Mass Spectrometry and Molecular Analysis

Practical application of LC and/or GC-based separation methods with intermediate complexity in respect to sample preparation, separation and detector integration/coupling: - Application structure-spedific sample preparation techniques for isolation of a panel of substances within complex sample matrices and subsequent preparation, enrichment or chemical derivatization - chromatographic method optimization based on specific key parameters for application of multi methods e.g. in trace analytics - Application of appropriate measures for method optimization in respect to separation power and efficient ionization of target analyt - Integraton of univeral and selective detectors for application of the aquired knowledge in the fields of spectrometric methods / mass spectrometry to qualitative problems in respect to substance identification - Practice with spectral databases and independent design of an data analysis method

UV/VIS spectrometry - principles of UV/VIS spectroscopy - principle structure and function of a UV/VIS spectrometer - chromophores and auxochromes - spectroscopical phenomena of chemical compounds - structural analysis Infrared and Raman spectrometry - principles of IR spectroscopy - principle structure and function of an IR and Raman spectrometer - characteristic vibrational spectra of chemical compounds - structural analysis Mass spectrometry - principles of mass spectrometry - principle structure and function of a mass spectrometer - techniques of ionisation of molecules and source design - main fragmentation reaction of organic compounds - performance of different technologies and their scope of application

- model procedures for interpretation of spectra of chemical compounds - interpretation and discussion of UV/VIS spectra with practical examples - interpretation and discussion of IR spectra with practical examples - theory of isotope distribution in mass spectrometry - advanced molecule-ion theory in mass spectrometry - priciple mechanisms of ion fragmentation in GC-MS ionization technique - priciple mechanisms of ion fragmentation in LC-MS ionization technique - interpretation and discussion of MS spectra with practical examples - postulation of molecular structure with the combined interpretation of UV/VIS, IR and MS spectra

Ethics in biomedicine (in the fields of gene technology, molecular diagnostics, gene therapy, planning of experimental and clinical studies, stem cells, personalized medicine), ethics committee, patient solicitors, ethics in transplantation, research, reproductive medicine, intensive care , palliative care, socioeconomical aspects, animal experiments

Prerequisites for the validation of an analytical method, validation parameters and their examination (reproducibility, repeatability, selectivity, sensitivity, recovery, precision, accuracy, detection and quantification limits, robustness), methods to characterize analytical methods, flow chart for method validation, release of method, documentation.

Design, apply and interpretation of selected molecular and gene technology methods including isolation of nucleic acid (e.g. from complex sample matrices like soil samples, waste water, breath and plasma), amplification and detection of nucleic acids by using different detection formats (e.g. digital PCR, qPCR, Sequenziertechnologien); Gene technology methods (vector and host systems, CRISPR-Cas9 based genome editing, mutagenesis, protein expression) and examination and influencing of gene regulation (real-time PCR, RNA interference,...) and high-throughput technologies criteria for choice of method; selection of the most suitable method for various applications (e.g. forensic science, waste water monitoring, antibody production).

Principles and advanced knowledge of molecular diagnostics, diagnostic strategies and procedures, carrier and test systems, biomarkers, criteria for method selection, practical examples in medicine, industry and environment ( detection of genetic diseases, forensic medicine, detection of genetically modified organsims, detection of pathogens in body fluids, drinking water, animal feeds and food); methods with a focus on their application in diagnostics: immunoassays (ELISA, immuno PCR, Westernblot), PCR (real time PCR, digital PCR), mutation analysis (SNP genotyping, DNA fingerprinting), microarray based methods (CGH arrays, SNP arrays, protein and antibody arrays), quality assurance

Introduction and use of different data bases (sequence, structure, genome and interaction data bases), prominent web portals (NCBI, ExPASy, KEGG), principles of sequence analysis (alignment, assembly, annotation), homologies, prediction programs (splice sites, promoter, mutations), simulation techniques, simulation of biological processes and systems, modelling of cellular systems.

