| 1. |
- Källback, Patrik
(författare)
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Development and Application of Software Tools for Mass Spectrometry Imaging
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mass spectrometry imaging (MSI) has been extensively used to produce qualitative maps of distributions of proteins, peptides, lipids, neurotransmitters, small molecule pharmaceuticals and their metabolites directly in biological tissue sections. Moreover, during the last 10 years, there has been growing demand to quantify target compounds in tissue sections of various organs. This thesis focuses on development and application of a novel instrument- and manufacturer-independent MSI software suite, msIQuant, in the open access format imzML, which has been developed specifically for quantitative analysis of MSI data. The functionality of msIQuant facilitates automatic generation of calibration curves from series of standards that can be used to determine concentrations of specific analytes. In addition, it provides many tools for image visualization, including modules enabling multiple interpolation, low intensity transparency display, and image fusion and sharpening. Moreover, algorithms and advanced data management modules in msIQuant facilitate management of the large datasets generated following rapid recent increases in the mass and spatial resolutions of MSI instruments, by using spectra transposition and data entropy reduction (at four selectable levels: coarse, medium, fine or superfine) before lossless compression of the data. As described in the thesis, implementation of msIQuant has been exemplified in both quantitative (relative or absolute) and qualitative analyses of distributions of neurotransmitters, endogenous substances and pharmaceutical drugs in brain tissue sections. Our laboratory have developed a molecular-specific approach for the simultaneous imaging and quantitation of multiple neurotransmitters, precursors, and metabolites, such as tyrosine, tryptamine, tyramine, phenethylamine, dopamine, 3-methoxytyramine, serotonin, gamma-aminobutyric acid (GABA), and acetylcholine, in histological tissue sections at high spatial resolution by matrix-assisted laser desorption ionization (MALDI) and desorption electrospray ionization (DESI) MSI. Chemical derivatization by charge-tagging primary amines of analytes significantly increased the sensitivity, enabling mapping of neurotransmitters that were not previously detectable by MSI. The two MSI approaches have been used to directly measure changes in neurotransmitter levels in specific brain structures in animal disease models, which facilitates understanding of biochemical mechanisms of drug treatments. In summary, msIQuant software has proven potency (particularly in combination with the reported derivatization technique) for both qualitative and quantitative analyses. Further developments will enable its implementation in multiple operating system platforms and use for statistical analysis.
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| 2. |
- Sköld, Karl, 1974-
(författare)
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Neuropeptidomics – Methods and Applications
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The sequencing of genomes has caused a growing demand for functional analysis of gene products. This research field named proteomics is derived from the term proteome, which by analogy to genome is defined as all proteins expressed by a cell or a tissue. Proteomics is however methodologically restricted to the analysis of proteins with higher molecular weights. The development of a technology which includes peptides with low molecular weight and small proteins is needed, since peptides play a central role in many biological processes. To study endogenous peptides and hormones, the peptidome, an improved method comprising rapid deactivation in combination with nano-flow liquid chromatography (LC) and mass spectrometry (MS) was developed. The method has been used to investigate endogenous peptides in brains of mouse and rat. Several novel peptides have been discovered together with known neuropeptides. To elucidate the post mortem time influence on peptides and proteins, a time course study was performed using peptidomics and proteomics technologies. Already after three minutes a substantial amount of protein fragments emerged in the peptidomics study and some endogenous peptides were drastically reduced with increasing post mortem time. Of about 1500 proteins investigated, 53 were found to be significantly changed at 10 minutes post mortem as compared to control. Moreover, using western blot the level of MAPK phosphorylation was shown to decrease by 95% in the 10 minutes post mortem sample. A database, SwePep (a repository of endogenous peptides, hormones and small proteins), was constructed to facilitate identification using MS. The database also contains additional information concerning the peptides such as physical properties. A method for analysis of LC-MS data, including scanning for, and further profiling of, biologically significant peptides was developed. We show that peptides present in different amounts in groups of samples can be automatically detected.The peptidome approach was used to investigate levels of peptides in two animal models of Parkinson’s disease. PEP-19, was found to be significantly decreased in the striatum of MPTP lesioned parkinsonian mice. The localization and expression was further investigated by imaging MALDI MS and by in situ hybridization. The brain peptidome of reserpine treated mice was investigated and displayed a number of significantly altered peptides. This thesis demonstrates that the peptidomics approach allows for the study of complex biochemical processes.
