<p>The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. </p><p>Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. </p><p>Fragment ion abundances are a quantifiable tool providing chiral recognition (R_Chiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. </p><p>The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding.</p><p>The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.</p>

Until first half of the XX century, sickle cell disease was practically limited to the malaria endemic areas and countries having known an important surge of African slaves. Today, migratory flows and progress of medicine have modified considerably the distribution of sickle cell disease which is from now on a frequent affection in Western Europe. The preventive implementation of medical care makes it possible to reduce morbidity and mortality associated with this pathology. Stake of a medical policy and economic interests, neonatal screening for hemoglobin disorders justifies then fully the implementation of powerful and adapted means. In order to initiate a newborn screening programme in our centre, we developed various immunological tests allowing to identify the sickle hemoglobin. We first of all developed an indirect immunoassay and led a population study on 46082 Belgian newborns and 1825 neonates from Central Africa. The performances of this assay were improved thereafter by conceiving a competitive test. Next, for reasons independent of our will, we had unfortunately to abandon the immunological approach. This methodology was thus supplanted in our center by an innovative method for this indication: the mass spectrometry. Our promising results currently authorize us to perennialize our policy in the neonatal screening for sickle cell disease and open the way for new developments in other fields. / Jusquà la première moitié du XXe siècle, la drépanocytose se limitait pratiquement aux zones dendémie palustre et aux pays ayant connu un important afflux desclaves dorigine africaine. Aujourdhui, les flux migratoires et les progrès de la médecine ont considérablement modifié la distribution de cette maladie qui est désormais une affection fréquente en Europe occidentale. La prise en charge précoce permet de réduire la morbidité et la mortalité associées à cette maladie. Enjeu dune politique sanitaire et dintérêts économiques, le dépistage néonatal de la drépanocytose justifie donc ainsi pleinement la mise en uvre de moyens performants et adaptés. Afin dinitier un programme de dépistage au sein de notre centre, nous avons initialement développé divers tests immunologiques permettant didentifier lhémoglobine anormale. Nous avons tout dabord mis au point un immunoessai indirect et conduit une étude de population sur 46082 nouveau-nés belges et 1825 bébés originaires dAfrique centrale. Les performances de lessai ont par la suite été améliorées en concevant un test compétitif. Lapprovisionnement laborieux danticorps nécessaires aux tests de détection a par la suite entravé notre programme. En effet, la commercialisation en a été interrompue et la production danticorps monoclonaux par nos moyens propres na pas été couronnée du succès escompté. Lapproche immunologique du dépistage néonatal de la drépanocytose a ainsi été supplantée dans notre centre par une méthode novatrice pour cette indication : la spectrométrie de masse. Nos résultats prometteurs nous autorisent actuellement à pérenniser notre nouvelle façon de faire dans le dépistage néonatal de la drépanocytose et ouvre la voie pour de nouveaux développements dans dautres domaines.

The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. Fragment ion abundances are a quantifiable tool providing chiral recognition (RChiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding. The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.

Bioinformatic methods were developed for improved identification of endogenous peptides using mass spectrometry. As a framework for these methods, a database for endogenous peptides, SwePep, was created. It was designed for storing information about endogenous peptides including tandem mass spectra. SwePep can be used for identification and validation of endogenous peptides by comparing experimentally derived masses of peptides and their fragments with information in the database. To improve automatic peptide identification of neuropeptides, targeted sequence collections that better mimic the peptidomic sample was derived from the SwePep database. Three sequence collections were created: SwePep precursors, SwePep peptides, and SwePep predicted. The searches for neuropeptides performed against these three sequence collections were compared with searches performed against the entire mouse proteome, and it was observed that three times as many peptides were identified with the targeted SwePep sequence collections. Applying the targeted SwePep sequence collections to identification of previously uncharacterized peptides yielded 27 novel potentially bioactive neuropeptides. Two fragmentations studies were performed using high mass accuracy tandem mass spectra of tryptic peptides. For this purpose, two databases were created: SwedCAD and SwedECD for CID and ECD tandem mass spectra, respectively. In the first study, fragmentation pattern of peptides with missed cleaved sites was studied using SwedCAD. It was observed that peptides with two arginines positioned next to each other have the same ability to immobilize two protons as peptides with two distant arginines. In the second study, SwedECD was used for studying small neutral losses from the reduced species in ECD fragmentation. The neutral losses were characterized with regard to their specificity and sensitivity to function as reporter ions for revealing the presence of specific amino acids in the peptide sequence. The results from these two studies can be used to improve identification of both tryptic and endogenous peptides. In summary, a collection of methods was developed that greatly improved the sensitivity of mass spectrometry peptide identification.

