This thesis describes bioanalytical methods for generating fingerprints of biological systems for extracting relevant information with (protein) drugs in focus. Similarities and differences between samples can reveal the hidden relevant information, which can be used to optimize the production and facilitate the quality control of such protein drugs during their development and manufacture. Metabolic fingerprinting and multivariate data analysis (MVDA) can also facilitate early diagnosis of diseases and the effects and toxicity of drugs. Currently, several protein drugs are available on the global market. Nevertheless, despite, the success of such biotherapeutics significant challenges remain to be overcome in maintaining their stability and efficacity throughout their production cycle and long-term storage. The native structure and functional activity of therapeutic proteins is affected by many variables from production to delivery, incl. variables assoc. with conditions in bioreactors, purification, storage and delivery. Thus, part of the work underlying this thesis focused on structural analysis of a protein drug using chemical labeling, peptide mapping, and evaluation of the charge state distributions of the whole protein generated by ESI. The other part focuses on non-targeted metabolomics with a view to optimizing the cell cultivation process and assessment of the drug’s toxicity. A combination of appropriate analytical methods and MVDA is needed to find markers that can facilitate optimization of the cultivation system and expression of the target proteins in early stages of process development. Rapid methods for characterizing the protein drugs in different stages of the process are also required for quality control. In order to obtain high quality fingerprints analytical separation techniques with high resolution (such as HPLC or UHPLC) and sensitive analytical detection techniques (such as ESI, quadrupole or TOF MS) have been used, singly or in combination. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript.

Although some physiological effects of toxic metal poisoning have been known for centuries, the specific chemical interactions between biological molecules and mercury(I), mercury(II) or lead(II) are not well understood. To date, only thirteen crystal structures of inorganic mercury-amino acid complexes and six crystal structures of lead-amino acid complexes have been reported with varying degrees of characterization. In order to improve our understanding of the coordination chemistry of mercury and lead in biological environments, a systematic method for the isolation of inorganic metal-amino acid complexes from acidic aqueous solutions has been developed. With this method we have prepared five new lead-amino acid complexes (with L-valine, L-isoleucine, L-phenylalanine, and L-arginine) and four new mercury-amino acid complexes (with L-alanine, D-alanine, L-proline, and N-methyl-L-alanine). These metal-amino acid complexes have been comprehensively characterized in the solid state, solution state and gas phase. The development of this isolation technique in conjunction with the exploration of a number of characterization techniques for studying metal-amino acid interactions greatly enhances the known methods by which metal-biological molecule systems are studied.

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ABSTRACT In this paper we describe the use of electrospray-assisted pyrolysis ionization/mass spectrometry (ESA-Py/MS) to selectively ionize trace polar compounds that coexist with large amounts of nonpolar hydrocarbons in synthetic polymer, crude oil, amber, humic substances, and rubber. Samples of different origins are distinguished rapidly by their ESA-Py mass spectra without prior separation or chemical pretreatment. During ESA-Py analysis, the samples in their solid or liquid states were pyrolyzed at 590 ¢XC using a commercial Curie-point pyrolytical probe; the gaseous pyrolysates were transferred into a glass reaction cell; the polar compounds (M) in the pyrolysates were then ionized in the form of protonated molecules (MH+), through their reactions with the charged species in the ESI plum. Although the major components of the pyrolysates are nonpolar hydrocarbons, their lack of functional groups that can receive a proton in the ESA-Py source results in no hydrocarbon ion signals being produced; thus, the ions detected in ESA-Py mass spectra all result from trace polar component in the pyrolysates.

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Um Proteine und Peptide ohne Verluste in der Trennleistung mit Hilfe der Kapillarelektrophorese zu analysieren, wurde der Innenkanal von fused silica Kapillaren mit 2-Hydroxyethylmethacrylat (HEMA) nach dem Prinzip der radikalischen Atomtransferpolymerisation beschichtet. Durch die Variation einiger Reaktionsparameter konnten dabei vier HEMA-Beschichtungen erhalten werden. Mit diesen wurden dann nach den Methoden der Kapillarzonenelektrophorese bei pH 3 und pH 9 und der isoelektrischen Fokussierung Vergleichsmessungen durchgeführt. Die Detektion erfolgte dabei teilweise mit einem Elektrosprayionisations-Flugzeit-Massenspektrometer. Es stellte sich heraus, dass sich die entwickelten Kapillarbeschichtungen im Bezug auf Trenneffizienz wie auch Stabilität im basischen Bereich teilweise stark voneinander unterschieden. Die Betrachtung der Polymerschichten mit Hilfe der Atomkraftmikroskopie zeigte, dass die Morphologie der HEMA-Beschichtung stark vom gewählten Reaktionsmedium abhängig ist.

This dissertation includes molecular and phytochemical investigations of the harmful, bloom-forming alga, Prymnesium parvum, including analysis of known polyketide metabolites as a function of salinity and growth. Initially, the development of molecular and phytochemical tools was necessary for the detection and quantification of P. parvum and its associated toxins. Suites of oligonucleotides and molecular beacons were designed for conventional and quantitative multiplex PCR to amplify four species- and gene-specific products simultaneously that were used for the detection and quantitation of P. parvum. This built-in redundancy provided increased confidence in reactions with the positive confirmation of four discrete products. Techniques were also developed for the chemical enrichment of toxins produced by P. parvum. Until now, isolation of “prymnesins” has never been reproduced. Polyketide prymnesins possess unique spectral properties that were used to generate an LC-MS fingerprint that comprised 13 ion species. Preliminary investigations using chemifluorimetric methods were also capable of detecting prymnesins in the pico- and nano-molar range. Environmental samples were tested as an independent assessment of these methods. Lastly, the roles of polyketide prymnesins were analyzed with respect to total hemolytic activity (HA) as a function of culture age and salinity. Variation in HA of supernatants was statistically significant relative to both variables (p << 0.05). Salinity was inversely related to HA wherein cultures growing in 5-25 psu were 150-200% more hemolytic. Total HA was inversely related to culture age during the first three weeks, but positively related to it during the next three weeks. Interestingly, no hemolysis was detected in fractions containing prymnesins from culture supernatants and the majority of hemolysins remained in the aqueous phase. Prymnesins extracted from cells varied significantly over the 6-week observation period (p << 0.05); HA was positively correlated during the first half and inversely related during the last half of the study. Salinity was directly related to HA from cell extracts, but these effects were not significantly different until the last three weeks. These investigations suggest that polyketide prymnesins are present at much lower quantities than previously believed, and they may not be the key compounds associated with hemolysis due to P. parvum. / text

Although some physiological effects of toxic metal poisoning have been known for centuries, the specific chemical interactions between biological molecules and mercury(I), mercury(II) or lead(II) are not well understood. To date, only thirteen crystal structures of inorganic mercury-amino acid complexes and six crystal structures of lead-amino acid complexes have been reported with varying degrees of characterization. In order to improve our understanding of the coordination chemistry of mercury and lead in biological environments, a systematic method for the isolation of inorganic metal-amino acid complexes from acidic aqueous solutions has been developed. With this method we have prepared five new lead-amino acid complexes (with L-valine, L-isoleucine, L-phenylalanine, and L-arginine) and four new mercury-amino acid complexes (with L-alanine, D-alanine, L-proline, and N-methyl-L-alanine). These metal-amino acid complexes have been comprehensively characterized in the solid state, solution state and gas phase. The development of this isolation technique in conjunction with the exploration of a number of characterization techniques for studying metal-amino acid interactions greatly enhances the known methods by which metal-biological molecule systems are studied.