You searched for subject:(Tandem mass spectrometry).
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Boston University
1.
Hogan, John.
Methods in automated glycosaminoglycan tandem mass spectra analysis.
Degree: PhD, Bioinformatics GRS, 2019, Boston University
URL: http://hdl.handle.net/2144/34811 
► Glycosylation is the process by which a glycan is enzymatically attached to a protein, and is one of the most common post-translational modifications in nature.…
(more)
▼ Glycosylation is the process by which a glycan is enzymatically attached to a protein, and is one of the most common post-translational modifications in nature. One class of glycans is the glycosaminoglycans (GAGs), which are long, linear polysaccharides that are variably sulfated and make up the glycan portion of proteoglycans (PGs). PGs are located on the cellular surface and in the extracellular matrix (ECM), making them important molecules for cell signaling and ligand binding. The GAG sulfation sequence is a determining factor for the signaling capacity of binding complexes, so accurate determination of the sequence is critical. Historically, GAG sequencing using
tandem mass spectrometry (MS2) has been a difficult, manual process; however, with the advent of faster computational techniques and higher-resolution MS2, high-throughput GAG sequencing is within reach.
Two steps in the pipeline of biomolecule sequencing using MS2 are discovery and interpretation of spectral peaks. The discovery step traditionally is performed using methods that rely on the concept of averagine, or the average molecular building block for the analyte in question. These methods were developed for protein sequencing, but perform considerably worse on GAG sequences, due to the non-uniform distribution of sulfur atoms along the chain and the relatively high isotope abundance of 34S. The interpretation step traditionally is performed manually, which takes time and introduces potential user error. To combat these problems, I developed GAGfinder, the first GAG-specific MS2 peak finding and annotation software. GAGfinder is described in detail in chapter two.
Another step in MS2 sequencing is the determination of the sequence using the found MS2 fragments. For a given GAG composition, there are many possible sequences, and peak finding algorithms such as GAGfinder return a list of the peaks in the MS2
mass spectrum. The many-to-many relationship between sequences and fragments can be represented using a bipartite network, and node-ranking techniques can be employed to generate likelihood scores for possible sequences. I developed a bipartite network-based sequencing tool, GAGrank, based on a bipartite network extension of Google’s PageRank algorithm for ranking websites. GAGrank is described in detail in chapter three.
Advisors/Committee Members: Zaia, Joseph (advisor).
Subjects/Keywords: Bioinformatics; Glycosaminoglycan; Networks; Sequencing; Tandem mass spectrometry
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APA (6th Edition):
Hogan, J. (2019). Methods in automated glycosaminoglycan tandem mass spectra analysis. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/34811
Chicago Manual of Style (16th Edition):
Hogan, John. “Methods in automated glycosaminoglycan tandem mass spectra analysis.” 2019. Doctoral Dissertation, Boston University. Accessed January 18, 2021.
http://hdl.handle.net/2144/34811.
MLA Handbook (7th Edition):
Hogan, John. “Methods in automated glycosaminoglycan tandem mass spectra analysis.” 2019. Web. 18 Jan 2021.
Vancouver:
Hogan J. Methods in automated glycosaminoglycan tandem mass spectra analysis. [Internet] [Doctoral dissertation]. Boston University; 2019. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/2144/34811.
Council of Science Editors:
Hogan J. Methods in automated glycosaminoglycan tandem mass spectra analysis. [Doctoral Dissertation]. Boston University; 2019. Available from: http://hdl.handle.net/2144/34811
Michigan State University
2.
Zhou, Xiao.
'Fixed charge' chemical derivatization and data dependent multistage tandem mass spectrometry for protein structural analysis.
Degree: 2012, Michigan State University
URL: http://etd.lib.msu.edu/islandora/object/etd:1256
► Thesis Ph. D. Michigan State University. Chemistry 2012.
Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. With…
(more)
▼ Thesis Ph. D. Michigan State University. Chemistry 2012.
Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. With the advantages in sensitivity, speed, and the capability of analyzing large/complex protein systems, mass spectrometry combined with protein labeling has found increasing utility for the characterization of protein surface. However, a common problem associated with the use of chemical labeling methods for mapping protein solvent accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed, the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e., the `needle in a haystack' problem). To address this challenge, an experimental strategy was developed involving the synthesis and application of a novel `fixed charge' sulfonium ion containing amine-specific protein modification reagent, S,S'-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-electrospray (ESI)-MS, automated collision induced dissociation (CID)-MS/MS, and data dependent neutral loss mode MS3 in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, Cellular Retinoic Acid Binding Protein II (CRABP II). After reaction with different reagent : protein ratios and digestion with Glu-C, modified peptides were selectively identified and the number of modifications within each peptide were determined by CID-MS/MS, via the exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state (i.e. proton mobility) of the peptide. The observation of these characteristic neutral losses were then used to automatically `trigger' the acquisition of an MS3 spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution structure of CRABP II. With the initial success demonstrated on a model protein, the experimental strategy was extended to reveal the mechanisms corresponding to oxidation induced inactivation of calcineurin (CN), from a structural perspective. CN is a Ca2+/calmodulin (CaM) activated phosphatase that participates in a wide variety of physiological processes. CaN is also reported to be inactivated by H2O2- or superoxide-induced oxidation both in vivo and in vitro. However, the mechanism is still under debate. Here, the relative rates of H2O2 induced oxidation of methionine residues within CN were first determined using a multi enzyme digestion strategy coupled with analysis using capillary HPLC-ESI-MS and CID/ETD-MS/MS. Then the developed experimental strategy, i.e., combining protein modification by DMBNHS with data dependent multistage tandem mass spectrometry, was applied to characterize changes in CN…
Advisors/Committee Members: Reid, Gavin E, Bruening, Merlin L, Jones, Arthur D, Baker, Gregory L.
Subjects/Keywords: Proteins – Analysis; Tandem mass spectrometry; Chemistry
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APA (6th Edition):
Zhou, X. (2012). 'Fixed charge' chemical derivatization and data dependent multistage tandem mass spectrometry for protein structural analysis. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:1256
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Zhou, Xiao. “'Fixed charge' chemical derivatization and data dependent multistage tandem mass spectrometry for protein structural analysis.” 2012. Thesis, Michigan State University. Accessed January 18, 2021.
http://etd.lib.msu.edu/islandora/object/etd:1256.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zhou, Xiao. “'Fixed charge' chemical derivatization and data dependent multistage tandem mass spectrometry for protein structural analysis.” 2012. Web. 18 Jan 2021.