Background and special considerations of Transcriptomics/(epi-) genomics/proteomics/glycomics/lipidomics/metabolomics: Biological Question, Experimental Design, Experiment, Image Analysis, Normalization, Data Mining, Verification and Interpretation; on the basis of applied tasks

Biological data management and knowledge management systems, data base structure and data formats, procedures of exploratory data analysis, normalization procedures and data reduction, data and structure analysis with multivariate statistical approaches (e.g. principal component analysis (PCA), independent component analysis (ICA), PLS discriminant analysis (PLS-DA), cluster analysis.

Tips and tricks for compiling written research papers (structure, referencing, graphical representation), professional abstract writing, short papers, full papers, posters and presentations in English language and planing of interdisciplinary grant proposals

Detailed mechanisms of gradient separation and isocratic separation, Special chromatographic extraction and enrichment, techniques (solid-phase extraction (SPE), in-tube extraction (ITEX), liquid-liquid extraction (LLE)) Special column materials (carrier materials and ligands) and their application, Mobile phases (mixtures and viscosity), Nano LC, Detailed discussion of applications in chromatography

Design of complex analysis workflows from selection of separation and detection method, preparation of necessary materials and standards including design of an analysis plan that considers the following aspects: - Sample stabilisation and storage - Enrichment / Isolation of analytes from complex matrices - Optimization of sample preparation (solvent selection, optimization of pH and ion strength of solvent) - Optimization strategies for eluents and stationary phases relevant for chromatographic separation - Demand-oriented optimization of instrument parameters for robust and sensitive detection of analytes - Calibration of required analysis systems - Chemometric methods for optimization of chromatographic processes - Demonstration of multivariate analysis and biostatistics during data analysis - Systematic error management

Theoretical background of mass analyzers Combination of ionizing techniques and mass analyzers Application of common MS systems High-resolution mass spectrometry Database supported identification of spectra Identification of unknown samples in MS Mass spectra of different classes of compounds Detailed mechanisms of ion fragmentation Potential and challenges of data processing Detailed sample preparation Potential of derivatization techniques MALDI-MS and SIMS-MS imaging Development of solution strategies with MS for problems in biology

Principles, methods and vectors in somatic gene therapy, advantages and disadvantages of the individual administration form, risks, legal aspects, other innovative therapy strategies, application examples

Criteria for the choice of biomarkers; procedures to identify new biomarkers (medical and environmental); single cell analysis; special knowledge in next generation sequencing, practical application and data evaluation.

Methods and specific aspects of personalized medicine including analytical challenges, possibilities and risks of individualized medicine.

Interdisciplinary applications in the field of molecular techniques incl. Diagnostic methods e.g. based on nanotechnology

Stem cells: Definition of different categories, Origin and Generation of stem cells, Growth, Differentiation/Development, Niches, manipulation/modification and characterization; Tissue engineering: Organisation and structure of tissue, immune tolerance, regeneration, wound healing, biomaterials and extracellular scaffolds; Culture conditions (2/3D-Models, bio-reactors, biomechanical stimulation), Applications (2/3D-Models, stemcell therapies, Tissue Eng.), Research project focused on regenerative medicine: Selection of novel therapeutic solutions for clinical problems, strategies for repair, replacement and regeneration of different tissues and organs; isolation of stem cells from organs and reprogramming, Setup of 3D- models (Organoids, Organ-on-a-chip,...), toxicity assays. Protein Engineering: Possibilities of targeted protein structure changes (focusing on protein design, synthetic biology, structural analysis, mutagenesis, demonstration of protein design software platforms), ...

Presentation and defence of master thesis, Exam in relation to study plan relevant contents

The aim of the master thesis is to define and examine an innovative problem using scientific methods with high level of independence, and to document and discuss the results in a thesis.

This seminar accompanies the writing process of the master thesis and provides guidelines for writing a master thesis. In addition, the students are offered professional and methodological support.

Application-oriented statistical foundations, descriptive statistics for the biometrics laboratory, tools and instruments for statistical data analysis and interpretation, quality assurance based on statistical procedures.

