The resistance of established medicines is rapidly increasing while the rate of discovery of new drugs and treatments have not increases during the last decades (Spiro et al. 2008). Systems pharmacology can be used to find new combinations or concentrations of established drugs to find new treatments faster (Borisy et al. 2003). A recent study aimed to use high resolution Liquid chromatography–mass spectrometry (LC-MS) for in vitro systems pharmacology, but encountered problems with unwanted variability and batch effects(Herman et al. 2017). This thesis builds on this work by improving the pipeline and comparing alternative methods and evaluating used methods. The evaluation of methods indicated that the data quality was often not improved substantially by complex methods and pipelines. Instead simpler methods such as binning for feature extraction performed best. In-fact many of the preprocessing method commonly used proved to have negative or neglect-able effects on resulting data quality. Finally the recently introduced Optimal Orthonormal System for Discriminant Analysis (OOS-DA) for batch removal was found to be a good alternative to the more complex Combat method.

Platelets are important for the healing of damaged blood vessels since they have an importantpart to play in the coagulation process. At the same time, the blood must be kept fluid and notcoagulate at the wrong time. Therefore there are factors that effect the aggregation of plateletsin a positive or a negative way. Previous investigations have shown that platelets during stirring conditions produce reactiveoxygen species (ROS) that weaken the inhibiting effect of nitric oxides (NO) on platelets andthat the drug Dexamethasone (Dex) can reduce the ROS-production. The aim of this project was to investigate if glucocorticoids, in this case Dexamethasone,could restore the inhibiting effect of NO on platelets and if there was any decrease in ROS-production. The result of the ROS-measurements showed a great variance and it was difficult to draw anyconclusions from them, but a clear decrease in ROS, as previous reported, was not shown. In the aggregation experiments the inhibiting effect of NO was observed through the drug S-nitroso-N-acetylpenicillamine (SNAP), a NO-donator. From the aggregation experiments, the result seemed to be that SNAP during longerincubation time lost its inhibiting effect, probably because the cells become desensitized.With superoxid dismutase (SOD), the effect of SNAP increased, both in the experiment withlonger and shorter incubation times. Dex seemed to reinforce the aggregation in relation toboth SOD and SNAP. To understand this relation further, more investigations must be done.Another interesting experiment would be to do combinations of experiments monitoring bothaggregation and ROS-production at the same time. / Trombocyterna, blodplättarna i blodet, är livsviktiga för att människor inte ska förblöda vid enskada. Samtidigt måste blodet hållas flytande och inte koagulera i onödan och därför finns deti kroppen en mängd faktorer som verkar pro- eller antiaggregerande. Tidigare undersökningar har visat på att trombocyter har en omrörningsberoendesyreradikalproduktion (ROS) som försvagar kväveoxids (NO) antiaggregerande effekt och attläkemedlet Dexametason (Dex) kan minska denna produktion. Detta projekt syftade till att ytterligare studera om glukokortikoider, i detta fall Dexametason,kunde återställa NO:s effekt på trombocyterna och om de i någon grad minskaderadikalproduktionen. Resultatet av ROS-mätningarna blev väldigt varierande och svårtolkade och några säkraslutsatser kunde inte dras, men en tydlig minskning i produktionen som tidigare observeratskunde inte upptäckas. I aggregationsförsöken observerades NO:s inhibitoriska verkan genomS-nitroso-N-acetylpenicillamine (SNAP), en NO-donator.Resultaten tyder på att SNAP under en längre inkuberingstid tappar sin inhiberande förmågapå trombocyterna, vilket förmodligen beror på att cellerna desensibiliseras.Superoxiddismutas (SOD) verkar ha en förstärkande effekt på SNAP oavsett ominkuberingstiden innan dosresponstillsats av trombin är lång eller kort, medan Dex tenderaratt förstärka aggregeringen både i förhållande till SNAP och SOD. För att få mer klarhet omdessa resultat är korrekta måste fler upprepningar göras och dessutom borde man genomförakombinationsförsök där man samtidigt övervakar ROS-produktion och aggregering.

