatic digestion of proteins provided complementary structural information on peptides and proteins, as well as their post-translational modifications.

As a result of increased terrorist activity around the world, the development of a canine training aid suitable for daily military operations is necessary to provide effective canine explosive detection. Since the use of sniffer dogs has proven to be a reliable resource for the rapid detection of explosive volatiles organic compounds, the present study evaluated the ability of the Human Scent Collection System (HSCS) device for the creation of training aids for plasticized / tagged explosives, nitroglycerin and TNT containing explosives, and smokeless powders for canine training purposes. Through canine field testing, it was demonstrated that volatiles dynamically collected from real explosive material provided a positive canine response showing the effectiveness of the HSCS in creating canine training aids that can be used immediately or up to several weeks (3) after collection under proper storage conditions. These reliable non-hazardous training aids allow its use in areas where real explosive material aids are not practical and/or available.

Various animal or vegetable origin bio-indicators are used for the assessment of the environmental contamination. The wild animals were chosen for monitoring of xenobiotic based organohalogen compounds. The district health facility staff collected the samples of wild boars in the territory of Central Bohemia. The controlled substances were isolated from the matrix by an extraction. The extraction was made by a petrolether and then it was purified by a column chromatography. A final cleansing of the extract was made by an acid hydrolysis. The determination of the selected analytes was finished by the method of gas chromatography with an electron capture detector. The results gave us basic information about the wild boar contamination of organohalogen pollutants.

Beryllium-7 (Be-7) only decays by electron capture into lithium-7 (Li-7) with a half life of 53 days. We study the effect of ionization on this decay rate. We do so by trapping a Be-7 ion plasma in a cylindrical Malmberg-Penning trap and measuring Be-7 and Li-7 concentrations as functions of time by using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). We have simulated these signals in a 2-dimensional electrostatic particle-in-cell (PIC) code. The two spectrum peaks merge at high ion densities whereas at low ion densities they can be resolved. The merged peak shifts linearly according to the relative abundances of these species. We have also simulated singly-ionized beryllium-7 hydride (BeH+) and Li-7 ion plasmas at high densities. These two separate peaks shift according to their relative abundances. We describe an analytical model that explains how these peaks shift.

This research paper fulfills the requirements of Geography 4C6. / This paper is an introductory study on the ability of a detention pond to reduce pollutant loading to a receiving water body. Three forms of water pollution are analysed in this study, trace metal (V, Ti and Mn in the water and on suspended solids and bottom sediments), organic and bacterial (bacterial indicators of fecal coliform and fecal streptococci are utilized) pollutants. Each pollutant type requires a different form of analysis to obtain concentrations for targeted pollutants. V, Ti and Mn concentrations were obtained from Instrumental Neutron Activation Analysis (INAA), organic concentrations were acquired by Electron Capture Gas Chromatography (ECGC) and bacterial concentrations were obtained from various laboratory techniques performed by technicians in the Microbiology Lab at McMaster University and in the Provincial Health Laboratories in Hamilton, Ontario. Suspended solid concentration are also analysed to determine the pond's effectiveness in reducing suspended solids load and thus the pollutants they carry. The Storm Water Management Model was used to estimate total pollutant loading into the pond via a combined sewer overflow (CSO). The pollutant concentrations obtained were analysed spatially through the sampling network and temporally between sampled dry and wet weather periods. The result of this study has led to the disturbing conclusion that the detention pond appears to have little or no effect on enhancing water quality. / Thesis / Bachelor of Science (BSc)