Objectives: Fusobacteria are prominent participants in the maturation of subgingival dental plaque biofilms in humans. A number of various species belonging to the Fusobacterium genus have been recovered from the subgingival microbiota of chronic periodontitis patients. However, conventional Fusobacterium species identification is labor-intensive, time-consuming, and complicated by shortcomings in phenotypic-based classification schemes, where many fusobacteria display overlapping and non-distinguishing morphologic features and biochemical properties. In addition, molecular identification of fusobacteria is plagued with difficulties of validating the specificity of nucleic acid probes and primers to various Fusobacterium species that have closely-related interspecies genetic profiles. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and its associated analytic software, was recently approved for clinical microbiology diagnostic use by the United States Food and Drug Administration. MALDI-TOF mass spectrometry has the potential to rapidly identify cultivable clinical isolates to a species level for 4,613 different bacterial species based on mass spectra of their bacterial protein profiles, including many Fusobacterium species. The purpose of this study was to use MALDI-TOF mass spectrometry to rapidly identify the patient distribution of fusobacteria isolated from the subgingival microbiota of chronic periodontitis patients. Methods: A total of 34 chronic periodontitis patients provided 96 fresh subgingival cultivable fusobacteria isolates (one to seven isolates per patient), which were presumptively identified by their chartreuse-positive colony autofluorescence under long-wave ultraviolet light on anaerobically-incubated, non-selective, enriched Brucella blood agar primary isolation plates. Each of the presumptive fusobacteria clinical isolates were subjected to MALDI-TOF mass spectrometry analysis using a bench top mass spectrometer, Bruker FlexControl 3.0 software, and MALDI Biotyper 3.1 software (Bruker Daltonics, Billerica, MA, USA), which contains mass spectra for a variety of fusobacteria in its reference library of bacterial protein profiles. Each clinical isolate underwent on-target plate formic acid protein extraction, and was taxonomically classified with MALDI-TOF mass spectrometry within an approximately 30-45 minute time period from the point of colony harvesting from primary isolation culture plates. A MALDI Biotyper log score of equal to or larger than 1.7 was required for reliable taxonomic classification of the clinical fusobacteria isolates. Results: A majority (58.8%) of the chronic periodontitis patients yielded two or three different species of subgingival Fusobacterium on non-selective enriched Brucella blood agar primary isolation plates. Fusobacterium naviforme was identified by MALDI-TOF mass spectrometry analysis in 14 (41.2%) chronic periodontitis study patients, Fusobacterium nucleatum subspecies vincentii in 13 (38.2%) patients, Fusobacterium nucleatum subspecies polymorphum in 9 (26.5%) patients, Fusobacterium nucleatum and Fusobacterium species each in 6 (17.6%) patients, Fusobacterium nucleatum subspecies nucleatum in 4 (11.8%) patients, and Fusobacterium nucleatum subspecies animalis in 3 (8.8%) patients. Three patients additionally yielded subgingival isolates of Fusobacterium canifelinum, normally an inhabitant of the oral cavity of dogs and cats. 52 (54.2%) of the fusobacteria clinical isolates revealed MALDI Biotyper log scores of equal to or larger than 1.7, the threshold for reliable taxonomic classification, while in comparison, 44 (45.8%) had log scores less than 1.7, indicating a less reliable species identification. No other microbial species, other than one of the Fusobacterium species, was listed by the MALDI-TOF mass spectrometry analytic software as the most likely organism for the tested clinical isolates. Conclusions: These findings indicate that a variety of Fusobacterium species may be identified with MALDI-TOF mass spectrometry in the subgingival microbiota of chronic periodontitis patients. F. naviforme and F. nucleatum subspecies vincentii were the most frequently isolated subgingival fusobacteria species in the evaluated study patients. Three chronic periodontitis patients also unexpectedly revealed subgingival isolates of the animal species F. canifelinum, which is normally in the oral cavity of dogs and cats. MALDI-TOF mass spectrometry may facilitate rapid identification of cultivable fusobacteria in human subgingival dental plaque biofilms, and enhance understanding of bacterial community structure in periodontal pockets. / Oral Biology

No / A novel ion trap time-of-flight hybrid mass spectrometer (qIT-TOF MS) has been applied for peptide sequencing in proteolytic digests generated from spore mixtures of Bacilli. The method of on-probe solubilization and in situ proteolytic digestion of small, acid-soluble spore proteins has been recently developed in our laboratory, and microorganism identification in less than 20 min was accomplished.1 In this study, tryptic peptides were generated in situ from complex spore mixtures of B. subtilis 168, B. globigii, B. thuringiensis subs. Kurstaki, and B. cereus T, respectively. MALDI analysis of bacterial peptides generated was performed with an average mass resolving power of 6200 and a mass accuracy of up to 10 ppm using a trap-TOF tandem configuration. Precursor ions of interest were usually selected and stored in the quadrupole ion trap with their complete isotope distribution by choosing a window of ±2 Da. Sequence-specific information on isolated protonated peptides was gained via tandem MS experiments with an average mass resolving power of 4450 for product ion analysis, and protein and bacterial sources were identified by database searching.