Vancouver:
Zhou X. 'Fixed charge' chemical derivatization and data dependent multistage tandem mass spectrometry for protein structural analysis. [Internet] [Thesis]. Michigan State University; 2012. [cited 2021 Jan 18].
Available from: http://etd.lib.msu.edu/islandora/object/etd:1256.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zhou X. 'Fixed charge' chemical derivatization and data dependent multistage tandem mass spectrometry for protein structural analysis. [Thesis]. Michigan State University; 2012. Available from: http://etd.lib.msu.edu/islandora/object/etd:1256
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Georgia
3.
Wang, Haofei.
Statistical analysis of mass spectrometry-assisted protein identification methods.
Degree: 2014, University of Georgia
URL: http://hdl.handle.net/10724/21396
► Mass spectrometry combined with database search utilities is a valuable protein identification tool. The success of database mining is dependent upon a series of variables…
(more)
▼ Mass spectrometry combined with database search utilities is a valuable protein identification tool. The success of database mining is dependent upon a series of variables such as mass accuracy, protein purity, peptide yield, and the genomic
complexity of the target organism as well as the size of database searched. Ten proteins are selected to quantify the dynamic interaction of the variables of interest using statistical methods. The ten proteins’ spectra and simulated randomized spectra
were searched using two searching programs. Statistically significant effects due to variation in mass accuracy, peptide coverage, level of impurity, database size and their interactions are found and quantified.
Subjects/Keywords: Mass spectrometry; MALDI-TOF; Tandem mass spectrometry; Proteomics; Peptide mapping; Database search; and Mass accuracy
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APA ·
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APA (6th Edition):
Wang, H. (2014). Statistical analysis of mass spectrometry-assisted protein identification methods. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/21396
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Haofei. “Statistical analysis of mass spectrometry-assisted protein identification methods.” 2014. Thesis, University of Georgia. Accessed January 18, 2021.
http://hdl.handle.net/10724/21396.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Haofei. “Statistical analysis of mass spectrometry-assisted protein identification methods.” 2014. Web. 18 Jan 2021.
Vancouver:
Wang H. Statistical analysis of mass spectrometry-assisted protein identification methods. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/10724/21396.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang H. Statistical analysis of mass spectrometry-assisted protein identification methods. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/21396
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Georgia
4.
Wang, Haofei.
Factors that affect protein identification by mass spectrometry.
Degree: 2014, University of Georgia
URL: http://hdl.handle.net/10724/21395
► Mass spectrometry combined with database search utilities is a valuable protein identification tool. The success of database mining is dependent upon mass accuracy, protein purity,…
(more)
▼ Mass spectrometry combined with database search utilities is a valuable protein identification tool. The success of database mining is dependent upon mass accuracy, protein purity, peptide yield, and the genomic complexity of the target
organism. Three proteins were selected to investigate the dynamic interaction of these variables and their effect on database mining. With variables of interest controlled, simulated spectra were searched using two searching programs. Results suggest
that high mass accuracy improves database searching confidence in the protein identification. With the addition of random noise peaks, some searching programs require a significant increase in the number of peptide ions and the mass accuracy required.
Placing limits on database searches usually improves searching efficiency by allowing fewer peptide ions for a successful identification.
Subjects/Keywords: Mass spectrometry; MALDI-TOF; Tandem mass spectrometry; Proteomics; Peptide mapping; Database search; and Mass accuracy
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APA ·
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APA (6th Edition):
Wang, H. (2014). Factors that affect protein identification by mass spectrometry. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/21395
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Haofei. “Factors that affect protein identification by mass spectrometry.” 2014. Thesis, University of Georgia. Accessed January 18, 2021.
http://hdl.handle.net/10724/21395.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Haofei. “Factors that affect protein identification by mass spectrometry.” 2014. Web. 18 Jan 2021.
Vancouver:
Wang H. Factors that affect protein identification by mass spectrometry. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/10724/21395.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang H. Factors that affect protein identification by mass spectrometry. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/21395
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Cincinnati
5.
Wetzel, Collin.
Global Identification and Mass Mapping of tRNA Isoacceptors
Using Targeted Tandem Mass Spectrometry.
Degree: PhD, Arts and Sciences: Chemistry, 2015, University of Cincinnati
URL: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1448037316
► This dissertation is focused on developing and implementing liquid chromatography-tandem mass spectrometry (LC-MS/MS) approaches for the high-throughput characterization of small RNAs in complex biological matrices.…
(more)
▼ This dissertation is focused on developing and
implementing liquid chromatography-
tandem mass spectrometry
(LC-MS/MS) approaches for the high-throughput characterization of
small RNAs in complex biological matrices. Non-coding ribonucleic
acids (ncRNA) have become increasingly recognized as important to a
number of biological functions, such as gene expression at both the
transcriptional and translational levels. Among the many classes of
ncRNAs, transfer ribonucleic acids (tRNA) are noted for their
significant role in the center of the central dogma of molecular
biology, translating the genetic code into functional proteins.
Naturally occurring chemical modifications are applied
post-transcriptionally to these polymers giving them added
structure and function. Despite biological relevance, the complex
nature of mixtures containing a pool of total tRNA typically
requires lengthy, impractical sample preparations steps. The
“digest and go” methods proposed in this dissertation should be
capable of helping advance the field of RNomics, much like the
lasting impact LC-MS based strategies have had on the rapidly
advancing field of proteomics; lending themselves to applications
from basic molecular biology studies to clinical applications
previously thought impractical. These advances were accomplished by
implementing targeted MS/MS based assays, which take advantage of
high-through-put data collection, taking one third the time of
previous LC-MS based approaches and capable of identifying more
individual tRNA isoacceptors, in conjunction with automated data
analysis.
Advisors/Committee Members: Limbach, Patrick (Committee Chair).
Subjects/Keywords: Analytical Chemistry; Mass Spectrometry; RNA; tRNA; RNA Mass Mapping; Tandem Mass Spectrometry
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APA ·
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APA (6th Edition):
Wetzel, C. (2015). Global Identification and Mass Mapping of tRNA Isoacceptors
Using Targeted Tandem Mass Spectrometry. (Doctoral Dissertation). University of Cincinnati. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=ucin1448037316
Chicago Manual of Style (16th Edition):
Wetzel, Collin. “Global Identification and Mass Mapping of tRNA Isoacceptors
Using Targeted Tandem Mass Spectrometry.” 2015. Doctoral Dissertation, University of Cincinnati. Accessed January 18, 2021.