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| 3. |
- Aerts, Jordan
(författare)
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Capillary electrophoresis mass spectrometry applied to structural proteomics and small molecule analysis
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Capillary electrophoresis with mass spectrometric (CE–MS) detection offers a separation method without equal in terms of flexibility, utility, and cost efficiency. Here we demonstrate precisely this through the application of several laboratory-built CE–MS instruments for the separation of brain metabolites in non-primates, enantioselective separations of synthetic anesthetic metabolites in fractionated pony urine, application in structural proteomics workflows, and identification of exogenous alkaloid biotransformationproducts in human cerebrospinal fluid (CSF).We outline a method for quickly and affordably etching austenitic steel tubing, which is widely used in electrospray sources for CE–MS. The stainless steel tapered tip emitters provide robust electrospray with low sheath liquid flow rates and can be easily fabricated in-house, offering flexibility and cost-efficiency when commercial options areunavailable. We contribute a CE–MS method for enantiomer separation, specifically targeting 6-hydroxynorketamine (HNK). By introducing chiral selectors into the separation capillary, the method enables efficient enantiomer separation and offers a newtool to assist with research on HNK as a cure for depression.We explore the feasibility of cold CE–MS in hydrogen deuterium exchange workflows. The utilization of a lab-designed Peltier-cooled CE device achieves deuterium back exchange rates on par with commercial liquid chromatography-based platforms, offering new possibilities for studying protein structures and interactions.We also demonstrate the wide ranging versatility of CE–MS with contributions to the identification of specific tobacco related metabolites in CSF samples during the development of a high throughput mass spectrometry diagnostic tool for Parkinson’sDisease.This thesis showcases the versatility and value of CE–MS in various applications, a true blessing for analytical chemistry.
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| 4. |
- Fridjonsdottir, Elva
(författare)
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Imaging neurochemical changes associated with Parkinson´s disease and L-DOPA-induced dyskinesia using mass spectrometry
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Parkinson’s disease (PD), caused by a loss of midbrain dopamine neurons, is the second most common neurodegenerative disease worldwide after Alzheimer’s disease. The primary treatment choice for PD is L-DOPA, the precursor for dopamine, which only affects symptoms and does not inhibit disease progression. Most patients develop motor complications during long-term L-DOPA treatment called L-DOPA-induced dyskinesia (LID), which are abnormal involuntary movements. LID has been associated with biochemical alterations in a number of signalling systems in the basal ganglia, including the dopaminergic, serotonergic, cholinergic and opioidergic systems, among others. Defining region-specific alterations of these signalling molecules and comprehensive metabolic pathways in the brain will help to improve our understanding of their involvement in LID. In the work upon which this thesis is based, we exploited the advantages of mass spectrometry imaging (MSI) to perform on-tissue mapping of a large number of molecules in a single experiment for investigating biochemical changes associated with LID. A novel matrix-assisted laser desorption/ionisation (MALDI) MSI on-tissue chemical derivatisation approach was developed that enabled imaging of primary amine and phenolic hydroxyl group containing neurotransmitters and their comprehensive metabolic pathways. In addition, a tissue clean-up protocol which improved the limit of detection of multiple neuropeptides involved in basal ganglia signalling was established. These methods were applied to neurotoxin-based animal models of PD and LID, including the gold-standard model, namely the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) administered non-human primate model. LID was found to be associated with extremely high levels of L-DOPA throughout the brain, but no significant increase in striatal dopamine was observed, contradicting the widely accepted hypothesis that LID is induced by elevated striatal dopamine levels. Furthermore, LID was associated with increased levels of signalling neuropeptides throughout the basal ganglia, where abnormally processed neuropeptides correlated with LID severity. Untargeted multivariate analysis revealed that LID was associated with increased abundance of the vasculature marker heme B in the striatum, suggesting angiogenesis and increased blood flow to this region. Moreover, important methyl donors, including S-adenosylmethionine, betaine and α-glycerophosphocholine were affected by MPTP exposure and LID. In conclusion, the studies included in this thesis provide methods for investigating multiple signalling molecules in single tissue sections and novel and comprehensive insights into the biochemical changes that occur in LID.