Laser-Ionization Time-of-Flight Mass Spectrometry (LI-TOF-MS) is a sophisticated tool for the molecular-weight determination and structural characterization of a variety of molecules. Advances in instrumentation and ionization methods have recently expanded its role in the analysis of high-mass analytes. Large multimetallic complexes, which are efficient solar-energy converters, rely heavily on their chemical structure for optimum operation. Molecular mass determinations of these multimetallic complexes have been problematic due to their lability and high molecular weights. This thesis describes the characterization of a LI-TOF-MS instrument and confirmation of theoretical time-of-flight mass-separation principles. Several test cases demonstrate the instrument's proper operation and calibration for a wide mass range of analytes. Mass spectral results of three organometallic compounds: i. [Ir(dpp)₂Cl₂](PF₆), ii. {[(bpy)₂Ru(dpp)]₂IrCl₂}(PF₆)₅, and iii. {[(bpy)₂Ru(dpp)]₂RuCl₂}(PF₆)₅ under a variety of laser ionization and sample preparation conditions are compared. A complete structural characterization of the monometallic complex, [Ir(dpp)₂Cl₂](PF₆), is presented. The two trimetallic analytes fragmented easily, but significant components of the molecules are successfully identified. After optimizing the ionization and analytical procedure, LI-TOF-MS proved useful in the analysis of high molecular mass metal complexes. / Master of Science

Kam, Kin Ting. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 169-192). / Abstracts in English and Chinese. / Chapter 1. --- Abstract --- p.ii / English --- p.ii / Chinese --- p.v / Chapter 2. --- Acknowledgments --- p.vii / Chapter 3. --- Abbreviations and N-glycan representation --- p.viii / Chapter 4. --- Introduction --- p.1 / Chapter 5. --- Review of Literatures --- p.2 / Chapter 5.1. --- Introduction to Liver Fibrosis --- p.2 / Chapter 5.1.1. --- Pathogenesis of Liver Fibrosis --- p.2 / Chapter 5.1.2. --- Changes of liver architecture - basis of liver fibrosis diagnosis --- p.4 / Chapter 5.2. --- Current Diagnosis of Liver Fibrosis - from Biopsy Examination to Serum Test --- p.5 / Chapter 5.3. --- Glycomics and its Potential as Biomarkers --- p.9 / Chapter 5.3.1. --- Overview of Biochemical and Functional Characteristics of Glycan --- p.13 / Chapter 5.3.2. --- N-linked and O-linked Glycosylations - A Valuable Source of Biomarkers --- p.15 / Chapter 5.3.3. --- Glycomics 一 An Uprising Approach for Biomarker Discovery --- p.17 / Chapter 5.3.4. --- Human Proteome Organisation Human Disease Glycomics/Proteome Initiative --- p.19 / Chapter 5.3.5. --- Recent Applications of Glycomics to Biomarker Discovery --- p.20 / Chapter 5.4. --- Current Technologies for Glycomic Study --- p.22 / Chapter 5.4.1. --- MALDI-TOF MS --- p.22 / Chapter 5.4.2. --- Lectin Microarray --- p.25 / Chapter 5.4.3. --- Liquid Chromatography --- p.27 / Chapter 5.4.4. --- Capillary Electrophoresis --- p.29 / Chapter 5.4.5. --- Quantitative Profiling of Tissue Glycome --- p.31 / Chapter 6 --- Project Rationales and Objectives --- p.36 / Chapter 7 --- Section 1: Methodology Development of Quantitative N- glycomic Profiling --- p.37 / Chapter 1. --- Introduction --- p.37 / Chapter 2. --- Method and Materials --- p.39 / Chapter 3. --- Results --- p.46 / Chapter 4. --- Discussion --- p.65 / Chapter 5. --- Conclusion --- p.71 / Chapter 8. --- Section 2: Serum N-glycomic Profile as Biomarker for Liver Fibrosis 一 Pilot Study --- p.73 / Chapter 1. --- Introduction --- p.73 / Chapter 2. --- Method and Materials --- p.75 / Chapter 3. --- Results --- p.79 / Chapter 4. --- Discussion --- p.86 / Chapter 5. --- Conclusion --- p.94 / Chapter 9. --- Section 3: Serum N-glycomic Profile as Biomarker for Liver Fibrosis -Verification Study --- p.96 / Chapter 1. --- Introduction --- p.96 / Chapter 2. --- Method and Materials --- p.98 / Chapter 3. --- Results --- p.104 / Chapter 4. --- Discussion --- p.137 / Chapter 5. --- Conclusion --- p.152 / Chapter 10. --- General Discussion --- p.153 / Chapter 11. --- Conclusion --- p.167 / Chapter 12. --- Original Data --- p.168 / Chapter 13. --- References --- p.169 / Chapter 14. --- Publications --- p.196