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1448037316.
MLA Handbook (7th Edition):
Wetzel, Collin. “Global Identification and Mass Mapping of tRNA Isoacceptors
Using Targeted Tandem Mass Spectrometry.” 2015. Web. 18 Jan 2021.
Vancouver:
Wetzel C. Global Identification and Mass Mapping of tRNA Isoacceptors
Using Targeted Tandem Mass Spectrometry. [Internet] [Doctoral dissertation]. University of Cincinnati; 2015. [cited 2021 Jan 18].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1448037316.
Council of Science Editors:
Wetzel C. Global Identification and Mass Mapping of tRNA Isoacceptors
Using Targeted Tandem Mass Spectrometry. [Doctoral Dissertation]. University of Cincinnati; 2015. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1448037316
University of Georgia
6.
Johnson, Darryl Lee.
The development of high efficiency separation techniques for the proteomic analysis of the canine prostate gland and exploration of the canine as an animal model of human prostate cancer.
Degree: 2014, University of Georgia
URL: http://hdl.handle.net/10724/29080
► Mass spectrometry (MS) is the most widely utilized analytical tool for the large-scale study of an organism’s proteome. This has created lofty expectations for the…
(more)
▼ Mass spectrometry (MS) is the most widely utilized analytical tool for the large-scale study of an organism’s proteome. This has created lofty expectations for the field of proteomics; however the study of biological systems continues to be
daunting task due to the extreme complexity and wide dynamic range of protein expression. Multidimensional separation techniques have been incorporated into MS-based proteomic workflows to overcome this challenge. Unfortunately, improvements in
separating power come at the expense of MS analysis time, thus implementation of highly efficient separation strategies becomes necessary to achieve high throughput. In this work, we describe the development of high efficiency reversed-phase liquid
chromatography (LC) separation methods. The use of superficially porous column packing materials permitted fast LC separations, and optimization of data-dependent acquisition (DDA) parameters allowed for the collection of high quality MS/MS spectra when
experiment time was reduced. The use of formic acid and ammonium formate (FA/AF) as a mobile phase modifier was found to be compatible with electrospray ionization, and provided a significant improvement in peptide separations over formic acid alone.
This combination of high efficiency LC separations and optimized DDA parameters lead to a significant reduction in experiment time and substantial increases in proteome coverage. The efficiency of 1D gel electrophoresis and LC (GeLC) separations were
evaluated to determine how to maximize protein identifications in a fixed instrument time format. This work demonstrates that the number of gel slices collected in GeLC analysis has very little impact on protein identifications. The most significant
factor is GeLC protein identification efficiency is the percentage of instrument time dedicated to LC gradient elution conditions. These newly developed, high efficiency GeLC separation methods were applied to the proteomic analysis of the canine
prostate gland. Canines and humans are the only two large mammals that spontaneously generate prostate cancer, thereby suggesting a potential predictive model of the human disease. Our work identified several proteins with association to prostate cancer
development and progression, suggesting the canine could be a relevant predictive model of androgen-insensitive, highly aggressive human prostate cancer.
Subjects/Keywords: Liquid Chromatography; Mass Spectrometry; Tandem Mass Spectrometry; Proteomics; Gel Electrophoresis; Animal Model; Canine; Prostate Cancer
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APA ·
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APA (6th Edition):
Johnson, D. L. (2014). The development of high efficiency separation techniques for the proteomic analysis of the canine prostate gland and exploration of the canine as an animal model of human prostate cancer. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/29080
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Johnson, Darryl Lee. “The development of high efficiency separation techniques for the proteomic analysis of the canine prostate gland and exploration of the canine as an animal model of human prostate cancer.” 2014. Thesis, University of Georgia. Accessed January 18, 2021.
http://hdl.handle.net/10724/29080.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Johnson, Darryl Lee. “The development of high efficiency separation techniques for the proteomic analysis of the canine prostate gland and exploration of the canine as an animal model of human prostate cancer.” 2014. Web. 18 Jan 2021.
Vancouver:
Johnson DL. The development of high efficiency separation techniques for the proteomic analysis of the canine prostate gland and exploration of the canine as an animal model of human prostate cancer. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/10724/29080.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Johnson DL. The development of high efficiency separation techniques for the proteomic analysis of the canine prostate gland and exploration of the canine as an animal model of human prostate cancer. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/29080
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Georgia
7.
Williamson, Leah Nicole.
Novel methods for the quantitation of central nervous system agents.
Degree: 2014, University of Georgia
URL: http://hdl.handle.net/10724/24319
► Humans can be exposed to central nervous system agents environmentally and/or therapeutically. Chronic exposure to these agents can cause damage to the central nervous system.…
(more)
▼ Humans can be exposed to central nervous system agents environmentally and/or therapeutically. Chronic exposure to these agents can cause damage to the central nervous system. In order to study the neurological effects of these agents,
sensitive and selective analytical methods must be developed and validated in biological matrices, such as brain tissue, plasma, and whole blood. Chlorpyrifos (CPF) is an organophosphate pesticide that inhibits acetylcholinesterase, which is an enzyme
that is necessary for normal function of the nervous system. CPF is metabolized by cytochrome P450 into chlorpyrifos-oxon (CPF-O) and TCP. CPF-O is about 3,000 times more potent than CPF in its inhibition of acetylcholinesterase activity, while TCP is
non-toxic and is eliminated by the kidneys. Therapeutically, chronic exposure to antipsychotic drugs can result in abnormalities in motor function. Additionally, it is important to determine the extent to which a correlation exists between plasma and
brain levels of these agents and cognitive function. Chapter 1 is the introduction and literature review that describes the layout of the dissertation and reviews the literature for analytical methods using liquid chromatography with time-of-flight mass
spectrometry (TOF-MS) for quantitation. Chapter 2 reviews the literature for analytical methods using gas chromatography and TOF-MS for quantitation. Chapters 3 and 4 present analytical methods for the quantitation of CPF and its metabolites in rat brain
tissue and blood using liquid chromatography and tandem mass spectrometry (LC-MS/MS). A TOF-MS analytical method for the quantitation of five antipsychotic drugs in rat plasma is presented in chapter 5.