Organic Chemistry: - Stereochemistry - Heterocycles - Structure of biomolecules and their chemical potential - Chemical bonding in organic molecules - Classification and properties of substance classes - Alkanes, alkenes and alkynes - Cycloalkanes and aromatics - Important functional groups and their reactions - Important reaction mechanisms of organic chemistry - Simple chemical synthesis processes Physical Chemistry: - Chemical catalysis - The Gibbs function and its role in chemical reactions - Kinetics of chemical reactions - Theory of chemical bonding - The laws of thermodynamics Stoichiometry: - Calculation of aqueous mixtures - Calculation of complex kinetic processes - Calculation of enzyme-catalyzed reactions - Working with equilibrium constants - Calculation of acid / base reactions - The pH concept and calculation of buffer systems - Calculate of redox reactions - Calculation of basic kinetic processes

Structure of prokaryotes and eukaryotes, structure and function of macromolecules (proteins, DNA, RNA, carbohydrates), genes, gene structure, chromosomes, information flow from gene to protein, DNA replication, transcription and translation, genetic codes, tools of molecular biology (bacteria, viruses, enzymes) vectors, synthetic oligonucleotides. Standard methods in molecular biology: Extraction of nucleic acids, determination of concentrations, detection of nucleic acids (blotting procedure), electrophoretic separation (nucleic acids and proteins), reverse transcription, PCR, blotting procedures, cloning, sequence analysis, foundations and applications of human and cytogenetics (mutations, heredity, diagnostics)

General chemistry: - basic laws of chemistry - foundations of the atomic theory and chemical bindings - the periodic table of elements - the law of mass action and the chemical equilibrium - types of chemical reaction (acid-base reactions, radical reactions, redox reactions) - terminology of chemical bindings Stoichiometry: - forming and paramterizing of chemical reaction equations - calculating chemical reactions - calculating serial dilutions - calculating aqueous mixtures

Legal bases of genetic engineering, differences in bacterial and mammalian genetics, possibilities of gene transfer in prokaryotes and eukaryotes, selection, protein expression systems, cell lysis/cell disruption, genetic regulatory mechanisms, cellular transport systems, protein degradation, cell-cell communication, mutagenesis, classical genetics and advanced genetics by the example of selected host organisms, basics of microbiology and virology, micro-organisms and viruses as tools of genetic engineering, species definition/taxonomy, laboratory animal science, analysis and cross-breeding of mouse lines, the production of transgenic organisms, special features of stem cells, discussion about the above-mentioned contents in specific fields of application

Foundations of chromatographic techniques: - Taxonomy of chromatographic procedures - principles of chromatographic separation - liquid chromatography - instrumentation - important parameters - Van Deemter equation - stationary phases - mobile phases - reversed-phase chromatography - normal-Phase chromatography - ion exchange chromatography - hydrophilic interaction chromatography - chiral chromatography - affinity chromatography - gel-permeation chromatography - principles of isocratic separation and gradient separation - detectors - Gas chromatography - instrumentation - important parameters - Raoult's law - separation columns - carrier gases - retention mechanisms - detectors - principles of temperature dependent separation of volatile and semi-volatile compounds Foundations of electrophoretical techniques: - principles of electrophoretical separation - capillary zone electrophoresis - instrumentation - retention mechanisms …

Search strategies for literature and other databases (introduction to relevant databases, selection of search keys, systematic approach, primary sources, scientific relevance, search documentation ); practical approach models for efficient and effective literature management, reference management software.

Development of attitudes and strategies that aid in increasing team performance and individual satisfaction and reduce conflict when collaborating in a team. The students get to know how to use digital media when working in a team and how to use professionally digital resources of the UAS JOANNEUM (audio/video conferencing, resource sharing, the LMS moodle, VPN access to resources of the university intranet), data protection and legal issues ( UAS JOANNEUM data protection guide).

Introduction and use of different data bases (sequence, structure, genome and interaction data bases), prominent web portals (NCBI, ExPASy, KEGG), principles of sequence analysis (alignment, assembly, annotation), homologies, prediction programs (splice sites, promoter, mutations), system theory and systems thinking, simulation techniques, simulation of biological processes and systems, modelling of cellular systems.