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| 5. |
- Nilsson, Anna, 1978-
(författare)
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Molecular Profiling and Imaging of Peptides, Proteins and Drugs in Biological Tissue using Mass Spectrometry
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biological functions within cells and organisms are mainly carried out by the translational products; proteins and peptides. The analysis and characterization of these biomolecules are of great importance for the progress in disease research and biomarker and drug discovery. The term peptidomics was introduced to describe the comprehensive analysis of peptides (e.g. neuropeptides) in biological tissues. In this thesis, a peptidomics approach using nanoflow liquid chromatography coupled to electrospray mass spectrometry (MS) has been developed for detection, identification, and quantification of neuropeptides in different disease models. A thoroughly controlled sample preparation technique and targeted neuropeptide sequence collections have been used to improve sample quality and to increase the number of identified neuropeptides. In particular, neuropeptide changes in experimental models of Parkinson’s disease (PD), with or without L-DOPA treatment, and the effect of antidepressant treatment on neuropeptide expression have been investigated. Several novel, potentially bioactive, neuropeptides have been identified and a number of peptides derived from precursors such as secretogranin-1, preproenkephalin-B, and somatostatin have been found differentially expressed. Some of them represent novel findings, not previously associated with PD or treatment with antidepressants.In addition, MALDI imaging MS (IMS), a technology that permits detection and spatial distribution determination of endogenous compounds and/or administered drugs directly on tissue sections, has been used in both small protein and drug applications. MALDI IMS on tissue samples from experimental models of PD revealed differential expression patterns of two small proteins involved in calcium regulation, PEP-19 and FKBP-12. Biomolecular interaction analysis was performed on FKBP-12 using surface plasmon resonance together with MS and several potential binding partners were identified.In a second approach, MALDI IMS was used to study the distribution of the anticholinergic bronchodilator tiotropium in rat lung following inhalation of the drug. The distribution of the drug was monitored in both MS and MS/MS mode and the levels where linearly quantifiable in the range of 80 fmol – 5 pmol.Conclusively, in this thesis mass spectrometry based technologies have successfully been developed to detect, identify, and characterize small proteins, peptides, and drugs in various tissue samples.
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| 6. |
- Vallianatou, Theodosia
(författare)
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Advanced Mass Spectrometry Imaging in Neuropharmacology
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mass spectrometry imaging (MSI) has emerged as a valuable approach for mapping multiple molecular species in sections of diverse tissues. It enables simultaneous detection of numerous compounds (from neurotransmitters to small proteins) in the brain at relatively high lateral resolution (>5 μm) on a routine basis. Matrix-assisted laser desorption/ionization (MALDI)-MSI and desorption electrospray ionization (DESI)-MSI are the most widely applied MSI techniques in tissue distribution studies. Recent advances in MSI instruments and software allow quantitative analysis of large numbers of compounds with high mass accuracy and high mass resolving power. Thus, in studies this thesis is based upon, MSI technology was used to address several challenging aspects of neuropharmacology. Restricted passage of potentially neuroactive substances into the brain, unpredictable multi-target effects, and the complexity of the central nervous system (CNS) physiology, are major obstacles in the development of efficient drugs. The simultaneous investigation of drugs’ delivery to the brain and potential effects on several CNS pathways in specific brain regions is, therefore, highly important. In addition, localization information is required for more comprehensive insights into CNS responses to both pharmaceutical agents and biological processes such as aging.MSI-based analysis of the transport of two selected drugs into the brain demonstrated effects of efflux membrane proteins on their distributions in the brain. The MDR1 substrate loperamide was found to localize specifically in the choroid plexus, indicating low brain entrance. In addition, MSI uncovered drug-drug interactions at the blood-brain barrier involving MDR1 inhibition. The technology was further used to explore neurochemical alterations induced by aging and acetylcholinesterase inhibition. First, MSI revealed that the cholinergic system’s responsivity in the retrosplenial cortex, a post-cingulate cortical area highly involved in cognition, to acetylcholinesterase inhibition significantly declined with age. Subsequently, simultaneous investigation of multiple brain metabolic pathways in specific brain areas with multivariate data analysis techniques demonstrated age-induced alterations in mitochondrial function, lipid signaling, and acetylcholine metabolism. Finally, MSI unveiled age-induced alterations in levels and distributions of the monoaminergic neurotransmitters and their metabolites in particular brain areas such as the ventral pallidum, caudate putamen, hippocampus, and cortical substructures. Age- and region-specific effects of acetylcholinesterase inhibition on the neurotransmitter systems were also detected. In conclusion, the studies provided novel insights into important brain pharmacokinetic and pharmacodynamic phenomena using advanced MSI techniques, as described and discussed in this thesis.
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