Subjects/Keywords: High performance liquid chromatography; tandem mass spectrometry; time-of-flight mass spectrometry; quantitation; chlorpyrifos; antipsychotics
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APA ·
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Export
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APA (6th Edition):
Williamson, L. N. (2014). Novel methods for the quantitation of central nervous system agents. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/24319
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Williamson, Leah Nicole. “Novel methods for the quantitation of central nervous system agents.” 2014. Thesis, University of Georgia. Accessed January 18, 2021.
http://hdl.handle.net/10724/24319.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Williamson, Leah Nicole. “Novel methods for the quantitation of central nervous system agents.” 2014. Web. 18 Jan 2021.
Vancouver:
Williamson LN. Novel methods for the quantitation of central nervous system agents. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/10724/24319.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Williamson LN. Novel methods for the quantitation of central nervous system agents. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/24319
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Johannes Gutenberg Universität Mainz
8.
Fachinger, Johannes Richard Werner.
Das Aerosol-Ionenfallen-Massenspektrometer (AIMS) : Aufbau, Charakterisierung und Feldeinsatz.
Degree: 2012, Johannes Gutenberg Universität Mainz
URL: http://ubm.opus.hbz-nrw.de/volltexte/2012/3278/
► Um die in der Atmosphäre ablaufenden Prozesse besser verstehen zu können, ist es wichtig dort vorhandene Partikel gut charakterisieren zu können. Dazu gehört unter anderem…
(more)
▼ Um die in der Atmosphäre ablaufenden Prozesse besser verstehen zu können, ist es wichtig dort vorhandene Partikel gut charakterisieren zu können. Dazu gehört unter anderem die Bestimmung der chemischen Zusammensetzung der Partikel. Zur Analyse insbesondere organischer Partikel wurde dazu in einer früheren Promotion das Aerosol-Ionenfallen-Massenspektrometer (AIMS) entwickelt.Im Rahmen dieser Arbeit wurden Entwicklungsarbeiten durchgeführt, um die Charakteristiken des Prototypen zu verbessern sowie es für den Feldeinsatz tauglich zu machen. Die durchgeführten Veränderungen betreffen mechanische und elektrische Komponenten sowie das LabView Steuerungsprogramm. So wurde z.B. die Ionenquelle derart modifiziert, dass die Ionen nicht mehr permanent erzeugt werden, sondern nur innerhalb des Zeitraums wenn sie auch in der Ionenfalle gespeichert werden können. Durch diese Modifikation konnte das Signal-zu-Rausch Verhältnis deutlich verbessert werden. Nach Beendigung der Umbauten wurden in ausführlichen Laborstudien die einzelnen Instrumentenparameter detailliert charakterisiert. Neben den Spannungen die zur Fokussierung oder zur Speicherung der Ionen in der Ionenfalle dienen, wurden die unterschiedlichen Arten der resonanten Anregung, mittels der die Ionen in der Ionenfalle gezielt zu Schwingungen angeregt werden können, sehr genau untersucht. Durch eine gezielte Kombination der unterschiedlichen Arten der resonanten Anregung ist es möglich MSn-Studien durchzuführen. Nach erfolgreicher Charakterisierung konnte in weiteren Laborstudien die MSn-Fähigkeit des AIMS demonstriert werden. Für Tryptophan (C11H12N2O2) wurde anhand von MS4-Studien ausgehend von m/z 130 ein möglicher Fragmentierungsweg identifiziert. Für die einzelnen Stufen der MS4-Studien wurden die Nachweisgrenzen abgeschätzt. Im Rahmen der PARADE (PArticles and RAdicals: Diel observations of the impact of urban and biogenic Emissions) Messkampagne im August/September 2011 auf dem kleinen Feldberg in der Nähe von Frankfurt am Main wurde die Feldtauglichkeit des AIMS demonstriert. Die Nachweisgrenzen liegen für eine Mittelungszeit von 60 Minuten für Organik bei 1,4 µg m-3, für Nitrat bei 0,5 µg m-3 und für Sulfat bei 0,7 µg m-3, was ausreichend ist um atmosphärisches Aerosol messen zu können. Dies ist ein signifikanter Fortschritt im Vergleich zum Prototypen, der aufgrund schlechter Reproduzierbarkeit und Robustheit noch nicht feldtauglich war. Im Vergleich zum HR-ToF-AMS, einem Standard-Aerosolmassenspektrometer, zeigte sich, dass beide Instrumente vergleichbare Trends für die Spezies Nitrat, Sulfat und Organik messen.
For a better understanding of atmospheric aerosol processes, a more detailed characterization, in particular of the chemical composition, is necessary. Therefore in the context of a former PhD thesis the Aerosol Ion-trap Mass Spectrometer (AIMS) has been developed. This thesis focuses on modifications to improve the characteristics of the prototype and to bring it into the field for the first time. These modifications include improvements of the…
Subjects/Keywords: Aerosol-Massenspektrometrie; Paul-Falle; Tandem-Massenspektrometrie; aerosol mass spectrometry; Paul trap; tandem mass spectrometry; Natural sciences and mathematics
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Manager
APA (6th Edition):
Fachinger, J. R. W. (2012). Das Aerosol-Ionenfallen-Massenspektrometer (AIMS) : Aufbau, Charakterisierung und Feldeinsatz. (Doctoral Dissertation). Johannes Gutenberg Universität Mainz. Retrieved from http://ubm.opus.hbz-nrw.de/volltexte/2012/3278/
Chicago Manual of Style (16th Edition):
Fachinger, Johannes Richard Werner. “Das Aerosol-Ionenfallen-Massenspektrometer (AIMS) : Aufbau, Charakterisierung und Feldeinsatz.” 2012. Doctoral Dissertation, Johannes Gutenberg Universität Mainz. Accessed January 18, 2021.
http://ubm.opus.hbz-nrw.de/volltexte/2012/3278/.
MLA Handbook (7th Edition):
Fachinger, Johannes Richard Werner. “Das Aerosol-Ionenfallen-Massenspektrometer (AIMS) : Aufbau, Charakterisierung und Feldeinsatz.” 2012. Web. 18 Jan 2021.
Vancouver:
Fachinger JRW. Das Aerosol-Ionenfallen-Massenspektrometer (AIMS) : Aufbau, Charakterisierung und Feldeinsatz. [Internet] [Doctoral dissertation]. Johannes Gutenberg Universität Mainz; 2012. [cited 2021 Jan 18].
Available from: http://ubm.opus.hbz-nrw.de/volltexte/2012/3278/.
Council of Science Editors:
Fachinger JRW. Das Aerosol-Ionenfallen-Massenspektrometer (AIMS) : Aufbau, Charakterisierung und Feldeinsatz. [Doctoral Dissertation]. Johannes Gutenberg Universität Mainz; 2012. Available from: http://ubm.opus.hbz-nrw.de/volltexte/2012/3278/
East Carolina University
9.