Need for quality standards by the Food and Drug Administration (FDA) and the Environmental Protection Agency (EPA); general criteria for operating test laboratories (ÖNORM EN 45001, ISO/IEC 17025); definition, explanation and commenting of quality assurance terminology, prerequisites for the validation of an analytical method, validation parameters and their examination (reproducibility, repeatability, selectivity, sensitivity, recovery, precision, accuracy, detection and quantification limits, robustness), methods to characterize analytical methods, flow chart for method validation, release of method, documentation.

putting theory into practice: instrumental main component and trace analytics: - creation of an analysis plan - production of standard solutions and serial dilutions - measuring of standard samples with chromatographical and spectrometrical techniques - creation of standard curves - analysis of a sample containing an unknown amount of a well-known analyte - sample collection - sample preparation - separation of complex mixtures with LC and GC - interpretation of the data - evaluation and logging In addition to handling of single procedures the focus is placed on the holistic aspect of the analytical procedure

- model procedures for interpretation of spetra of chemical compounds - interpretation and discussion of UV/VIS spectra with practical examples - interpretation and discussion of IR spectra with practical examples - theory of isotope distribution in mass spectrometry - advanced molecule-ion theory in mass spectrometry - priciple mechanisms of ion fragmentation in GC-MS ionization technique - priciple mechanisms of ion fragmentation in LC-MS ionization technique - interpretation and discussion of MS spectra with practical examples - postulation of molecular structure with the combined innterpretation of UV/VIS, IR and MS spectra

UV/VIS spectrometry - principles of UV/VIS spectroscopy - principle structure and function of a UV/VIS spectrometer - chromophores and auxochromes - spectroscopical phenomena of chemical compounds - structural analysis Infrared and Raman spectrometry - principles of IR spectroscopy - principle structure and function of an IR and Raman spectrometer - characteristic vibrational spectra of chemical compounds - structural analysis Mass spectrometry - principles of mass spectrometry - principle structure and function of a mass spectrometer - techniques of ionisation of molecules and source design - main fragmentation reaction of organic compounds - performance of different technologies and their scope of application

Transcriptomics/(epi-) genomics/proteomics/glycomics/lipidomics/metabolomics: Biological Question, Experimental Design, Experiment, Image Analysis, Normalization, Data Mining, Verification and Interpretation; on the basis of concrete tasks

Principles and advanced knowledge of molecular diagnostics, diagnostic strategies and procedures, carrier and test systems, biomarkers, criteria for method selection, practical examples in medicine, industry and environment ( detection of genetic diseases, forensic medicine, detection of genetically modified organsims, detection of pathogens in body fluids, drinking water, animal feeds and food); methods with a focus on their application in diagnostics: immunoassays (ELISA, immuno PCR, Westernblot), PCR (real time PCR, digital PCR), mutation analysis (SNP genotyping, DNA fingerprinting), microarray based methods (CGH arrays, SNP arrays, protein and antibody arrays), quality assurance

Isolation of nucleic acid (e.g. from complex sample matrices like soil samples, waste water, breath and plasma), amplification and detection of nucleic acids by using different detection formats (e.g. digital PCR, qPCR, in situ…) selection of suitable vector and host systems, examination and influencing of gene regulation (real-time PCR, RNA interference,...) mutagenesis, high-throughput technologies (generation of libraries, next generation sequencing, RNAseq, micro-arrays (oligonucleotide, peptide arrays), ChIP-Seq, methylation analysis), protein expression systems, in situ detection of proteins, principles of protein design; criteria for choice of method; selection of the most suitable method for a concrete question (e.g. forensic science, waste water monitoring, antibody production).

Nanotechnology in medicine, medical technology and environment: molecular targeting, molecular imaging, drug delivery, surface coating, nanotoxicology, environmental monitoring

Biological data management and knowledge management systems, data base structure and data formats, procedures of exploratory data analysis, normalization procedures and data reduction, data and structure analysis with multivariate statistical approaches (principal component analysis (PCA), independent component analysis (ICA), PLS discriminant analysis (PLS-DA), cluster analysis.