Advancements in the field of modified messenger RNA (mRNA) has led to new ventures in the pharmaceutical industry. However, new drug products demand new analytical methods to ensure the efficacy and purity of the drug. Capillary gel electrophoresis (CGE) with UV detection shows great potential for separation of mRNA samples due to the equal mass-to-charge ratio of mRNA and the flexible parameters of the CGE methods. This thesis investigates the optimal parameters of the capillary electrophoresis method, sample treatment procedure and sieving medium composition for enhanced shortmers separation of mRNA by CGE analysis. An RNA ladder with 100-1000 nucleotides and EPO mRNA with 900 nucleotides were used as model compounds. The effect of capillary dimensions and separation temperature on the resolution of the RNA peaks was established through comparative experiments. Sample treatment processes were evaluated to achieve an optimal conformation of the mRNA for CGE analysis. By heating the mRNA sample for 15 min at 80°C all multimers were seemingly eradicated. Moreover, it was found that addition of 4 M of urea to mRNA sample before heating resulted in improved peak shape. A sieving medium consisting of a mix of the two polymers polyvinylpyrrolidine (PVP) and hydroxyethyl cellulose (HEC) proved to have beneficial qualities for separation. The addition of sucrose as viscosity modifier in the sieving medium surprisingly further enhanced the resolution. Moreover, during the project a heavy wash was established which drastically improved repeatability of the analyses through more efficient regeneration of the capillary. ISSN:

Ultra-high performance liquid chromatography (UHPLC) provides a considerable increase in throughput compared to HPLC and a reduced solvent consumption. The implementation of UHPLC in pharmaceutical analysis, e.g. quality control, has accelerated in recent years and there is currently a mix of HPLC and UHPLC instrumentation within pharmaceutical companies. There are, however, technical and regulatory challenges converting a HPLC method to UHPLC making it difficult to take full advantage of UHPLC in regulatory-focused applications like quality control in pharmaceutical production. Using chromatographic modelling and fundamental theory, this thesis investigated method conversion between HPLC and UHPLC. It reports on the influence of temperature gradients due to viscous heating, pressure effects and stationary phase properties on the separation performance. It also presents a regulatory concept for less regulatory interaction for minor changes to approved methods to support efficient life cycle management. The higher pressure in UHPLC gave a retention increase of up to 40% as compared to conventional HPLC while viscous heating, instead, reduced retention and the net result was very solute dependent. Selectivity shifts were observed even between solutes with similar structure when switching between HPLC and UHPLC and an experimental method to predict such selectivity shifts was therefore developed. The peak shape was negatively affected by the increase in pressure for some solutes since secondary interactions between the solute and the stationary phase increased with pressure. With the upcoming ICH Q12 guideline, it will be possible for the industry to convert existing methods to UHPLC in a more flexible way using the deeper understanding and the regulatory concept presented here as a case example. / Ultra-high performance liquid chromatography (UHPLC) provides a considerable increase in throughput compared to conventional HPLC and a reduced solvent consumption. The implementation of UHPLC in pharmaceutical analysis has accelerated in recent years and currently both instruments are used. There are, however, technical and regulatory challenges converting a HPLC method to UHPLC making it difficult to take full advantage of UHPLC in regulatory-focused applications like quality control in pharmaceutical production. In UHPLC, the column is packed with smaller particles than in HPLC resulting in higher pressure and viscous heating. Both the higher pressure and the higher temperature may cause changes in retention and selectivity making method conversion unpredictable. Using chromatographic modelling and fundamental theory, this thesis investigates method conversion between HPLC and UHPLC. It reports on the influence of temperature gradients due to viscous heating, pressure effects and stationary phase properties on the separation performance. It also presents a regulatory concept for less regulatory interaction for minor changes to approved quality control methods and how predicable method conversion is achieved by improved understanding.