Kobet, Robert A.
DIFFERENTIATION OF J-SERIES PROSTAGLANDINS AS PRO-APOPTOTIC PRODUCTS OF CANCER CELL METABOLISM.
Degree: MS, MS-Chemistry, 2016, East Carolina University
URL: http://hdl.handle.net/10342/6003
► Cyclopentenone J-series prostaglandins and prostaglandin-ethanolamide conjugates have been shown to selectively induce endoplasmic reticulum stress-apoptosis in different cancer cell types. These lipids have been identified…
(more)
▼ Cyclopentenone J-series prostaglandins and prostaglandin-ethanolamide conjugates have been shown to selectively induce endoplasmic reticulum stress-apoptosis in different cancer cell types. These lipids have been identified as the downstream products of COX-2 metabolism of arachidonic acid and arachidonoyl ethanolamide, respectively. While techniques such as ELISA and UV-Vis spectroscopy can detect these molecules based on their class, they fail to offer the specificity necessary to differentiate those prostaglandins that are isomeric in structure. The J-series prostaglandins PGJ2 and [Delta]12PGJ2 are structural isomers that differ in the position of a single double bond. The differentiation of these prostaglandins is an important step in the elucidation of the metabolic pathway mediated by COX-2 and the mechanism of action of the downstream products.
Mass spectrometry has been shown to be a powerful method in the study of biological lipids due to the sensitivity and specificity it offers.
Tandem mass spectrometry (MS/MS) offers the ability to isolate molecules of identical masses and obtain information regarding their individual fragmentation patterns as well as energetics and stability characteristics. The goal of this project is to differentiate the prostaglandin isomers PGJ2 and [Delta]12PGJ2 using a variety of MS/MS methods. MS/MS experiments were performed on prostaglandin standard solutions using a linear quadrupole-time of flight (Q-ToF)
mass spectrometer and a quadrupole ion trap (QIT). An initial set of experiments aimed to identify product ions specific to either isomer using MS/MS and pseudo-MS3 on the Q-ToF and MSn analysis using the QIT. Our results indicate that neither method yielded product ions with significant intensity and reproducibility to be designated as specific to either isomer. Our focus then shifted to attempting to exploit differences in the energies of onset of some of the common product ions (energy-resolved
mass spectrometry). Under controlled sample preparation and ESI source parameters, this method was also shown to be unsuccessful in providing information specific to either PGJ2 or [Delta]12PGJ2. These results are predicted to be the result of in-source isomerization of PGJ2 to the conjugated [Delta]12 isomer. In order to confirm unique fragmentation of the double bond isomers using the established LC-ESI-MS/MS method initially used to identify these metabolic products, offline derivatization methods will likely be necessary to fix the double bond position in order to prevent the in-source isomerization that is believed to have hindered our ability to differentiate these molecules.
Advisors/Committee Members: Danell, Allison S. (advisor).
Subjects/Keywords: energy-resolved mass spectrometry; collision-induced dissociation; Cancer cells; Mass spectrometry; Prostaglandins; Tandem mass spectrometry; Cancer – Research
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APA (6th Edition):
Kobet, R. A. (2016). DIFFERENTIATION OF J-SERIES PROSTAGLANDINS AS PRO-APOPTOTIC PRODUCTS OF CANCER CELL METABOLISM. (Masters Thesis). East Carolina University. Retrieved from http://hdl.handle.net/10342/6003
Chicago Manual of Style (16th Edition):
Kobet, Robert A. “DIFFERENTIATION OF J-SERIES PROSTAGLANDINS AS PRO-APOPTOTIC PRODUCTS OF CANCER CELL METABOLISM.” 2016. Masters Thesis, East Carolina University. Accessed January 18, 2021.
http://hdl.handle.net/10342/6003.
MLA Handbook (7th Edition):
Kobet, Robert A. “DIFFERENTIATION OF J-SERIES PROSTAGLANDINS AS PRO-APOPTOTIC PRODUCTS OF CANCER CELL METABOLISM.” 2016. Web. 18 Jan 2021.
Vancouver:
Kobet RA. DIFFERENTIATION OF J-SERIES PROSTAGLANDINS AS PRO-APOPTOTIC PRODUCTS OF CANCER CELL METABOLISM. [Internet] [Masters thesis]. East Carolina University; 2016. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/10342/6003.
Council of Science Editors:
Kobet RA. DIFFERENTIATION OF J-SERIES PROSTAGLANDINS AS PRO-APOPTOTIC PRODUCTS OF CANCER CELL METABOLISM. [Masters Thesis]. East Carolina University; 2016. Available from: http://hdl.handle.net/10342/6003
NSYSU
10.
Wang, Ter-min.
Determination of the triarylmethanes and corresponding metabolites in aquatic animal tissues by high-performance liquid chromatography-tandem mass spectrometry.
Degree: Master, Marine Biotechnology and Resources, 2008, NSYSU
URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0901108-120157
► 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…
(more)
▼ 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)â 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 (CCα) were 0.16 ± 0.07 μg/kg(MG), 0.15 ± 0.04 μg/kg(LMG), 0.20 ± 0.13 μg/kg(CV) and 0.23 ± 0.12 μg/kg(LCV), and detection capabilities (CCβ) were 0.20 ± 0.09 μg/kg(MG), 0.18 ± 0.05 μg/kg(LMG), 0.24 ± 0.16 μgkg-1(CV) and 0.29 ± 0.15 μg/kg(LCV).
Advisors/Committee Members: Chi-Hsin Hsu (chair), Wei-Hsien Wang (committee member), Jung-Hui Chen (chair).
Subjects/Keywords: LC-MS/MS; high-performance liquid chromatography-tandem mass spectrometry; triarylmethane
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APA (6th Edition):
Wang, T. (2008). Determination of the triarylmethanes and corresponding metabolites in aquatic animal tissues by high-performance liquid chromatography-tandem mass spectrometry. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0901108-120157
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Ter-min. “Determination of the triarylmethanes and corresponding metabolites in aquatic animal tissues by high-performance liquid chromatography-tandem mass spectrometry.” 2008. Thesis, NSYSU. Accessed January 18, 2021.
http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0901108-120157.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Ter-min. “Determination of the triarylmethanes and corresponding metabolites in aquatic animal tissues by high-performance liquid chromatography-tandem mass spectrometry.” 2008. Web. 18 Jan 2021.