Chan Pui Kwan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 98-104). / Abstracts in English and Chinese. / TABLE OF CONTENTS --- p.i / LIST OF FIGURES --- p.iv / LIST OF TABLES --- p.vii / ABBREVIATIONS --- p.viii / Chapter Chapter one --- Research Background / Chapter 1.1 --- Carbohydrates --- p.2 / Chapter 1.2 --- Impact of molecular weight of polysaccharides --- p.5 / Chapter 1.3 --- Molecular Weight Determination of polysaccharides --- p.6 / Chapter 1.3.1 --- Laser Scattering --- p.6 / Chapter 1.3.2 --- Gel Permeation Chromatography --- p.7 / Chapter 1.3.3 --- Mass spectrometry --- p.9 / Chapter 1.4 --- Matrix assisted laser desorption/ ionization (MALDI) --- p.10 / Chapter 1.4.1 --- Laser desorption --- p.10 / Chapter 1.4.2 --- Matrix-assisted laser desorption / ionization (MALDI) --- p.11 / Chapter 1.5 --- MALDI-TOFMS analysis of polymers --- p.14 / Chapter 1.6 --- Outline of the present work --- p.16 / Chapter Chapter two --- Experimental and Instrumentation / Chapter 2.1 --- Matrix-assisted laser desorption/ ionization Time of flight Mass Spectrometry (MALDI-TOFMS) --- p.18 / Chapter 2.2 --- Delayed extraction --- p.20 / Chapter 2.3 --- Time of flight mass spectrometry (TOFMS) --- p.20 / Chapter 2.3.1 --- Linear time-of-flight mass spectrometry --- p.20 / Chapter 2.3.2 --- Reflectron --- p.21 / Chapter 2.4 --- Instrumentation --- p.23 / Chapter 2.4.1 --- Laser system --- p.24 / Chapter 2.4.2 --- Ion source --- p.26 / Chapter 2.4.3 --- Ion deflection --- p.26 / Chapter 2.4.4 --- Detection --- p.27 / Chapter 2.4.5 --- Reflector --- p.27 / Chapter 2.4.6 --- Data acquisition --- p.29 / Chapter 2.5 --- Experimental --- p.29 / Chapter 2.5.1 --- Sample preparation --- p.29 / Chapter 2.5.2 --- Calibration --- p.33 / Chapter 2.6 --- Data analysis --- p.33 / Chapter Chapter three --- Use of ammonium fluoride as co-matrix / Chapter 3.1 --- Introduction --- p.35 / Chapter 3.2 --- Results and discussion --- p.37 / Chapter 3.2.1 --- Effect of co-matrix --- p.45 / Chapter 3.2.2 --- Effect of sample preparation --- p.49 / Chapter 3.2.3 --- Analysis of dispersed dextran --- p.52 / Chapter 3.3 --- Conclusion --- p.55 / Chapter Chapter four --- Effect of sample preparation / Chapter 4.1 --- Introduction --- p.57 / Chapter 4.2 --- Experimental --- p.57 / Chapter 4.2.1 --- Sample preparation --- p.57 / Chapter 4.3 --- Results and discussion --- p.59 / Chapter 4.4 --- Conclusion --- p.71 / Chapter Chapter five --- Development of liquid matrix systems / Chapter 5.1 --- Introduction --- p.73 / Chapter 5.2 --- Experimental --- p.75 / Chapter 5.2.1 --- Sample preparation --- p.75 / Chapter 5.3 --- Results and discussion --- p.76 / Chapter 5.3.1 --- Formulation of matrix solutions --- p.76 / Chapter 5.3.2 --- Use of liquid matrix system --- p.87 / Chapter 5.3.3 --- Analysis of dispersed dextran --- p.90 / Chapter 5.4 --- Conclusion --- p.93 / Chapter Chapter six --- Conclusion / Chapter 6.1 --- Conclusion --- p.95 / References --- p.98 / Appendix / Appendix 1 Chemical structure of matrices / Appendix 2 Chemical structure of solubilizing agents / Appendix 3 Chemical structure of liquid supports / Appendix 4 Chemical structure of additives