A new method for analysis of acidic herbicides, mostly phenoxy acids and their esters, in cereals with liquid chromatography-tandem quadrupole mass spectrometry (LS-MS/MS) has been developed. Samples were hydrolyzed with sodium hydroxide in order to release covalently bound compounds followed by neutralization and finally extraction with acidified ethyl acetate. The extraction efficiency for both ester formulations and acids were studied. Acceptable results (70-120 %) were obtained for 2,4-D, dichlorprop, MCPA and mecoprop for both esters and acids. However, low recoveries were observed for ester formulations of dicamba, fluroxypyr, fluazifop and haloxyfop, possibly due to the complex structure of the compounds in combination with the matrix and/or incomplete hydrolysis step. The limit of quantification (LOQ) for targeted pesticides was 0.01 mg/kg. The method has been tested in the EU Proficiency Test for cereals with good results.

There are two purposes in this research, one is the development of the new method which can be used for detection and quantification of triarylmethanes in fish tissues. The other is that we confirmed validation and utility of triarylmethanes by the method that is according to Commission Decision 2002/657/EC. Homogenized fish tissues were extracted twice with acetonitrile and defatted with n-hexane. HPLC separation was conducted with the RP-18 column. The mobile phases consisted of 0.5 mM ammonium acetate buffer (pH 3.8, adjusted with acetic acid)¡V ACN (contained 0.1% formic acid) solution. Triarylmethane was determined by LC-ESI-MS/MS in positive mode. The correlation coefficients of calibration curves with triarylmethane in fish tissues were 0.998 ~ 0.999. The decision limits (CC£\) were 0.16 ¡Ó 0.07 £gg/kg(MG), 0.15 ¡Ó 0.04 £gg/kg(LMG), 0.20 ¡Ó 0.13 £gg/kg(CV) and 0.23 ¡Ó 0.12 £gg/kg(LCV), and detection capabilities (CC£]) were 0.20 ¡Ó 0.09 £gg/kg(MG), 0.18 ¡Ó 0.05 £gg/kg(LMG), 0.24 ¡Ó 0.16 £ggkg-1(CV) and 0.29 ¡Ó 0.15 £gg/kg(LCV).

Sphingolipids are a highly diverse category of compounds that serve not only as components of biologic structures but also as regulators of numerous cell functions. Because so many of the structural features of sphingolipids influence their biological activity, there is a need for comprehensive methods for quantitation of as many individual subspecies as possible. This dissertation describes methods that have been developed and validated for the extraction, liquid chromatographic separation, identification and quantitation of sphingolipids by electrospray ionization (ESI), tandem mass spectrometry (MS/MS) using an internal standard cocktail developed by the LIPID MAPS Consortium. The compounds that can be readily analyzed are sphingoid bases and sphingoid base 1-phosphates, as well as more complex species such as ceramides, ceramide 1-phosphates, sphingomyelins, and mono- and di-hexosylceramides. For broader utility, the methods have been optimized for two categories of tandem mass spectrometers. With minor modifications, these methods can be applied to the analysis of isomers such as glucosylceramide and galactosylceramide, and with the availability of additional internal standards, more complex species such as sulfatides can also be quantified. Using these methods 46 species of these compounds have been quantified in RAW264.7 cells, a macrophage cell line. Quantitation of individual sphingolipid metabolites is possible using liquid chromatography, tandem mass spectrometry, and stable isotope labeling with [13C]palmitic acid can be used to differentiate between metabolites produced by de novo synthesis versus turnover. This approach is more accurate when one knows the isotope enrichment of the precursor pool (in this case, [13C]-palmitoyl-CoA); therefore this dissertation describes methods to analyze both the various isotopic forms of palmitoyl-CoA and sphingolipids through sphingomyelins and monohexosylceramides using two cell models, HEK293 cells and RAW264.7 cells treated with Kdo2-Lipid A. The sphingolipid analysis was simplified by the fragmentation of most of the metabolites to backbone product ions. For example the presence of the isotopic label in the long chain base, N-acyl linked fatty acid, or both was determined via, m/z 264 for [12C]sphingosine (d18:1) and m/z 280 for [13C]sphingosine (m+16, d18:1), versus the m/z of the isotopically labeled precursor, (m+16 versus m+32).