Vancouver:
Wang T. Determination of the triarylmethanes and corresponding metabolites in aquatic animal tissues by high-performance liquid chromatography-tandem mass spectrometry. [Internet] [Thesis]. NSYSU; 2008. [cited 2021 Jan 18].
Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0901108-120157.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang T. Determination of the triarylmethanes and corresponding metabolites in aquatic animal tissues by high-performance liquid chromatography-tandem mass spectrometry. [Thesis]. NSYSU; 2008. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0901108-120157
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Universiteit Utrecht
11.
Ahmed, M.M.
Recent Advances in Phosphoproteomics: Principles and Applications.
Degree: 2012, Universiteit Utrecht
URL: http://dspace.library.uu.nl:8080/handle/1874/258961
► Protein phosphorylation is a reversible modification of cellular proteins that regulate protein function, cellular localization and formation of protein complexes. It is involved in almost…
(more)
▼ Protein phosphorylation is a reversible modification of cellular proteins that regulate protein function, cellular localization and formation of protein complexes. It is involved in almost all cellular processes and deregulation of protein phosphorylation has been implicated in the development of many diseases. Currently,
mass spectrometry (MS) is the method of choice for studying cellular phosphorylation events, as the state-of-art MS techniques are able to analyze thousands of phosphopeptides present in complex biological samples in one experiment, in a rapid and highly sensitive fashion. However, phosphorylation analysis with MS is challenged by the substoichiometric levels of phosphorylated peptides, suppression of phosphopeptide ionization inside
mass spectrometers and the loss of the phosphate group during peptide ion fragmentation in
tandem mass spectrometry (MS/MS). With this respect, various developments in sample preparation strategies, instrumentation, quantitative methodologies and data analysis tools have been achieved to enhance MS-based phosphorylation analysis. Selective isolation and enrichment of phosphorylated proteins/peptides in analytical samples can be achieved prior to MS analysis by techniques such as, immobilized metal affinity chromatography (IMAC) using metal ions, metal oxide chromatography (MOAC) using metal oxides, other chromatographic methods such strong cation exchange (SCX) chromatography or the use of specific antibodies directed against specific phosphorylated residues in immunoprecipitation, while, combining different enrichment techniques are frequently employed to enhance the efficiency of enrichment and the subsequent phosphorylation analysis. Several MS approaches were developed to facilitate the analysis of phosphopeptides which can be difficult due the loss of the phosphate group. These include multi-stage MS with additional activation steps (e.g. MS3),
mass spectrometers with high-energy implementations and special scan modes and the employment of ion fragmentation techniques that avoid the phosphate group loss, such as electron-based dissociation techniques. In this literature review, the principles and applications of the state-of-art MS methodologies, current challenges and future directions in phosphoproteomics are described. In addition, some of the advances made in chemical biology tools for studying protein phosphorylation are discussed.
Advisors/Committee Members: Rijkers, D. T. S..
Subjects/Keywords: Phosphoproteomics; Enrichment strategies; Phosphopeptide Fragmentation; Tandem mass spectrometry
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APA (6th Edition):
Ahmed, M. M. (2012). Recent Advances in Phosphoproteomics: Principles and Applications. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/258961
Chicago Manual of Style (16th Edition):
Ahmed, M M. “Recent Advances in Phosphoproteomics: Principles and Applications.” 2012. Masters Thesis, Universiteit Utrecht. Accessed January 18, 2021.
http://dspace.library.uu.nl:8080/handle/1874/258961.
MLA Handbook (7th Edition):
Ahmed, M M. “Recent Advances in Phosphoproteomics: Principles and Applications.” 2012. Web. 18 Jan 2021.
Vancouver:
Ahmed MM. Recent Advances in Phosphoproteomics: Principles and Applications. [Internet] [Masters thesis]. Universiteit Utrecht; 2012. [cited 2021 Jan 18].
Available from: http://dspace.library.uu.nl:8080/handle/1874/258961.
Council of Science Editors:
Ahmed MM. Recent Advances in Phosphoproteomics: Principles and Applications. [Masters Thesis]. Universiteit Utrecht; 2012. Available from: http://dspace.library.uu.nl:8080/handle/1874/258961
University of Alberta
12.
Fentabil, Messele.
Characterization of glycoproteins and oligosaccharides using
mass spectrometry.
Degree: MS, Department of Chemistry, 2010, University of Alberta
URL: https://era.library.ualberta.ca/files/6d56zz33j
► This thesis describes the application of mass spectrometry (MS) to glycoprotein and oligosaccharide analysis. Glycosylated proteins are involved in cell-cell and cell-matrix recognition. Applications of…
(more)
▼ This thesis describes the application of mass
spectrometry (MS) to glycoprotein and oligosaccharide analysis.
Glycosylated proteins are involved in cell-cell and cell-matrix
recognition. Applications of trypsin and proteinase K to hydrolyze
glycoproteins into glycopeptides that are compatible with MS and
MS/MS analysis are investigated. For successful site-specific
analysis of glycans, glycopeptides with short peptide (3-8
residues) are needed. Although trypsin is an important enzyme for
protein identification, proteinase K is superior for site-specific
glycan analysis due to its potential to hydrolyze every
glycoprotein to short glycopeptides. The gas-phase dissociation
pathways, kinetics and energetics of protonated oligosaccharides
are described. The oligosaccharides dissociate via cleavage at the
glycosidic linkages during thermal activation. Using double
resonance experiments, it was established that oligosaccharides
undergo sequential and parallel fragmentation reactions.
Furthermore, dissociation of product ions to secondary ions was
confirmed. Arrhenius activation parameters, Ea and A for protonated
alpha- and beta-linked D-glucopyranose oligosaccharides are
reported.
Subjects/Keywords: Glycoproteins; Mass spectrometry; Oligosaccharide gas phase dissociations; Tandem MS
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APA (6th Edition):
Fentabil, M. (2010). Characterization of glycoproteins and oligosaccharides using
mass spectrometry. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/6d56zz33j
Chicago Manual of Style (16th Edition):
Fentabil, Messele. “Characterization of glycoproteins and oligosaccharides using
mass spectrometry.” 2010. Masters Thesis, University of Alberta. Accessed January 18, 2021.
https://era.library.ualberta.ca/files/6d56zz33j.
MLA Handbook (7th Edition):
Fentabil, Messele. “Characterization of glycoproteins and oligosaccharides using
mass spectrometry.” 2010. Web. 18 Jan 2021.