General and statistical planning of experiments in (pre-) clinical and analytical- technical contexts, experimental strategies and creating experimental designs (2k - fractional factorial designs, full factorial designs, response surface designs), evaluation of experimental data with analysis of variance and /or regression, critical success factors in DOE.

Implementation of an independent project (in team work) with a clear initial research question, information and literature search, designing and conducting appropriate experiments, data evaluation and interpretation of the results, write-up and presentation of the results.

Tips and tricks for compiling written research papers (structure, referencing, graphical representation), professional abstract writing, short papers, full papers, posters and presentations in English language.

Detailed mechanisms of gradient separation and isocratic separation Special chromatographic extraction and enrichment techniques (solid-phase extraction (SPE), in-tube extraction (ITEX), liquid-liquid extraction (LLE)) Special column materials (carrier materials and ligands) and their application Mobile phases (mixtures and viscosity) Nano LC Injection techniques in gas chromatography Detailed discussion of applications in chromatography

The students work out representative analytical methods according to the given requirements. They cover the complete process from formulating the research question, searching for relevant literature and resources, preparing the samples to carrying out the analytical procedure and evaluating and disseminating the results. Case studies enhance their awareness of the complexity of bioanalytical problems. Thus, the students are enabled to draft independently application oriented solution possibilities to complex analytical problems. In this course the students need to compile and present their own project papers and must answer questions about the analytic process that they have dealt with.

Techniques of sample collection Stabilizing and storage of samples Concentration and isolation of analytes from complex matrices Optimization of sample preparation (choice of suitable solvents, optimizing of pH value and ion strength of a solvent) Optimization strategies for eluents and stationary phases Selectivity of columns in chromatography Optimization of reversed phase chromatography Optimization of normal phase chromatography Using principal component analysis (PCA) to evaluate chromatographical procedures Chemometrical methods for optimizing the chromatographic process Optimization techniques in gas chromatography Systematic search for errors in LC-MS and GC-MS

Planning of complex analysis processes and choosing the appropriate LC/MS and GC/MS techniques Preparation of tools and standard samples and calibration of the required analysis systems Optimization of parameters of the analytic devices that meet the requirements for safe and sensitive detection of targeted analytes Experimental identification of limit of detection and limit of quantitation of the analytes Separation of complex substance mixtures using computer-assisted mass spectrometry techniques Identification of characteristic ions for qualitative and quantitative measurement of analytes Application of appropriate procedures for method optimization with regard to separation and effective ionization of target analytes Computer-aided data processing and reporting

Theoretical background of mass analyzers Combination of ionizing techniques and mass analyzers Application of common MS systems High-resolution mass spectrometry Database supported identification of spectra Identification of unknown samples in MS Mass spectra of different classes of compounds Detailed mechanisms of ion fragmentation Potential and challenges of data processing Detailed sample preparation Potential of derivatization techniques MALDI-MS and SIMS-MS imaging Development of solution strategies with MS for problems in biology

Ethics in biomedicine (in the fields of gene technology, molecular diagnostics, gene therapy, planning of experimental and clinical studies, stem cells, personalized medicine)

Principles, methods and vectors in somatic gene therapy, advantages and disadvantages of the individual administration form, risks, legal aspects, other innovative therapy strategies like cloning or stem cell therapy, application examples

functional genomics; multidsiciplinary networking and interdisciplinary practical examples of molecular techniques

Criteria for the choice of biomarkers; procedures to identify new biomarkers (medical and environmental); single cell analysis; special knowledge in next generation sequencing, practical application and data evaluation.

Foundations of pharmacogenomics; methods/ background; opportunities and risks of individualized medicine

In silico modelling, possibilities of structure change (mutagenseis, synthetic biology, tags, fusion proteins) production systems, practical examples from vaccine development, dietary supplements, medication.

The aim of the master thesis is to work out independently an innovative job-specific topic, to examine it scientifically and to record the results in a thesis.

The aim of the master thesis is to work out independently an innovative job-specific topic, to examine it scientifically and to record the results in a thesis.