Thesis (Ph. D.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 206-208). Also available on the World Wide Web.

The ubiquity of pharmaceuticals and personal care products in water systems is well known. With the increasing implementation of water reuse schemes in the US, concern about potential health effects of these compounds in humans has risen. While potential synergistic effects of chronic low doses exposure to a cocktail of these compounds is still being studied, it is prudent to monitor and attenuate these trace organic compounds (TOrCs) from our water sources. This research initially focused on identifying suitable `indicator' TOrCs based on theoretical physico-chemical parameters and actual experimental data. It was concluded that an indicator list will be specific to the goal targeted with dependence on treatment process, occurrence and analytical ease. Quantification of these TOrCs are part per trillion levels in water requires accurate, precise and robust analytical techniques. The next part of this research was spent on developing three different analytical methods with LC-MS/MS for the sensitive detection of TOrCs in several different water matrices including raw sewage and final drinking water. The treatment efficacy of granular activated carbon for attenuation of TOrCs is studied in detail with emphasis on developing correlations between TOrC removal and bulk organic parameters of water like UV absorbance and fluorescence by using rapid small-scale column testing. The results indicate a correlation between removal of TOrCs and bulk organic parameters that is independent of water quality. The effectiveness of commercially available activated carbon based point-of-use (POU) devices for removal of a set of TOrCs from water was evaluated. The data indicated that POUs are a viable option for treatment of TOrCs but specific removal depends on type of device, water quality and amount of water treated. Finally, further research was targeted at identifying transformation products as a result of oxidation of polyfluorinated precursor materials in reclaimed waters. The results illustrated that toxic perfluorocarboxylic acids can be formed on oxidation of fluorotelomer unsaturated carboxylic acids that are known to be present in water.

As DNA sequence information becomes increasingly available, researchers are now tackling the great challenge of characterizing and identifying peptides and proteins from complex mixtures. Automatic database searching algorithms have been developed to meet this challenge. This dissertation is aimed at improving these algorithms to achieve more accurate and efficient peptide and protein identification with greater confidence by incorporating peak intensity information and peptide cleavage patterns obtained in gas-phase ion dissociation research. The underlying hypothesis is that these algorithms can benefit from knowledge about molecular level fragmentation behavior of particular amino acid residues or residue combinations.SeQuence IDentification (SQID), developed in this dissertation research, is a novel Bayesian learning-based method that attempts to incorporate intensity information from peptide cleavage patterns in a database searching algorithm. It directly makes use of the estimated peak intensity distributions for cleavage at amino acid pairs, derived from probability histograms generated from experimental MS/MS spectra. Rather than assuming amino acid cleavage patterns artificially or disregarding intensity information, SQID aims to take advantage of knowledge of observed fragmentation intensity behavior. In addition, SQID avoids the generation of a theoretical spectrum predication for each candidate sequence, needed by other sequencing methods including SEQUEST. As a result, computational efficiency is significantly improved.Extensive testing has been performed to evaluate SQID, by using datasets from the Pacific Northwest National Laboratory, University of Colorado, and the Institute for Systems Biology. The computational results show that by incorporating peak intensity distribution information, the program's ability to distinguish the correct peptides from incorrect matches is greatly enhanced. This observation is consistent with experiments involving various peptides and searches against larger databases with distraction proteins, which indirectly verifies that peptide dissociation behaviors determine the peptide sequencing and protein identification in MS/MS. Furthermore, testing SQID by using previously identified clusters of spectra associated with unique chemical structure motifs leads to the following conclusions: (1) the improvement in identification confidence is observed with a range of peptides displaying different fragmentation behaviors; (2) the magnitude of improvement is in agreement with the peptide cleavage selectivity, that is, more significant improvements are observed with more selective peptide cleavages.