There is an alarming increase of explosions with devastating consequences, the ultimate being loss of life. Furthermore, these kinds of substances have a toxic effect on animals, nature and humans if they are incorrectly disposed. In order to counteract the rising trend and increase the feeling of security within the society, the Swedish Defense Research Agency (FOI) has started a new project which in the future might be used by the police in order to prevent possible terrorist attacks. The aim with this new project is to perform trace analysis of explosives in wastewater in order to receive an indication of where illegal production of explosives takes place. This method has the potential to be used for other matrixes, such as soil instead of wastewater or other water matrixes, thereby exposing possible harmful and contaminated places.   The aim with this thesis was to develop a method for an Ultra-High-Performance Liquid Chromatography (UHPLC) instrument in order to perform trace analysis of explosives in wastewater. Furthermore, the aim was also to develop a method for an automated solid phase extraction (SPE) instrument for sample clean-up. Lastly mass spectrometry was performed with a triple-quadrupole. A performance analysis was made for the developed UHPLC-method which resulted in a good repeatability. Furthermore, several experiments were conducted on the SPE-instrument in order to receive a yield close to 100%. The different experiments included comparison between the most beneficial eluent, volume of eluent and evaporation step. The highest yield was received with 3 ml acetonitrile without any evaporation step. A performance analysis was made of the developed method for the SPE-robot, which resulted in a good accuracy and precision. In hopes of lowering the detection limit, mass spectrometry was conducted by a preciously validated instrument based at FOI. A lower detection limit was received for all substances; R-salt 0,025 µg/ml, TNT 0,094 µg/ml and PETN 0,103 µg/ml.

Atmospheric deposition has been suggested to be a major input pathway of perfluoroalkyl acids (PFAAs) to the Baltic Sea catchment area and to the Baltic Sea itself. However, the sources of PFAAs to the atmosphere are not well characterized. In this study we investigated if waste incineration plants in Sweden could be a source of PFAAs to the atmosphere and to the environment in general. Samples of the end products from waste incineration were collected at four different incineration plants. The plants differed in size and technical advancement and were considered to be representative for the majority of waste incineration plants in Sweden. The collected samples were slag from the furnaces, fly ash from the flue gases, “bambergkaka” (a mix of fly ash and sludge from wastewater treatment) as well as condensate and wastewater from the cleaning process of the flue gases. Two methods were developed, one for analysis of PFAAs in solid samples and one for water samples. Method validation showed good performance for both methods in terms of precision and accuracy, despite low recoveries obtained for the method for solid samples. The results from sample analysis revealed that PFAAs were present in all solid samples at concentrations in the low to sub ng/g range and in all but one condensate and wastewater samples at concentrations in the low to sub ng/L range. The quantified concentrations were used to estimate the potential annual discharges of PFAAs from waste incineration plants to the environment. Emission scenarios via landfills, via wastewater treatment plants and to the atmosphere were considered. The main conclusion of this study is that waste incineration in Sweden is not a significant source of PFAAs to the atmosphere or to the environment in general.

New psychoactive substances are becoming increasingly common in many parts of the world, and some of them are marketed as “legal highs” and are produced to circumvent the drug legislation, and they come in many unregulated forms. The aim of this research was to characterize the metabolites of a new psychoactive substance and hence provide the fundamental data needed for further research of toxicity and future drug testing. The synthetic cannabinoid 4-fluoro-CUMYL-5-fluoro-PICA was incubated in cryopreserved hepatocytes for 1, 3 and 5 hour and then the formed metabolites was analyzed with an LC-QTOF-MS method, data analysis was performed by using the software MassHunter Qualitative Analysis. For 4-fluoro-CUMYL-5-fluoro-PICA a total of ten metabolites were identified, with three hydroxylations, two oxidative defluorinations to carboxylation, three oxidative defluorination and two fluoropentyl dealkylation. The metabolite with the highest intensity was oxidative defluorination.