Vancouver:
Fentabil M. Characterization of glycoproteins and oligosaccharides using
mass spectrometry. [Internet] [Masters thesis]. University of Alberta; 2010. [cited 2021 Jan 18].
Available from: https://era.library.ualberta.ca/files/6d56zz33j.
Council of Science Editors:
Fentabil M. Characterization of glycoproteins and oligosaccharides using
mass spectrometry. [Masters Thesis]. University of Alberta; 2010. Available from: https://era.library.ualberta.ca/files/6d56zz33j
Texas A&M University
13.
Kmiec, Kevin.
Factors Affecting the Fragmentation of Peptide Ions: Metal Cationization and Fragmentation Timescale.
Degree: PhD, Chemistry, 2012, Texas A&M University
URL: http://hdl.handle.net/1969.1/ETD-TAMU-2012-08-11243
► The factors affecting peptide fragmentation have been extensively studied in the literature in order to better predict the fragment ion spectra of peptides and proteins.…
(more)
▼ The factors affecting peptide fragmentation have been extensively studied in the literature in order to better predict the fragment ion spectra of peptides and proteins. While there are countless influences to consider, metal cation binding in the gas-phase is particularly interesting. Herein, a comparison of fragmentation patterns of a model peptide series with various charge carriers (H+, Li+, Na+, K+, and Cu+) will assist in determining the location of the preferred binding site of the metal cation and in assessing differences in the fragmentation pattern as a result of this binding site. An interesting observation from these studies reveals abundant x-type fragment ions occurring from the fragmentation of alkali-metal cationized peptides. As these fragment ions have been observed in previous studies by others but not addressed, the factors affecting the formation of these x-type fragment ions are explored.
Additionally, a home-built 193-nm photodissociation
tandem time-of-flight
mass spectrometer is utilized to study how peptide fragmentation kinetics affect the fragmentation pattern observed. Initially, the fragmentation timescales of various peptides are investigated. Results indicate that longer fragmentation timescales (~10 microseconds) result in an increased number of identified peaks with internal and ammonia loss fragment ions being the most common in comparison to 'prompt' fragmentation timescales (~1 microsecond). Furthermore, b-type fragment ion formation is also favored at longer timescales for the arginine containing peptides investigated.
The fragmentation pattern of several proline containing peptides is examined by collision-induced dissociation and 193-nm photodissociation. Unique fragment ions are observed with each occurring at a proline residue. Few differences are detected between CID and 193-nm photodissociation spectra, indicating that the proline residues direct fragmentation rather than the dissociation method.
In an effort to improve the performance of the photodissociation
tandem TOF instrument, the addition of a second source and a dual-stage reflectron are incorporated. The modifications result in improved
mass range, signal-to-noise, and increased fragment ion collection efficiencies. High quality
mass spectra are acquired across a range of
mass-to-charge ratios from ~600 to 1900. Furthermore, the modifications continue to allow investigation of various fragmentation timescales with the addition of an additional timeframe of ~3 microseconds.
Advisors/Committee Members: Russell, David H. (advisor), Hardin, Paul E. (committee member), North, Simon W. (committee member), Schweikert, Emile A. (committee member).
Subjects/Keywords: mass spectrometry; peptides; fragmentation; photodissociation; tandem MS; metal cationization
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Export
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Manager
APA (6th Edition):
Kmiec, K. (2012). Factors Affecting the Fragmentation of Peptide Ions: Metal Cationization and Fragmentation Timescale. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2012-08-11243
Chicago Manual of Style (16th Edition):
Kmiec, Kevin. “Factors Affecting the Fragmentation of Peptide Ions: Metal Cationization and Fragmentation Timescale.” 2012. Doctoral Dissertation, Texas A&M University. Accessed January 18, 2021.
http://hdl.handle.net/1969.1/ETD-TAMU-2012-08-11243.
MLA Handbook (7th Edition):
Kmiec, Kevin. “Factors Affecting the Fragmentation of Peptide Ions: Metal Cationization and Fragmentation Timescale.” 2012. Web. 18 Jan 2021.
Vancouver:
Kmiec K. Factors Affecting the Fragmentation of Peptide Ions: Metal Cationization and Fragmentation Timescale. [Internet] [Doctoral dissertation]. Texas A&M University; 2012. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2012-08-11243.
Council of Science Editors:
Kmiec K. Factors Affecting the Fragmentation of Peptide Ions: Metal Cationization and Fragmentation Timescale. [Doctoral Dissertation]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2012-08-11243
North Carolina State University
14.
Viswakumar, Anjali.
Development of a Gas Chromatography-Tandem Mass Spectrometry Method for the Simultaneous Analysis of 19 Taste and Odor Compounds.
Degree: MS, Civil Engineering, 2010, North Carolina State University
URL: http://www.lib.ncsu.edu/resolver/1840.16/6304
► An analytical method was developed to detect and quantify 19 compounds commonly associated with taste and odor (T&O) problems in drinking water. The method can…
(more)
▼ An analytical method was developed to detect and quantify 19 compounds commonly associated with taste and odor (T&O) problems in drinking water. The method can be used by utilities during T&O episodes to quickly and reliably detect T&O compounds and determine their concentrations. Knowledge about the identity and concentration of T&O compounds will greatly aid utilities in the selection of appropriate treatment strategies. Head space solid phase microextraction (SPME) was used to concentrate T&O compounds, and gas chromatography (GC) followed by
tandem mass spectrometry (MS/MS) was used to separate, detect, and quantify the T&O compounds. Method development included (1) determination of parent ion
mass and retention time, (2) optimization of the ion trap MS/MS instrumental parameters, (3) development of calibration curves, and (4) determination of the method detection limits (MDLs) and limits of quantitation (LOQs) for each compound. For 12 of the 17 targeted T&O compounds with known odor threshold concentrations (OTCs), LOQs were below the OTC. This result suggests that the developed method is capable of detecting developing T&O problems for these 12 compounds and allow utilities to implement treatment strategies before consumers can detect objectionable tastes and odors in their water. The developed method was tested by analyzing three water samples from North Carolina ponds and lakes that experienced algae/cyanobacteria blooms. In addition, Raleigh source and tap water samples were analyzed. Of the 19 targeted T&O compounds, all but 2,4,6 tribromoanisole were detected in the collected samples. In the bloom samples, geosmin, β-ionone, and trans-2,cis-6-nonadienal most frequently occurred at concentrations that exceeded their OTCs, sometimes by a factor of >100. A comparison of results for non-filtered and filtered (0.45 µm membrane) samples suggests that many T&O compounds were predominantly present inside algae/cyanobacteria cells. Only geosmin and β-cyclocitral were present at measurable levels in Raleigh source and tap water. Concentrations in the raw and tap water samples were similar and at levels that were at or below the OTCs of geosmin and β-cyclocitral.