Lignocellulosic biomass (e.g., non food-based agricultural resides and forestry wastes) has recently been promoted for use as a source of bioethanol instead of food-based materials (e.g., corn and sugar cane), however to fully realize these benefits an improved understanding of lignocellulosic recalcitrance must be developed. The primary goal of this thesis is to gain fundamental knowledge about the surface of the plant cell wall, which is to be integrated into understanding biomass recalcitrance. Imaging mass spectrometry by TOF-SIMS and MALDI-IMS is applied to understand detailed spatial and lateral changes of major components in the surface of biomass under submicron scale. Using TOF-SIMS analysis, we have demonstrated a dilute acid pretreated poplar stem represented chemical differences between surface and bulk compositions. Especially, abundance of xylan was observed on the surface while sugar profile data showed most xylan (ca. 90%) removed from the bulk composition. Water only flowthrough pretreated poplar also represented difference chemistry between surface and bulk, which more cellulose revealed on the surface compared to bulk composition. In order to gain the spatial chemical distribution of biomass, 3-dimensional (3D) analysis of biomass using TOF-SIMS has been firstly introduced in the specific application of understanding recalcitrance. MALDI-IMS was also applied to visualize different molecular weight (e.g., DP) of cellulose oligomers on the surface of biomass.

Surface-assisted laser desorption/ionization mass spectrometry (SALDI MS) is a novel technique for direct analysis of organic and biological molecules. Amino acids, dipeptides, and organoselenium compounds were successfully detected by SALDI on carbon and silicon surfaces. Surface effects, solvent effects, temperature effects and pH effects were studied. A possible mechanism of SALDI is proposed based on observed results. In general, stimulated desorption results in neutral yields that are much larger than ion yields. Thus, we have exploited and further developed laser desorption single photon ionization mass spectrometry (LD/SPI MS) as a means of examining biomolecules. The experimental results clearly demonstrate that LD/SPI MS is a very useful and fast analysis method with uniform selectivity and high sensitivity. Selenium (Se) is an essential ultra-trace element in the human body. In efforts to obtain more useful information of selenium metabolites in human urine, mass determination of unknown organoselenium compounds in biological matrices using SALDI MS was investigated. In another approach, several selenium metabolites in human urine were successfully detected by LD/SPI MS. A HPLC-MS/MS method was also developed for a quantitative case study of selenium metabolites in human urine after ingestion of selenomethionine. Low-energy electrons (LEE, 3-20 eV) have been shown to induce single and double strand breaks (SSB and DSB) in plasmid DNA. To understand the genotoxic effects due to secondary species of high-energy radiation, we investigate the role of transient negative ions and the specificity in LEE-DNA damage by examining the neutral product yields using low electron stimulated dissociation SPI MS. The neutral yields as a function of incident electron energy are also correlated with the SSBs and DSBs measured using post-irradiation gel electrophoresis. The results provide further insight concerning the mechanisms of LEE-induced damage to DNA. Overall, this research provided an in-depth understanding of non-thermal surface processes and the development of new mass spectrometric techniques for the analysis of biomolecules.

Identification of fungi is based on macroscopic observations of morphology and microscopic characteristics. These conventional methods are time-consuming and requires expert knowledge. For the past years Matrix-assisted laser desorption ionization-time of flight mass spectrometry has been used for routine bacterial identification in clinical laboratories but not yet in the same extension for fungi. In this study three preanalytic preparation methods for fungi were evaluated in order to shorten the processing time in routine laboratory performance. Clinically relevant strains (n=18) of molds and dermatophytes were cultivated on agar plates and prepared according to the different preparation methods for protein extraction. Each strain was analyzed in quadruplicate by the MALDI Biotyper and the database Filamentous Fungi Library 1.0. The results showed that the genus and species identification rates of the least time-consuming direct extraction method were 33% and 11% respectively. Using the formic acid extraction method, the genus and species identification rates were 83% and 44%, respectively. For the longest sample preparation method, liquid media culturing before formic acid extraction, successfully identified all strains except one, which resulted in an identification rate of 94% and 78% respectively. This study shows that preparing samples in cultured liquid media MADLI-TOF MS effectively identified fungal strains to both genus- and species-level. This method was however too time-consuming and cumbersome to be recommended as a replacement to the conventional method. Future studies should be aimed at expanding the reference library and making the direct extraction method more reproducible in terms of obtaining more reliable identification rates.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 7 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2005. / Härtill 5 uppsatser.