The selection of a representative sample is a delicate problem when drug seizures comprised of large number of units arrive at the Swedish National Forensic Centre (NFC). If deviating objects in the selected sample size are found, additional analyzes are required to investigate how representative the results are for the entire population. This generates further pressure on operational analysis flow. With the goal to provide a tool which forensic scientists at NFC can base their assessment of the representative nature of the selected sampling of large drug seizures on, this project investigated the possibilities of evaluating the level of homogeneity in drug seizures using near-infrared (NIR) hyperspectral imaging along with principal component analysis (PCA). A total of 27 sample groups (homogeneous, heterogeneous and seized sample groups) were analyzed and different predictive models were developed. The models were either based on quantifying the variation in NIR spectra or in PCA scores plots. It was shown that in the spectral range of 1300-2000 nm, using a pre-processing combination of area normalization, quadratic (second polynomial) detrending and mean centering, promising predictive abilities of the models in their evaluation of the level of homogeneity in drug seizures were achieved. A model where the approximated signal-dependent variation was related to the quotient of significant and noise explained variance given by PCA indicated most promising predictive abilities when quantifying the variation in NIR spectra. Similarly, a model where a rectangular area, defined by the maximum distances along PC1 and PC2, was related to the cumulative explained variance of the two PCs showed most promising predictive abilities when quantifying the variation in PCA scores plots. Different zones for which within sample groups are expected to appear based upon their degree of homogeneity could be established for both models. The two models differed in sensitivity. However, more comprehensive studies are required to evaluate the models applicability from an operational point-of-view.

Male butterflies have some certain pathways to prevent the female butterfly which has mated with them from mating with other butterflies. Research shows that some proteins from the male butterflies may play an important role in this mechanism. To investigate how the pathway works, the proteins contained in the spermatophore which is injected into the female butterfly by the male one during mating are very important. In this study, the butterfly spermatophore proteins were mainly studied. The proper procedures to obtain the spermatophore from the female body were developed. Since capillary electrophoresis (CE) has many advantages for separation and detection of low amounts of sample, it was used in this study in order to separate the proteins obtained from spermatophores. Finally, Mass Spectrometry (MS) was performed to analyze the proteins after separation in order to identify the proteins. This thesis mainly introduced the following points: 1. The method for obtaining spermatophores from butterfly bodies and the procedures for extracting proteins from spermatophores. 2. Optimized methods and conditions of Capillary Zone Electrophoresis (CZE) for butterfly spermatophore proteins. Several CZE methods and sets of conditions were compared in order to find the optimized ones. 3. Protein samples were applied to Mass Spectrometry (MS) to try to analyze and identify them. Moreover, the effect of using ZiptipsTM for sample pretreatment was discussed.

Allt eftersom problemen med fossila ämnen blir mer tydliga dras industrins uppmärksamhet till trä som en förnybar råvara och energikälla. I Sverige finns stora resurser av barrträd, vilket har betytt mycket för landets ekonomi och kommer förmodligen att göra det i framtiden också. Ett stort problem vid nyplantering av barrträd är dock angrepp av skadeinsekter, som kan leda till att så mycket som 40 % av trädplantorna dör inom ett år. Nyligen har ett ämne som förekommer i barrträd, metyljasmonat, uppmärksammats för sina skyddande effekter. Då det är naturligt och helt bionedbrytbart har det föreslagits som ett miljövänligt alternativ till traditionella pesticider. För kommersialisering och vidare utveckling bör dock ämnets påverkan på trädet undersökas.  Vi undersökte sammansättningen av aminosyror i barken hos behandlade och obehandlade plantor med kapillärelektrofores. Metoden som användes visade sig dock ha dålig reproducerbarhet, vilket gjorde resultaten opålitliga. De tydde på att metyljasmonatbehandlingen inte ändrade sammansättningen dramatiskt, men det krävs en mer robust metod för att dra säkra slutsatser. Vi undersökte även förekomst och mängd av terpener i barkproverna med GC-MS. Fem stycken terpener karakteriserades: 3-karen, D-limonen, β-fellandren, geranyl linalool och thunbergol. Metoden visade god reproducerbarhet och tillförlitlighet, men mer data behövdes för att kunna dra slutsatser med statistisk säkerhet. Samtliga prover visade sig innehålla mätbara halter av 3-karen, β-fellandren och thunbergol. Resultaten antyder att koncentrationen av terpener överlag ökade efter metyljasmonatbehandling och detta var särskilt tydligt för β-fellandren. Det fanns anledning att tro att genetiska faktorer påverkade resultatet av behandlingen, då vissa kloner svarade starkare på behandlingen än andra.