Advisors/Committee Members: Detelf Knappe, Committee Member (advisor), Joel Ducoste, Committee Member (advisor), Francis L. de los Reyes III, Committee Member (advisor).
Subjects/Keywords: Taste and Odor Compounds; Gas chromatography; Tandem Mass Spectrometry
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APA ·
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Export
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APA (6th Edition):
Viswakumar, A. (2010). Development of a Gas Chromatography-Tandem Mass Spectrometry Method for the Simultaneous Analysis of 19 Taste and Odor Compounds. (Thesis). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/6304
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Viswakumar, Anjali. “Development of a Gas Chromatography-Tandem Mass Spectrometry Method for the Simultaneous Analysis of 19 Taste and Odor Compounds.” 2010. Thesis, North Carolina State University. Accessed January 18, 2021.
http://www.lib.ncsu.edu/resolver/1840.16/6304.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Viswakumar, Anjali. “Development of a Gas Chromatography-Tandem Mass Spectrometry Method for the Simultaneous Analysis of 19 Taste and Odor Compounds.” 2010. Web. 18 Jan 2021.
Vancouver:
Viswakumar A. Development of a Gas Chromatography-Tandem Mass Spectrometry Method for the Simultaneous Analysis of 19 Taste and Odor Compounds. [Internet] [Thesis]. North Carolina State University; 2010. [cited 2021 Jan 18].
Available from: http://www.lib.ncsu.edu/resolver/1840.16/6304.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Viswakumar A. Development of a Gas Chromatography-Tandem Mass Spectrometry Method for the Simultaneous Analysis of 19 Taste and Odor Compounds. [Thesis]. North Carolina State University; 2010. Available from: http://www.lib.ncsu.edu/resolver/1840.16/6304
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Boston University
15.
Ke, Yiling.
Detection and quantitation of nine fentanyl analogs in urine and oral fluid using QSight Triple Quad LC-MS/MS.
Degree: MS, Biomedical Forensic Sciences, 2020, Boston University
URL: http://hdl.handle.net/2144/41277
► The opioid epidemic has become a serious public health problem in the United States. The increasing abuse of synthetic opioids has raised concerns in the…
(more)
▼ The opioid epidemic has become a serious public health problem in the United States. The increasing abuse of synthetic opioids has raised concerns in the society. Fentanyl is a synthetic opioid analgesic which has resulted in an increasing number of drug overdoses since 2013. In addition, fentanyl analogs, originally manufactured for use as analgesics or animal tranquilizers, have emerged in the United States drug market. Fentanyl and its analogs, similar to other opioids, work as full µ-agonists, binding with µ-receptors in the brain. Fentanyl and its analogs elicit more potent effects compared to the traditional opioids being abused such as morphine or heroin. With the emergence of fentanyl analogs in the drug market, identifying and differentiating those analogs becomes a challenge due to their structural similarities to fentanyl.
The purpose of this research was to develop a method of identifying and quantifying nine fentanyl analogs in urine and oral fluid using the QSight® Triple Quad LC-MS/MS, coupled with a Halo® C18, 2.7µm column. The method was validated based on AAFS Standards Board (ASB) Standard 036, Standard Practices for Method Validation in Forensic Toxicology. The analytes in this research included fentanyl, norfentanyl, acetyl fentanyl, carfentanil, cyclopropyl fentanyl, methoxyacetyl fentanyl, valeryl fentanyl, furanyl fentanyl and 4-anilino-N-phenethylpiperdine (4ANPP). All samples, calibrators, and quality controls (QC) were prepared by spiking certified reference standards into donated human urine or human oral fluid. Supported liquid extraction (SLE) was performed as the sample preparation method using ISOLUTE® SLE+ 1mL columns followed by evaporation. All samples were reconstituted with 200 µL methanol. The mobile phases used in this method were 5mM ammonium formate in Millipore water with 0.1% formic acid and methanol with 0.1% formic acid.
A 10-minute LC method achieved complete resolution of the analytes, with specific retention times ranging from 3.5 to 5.7 minutes. For urine and oral fluid analysis, the calibration range for all analytes was established from 1 to 70 ng/mL. The resulting r2 values were greater than 0.988 for all analytes. Bias and precision were evaluated at 3, 25 and 60 ng/mL, and bias and percent coefficient of variation (%CV) for within and between run precision had acceptable values within ±20%. The limit of detection (LOD) was 0.1 ng/mL for most fentanyl analogs, with a LOD of 0.01 ng/mL for valeryl fentanyl and furanyl fentanyl. Carryover was not detected for any analytes in either matrix. Recovery of all compounds following SLE for both urine and oral fluid was above 50%. For urine, the ion enhancement and suppression of all analytes was within 25%. For oral fluid, the ion enhancement and suppression of most analytes was within 25% except valeryl fentanyl, which experienced suppression of 35%. The matrices analyzed had no interference effect on the detection or quantitation of analytes in this method. The interference effects of different commonly encountered…
Advisors/Committee Members: Botch-Jones, Sabra R. (advisor).
Subjects/Keywords: Toxicology; Fentanyl analogs; HPLC; Supported liquid extraction; Tandem mass spectrometry
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Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Ke, Y. (2020). Detection and quantitation of nine fentanyl analogs in urine and oral fluid using QSight Triple Quad LC-MS/MS. (Masters Thesis). Boston University. Retrieved from http://hdl.handle.net/2144/41277
Chicago Manual of Style (16th Edition):
Ke, Yiling. “Detection and quantitation of nine fentanyl analogs in urine and oral fluid using QSight Triple Quad LC-MS/MS.” 2020. Masters Thesis, Boston University. Accessed January 18, 2021.
http://hdl.handle.net/2144/41277.
MLA Handbook (7th Edition):
Ke, Yiling. “Detection and quantitation of nine fentanyl analogs in urine and oral fluid using QSight Triple Quad LC-MS/MS.” 2020. Web. 18 Jan 2021.
Vancouver:
Ke Y. Detection and quantitation of nine fentanyl analogs in urine and oral fluid using QSight Triple Quad LC-MS/MS. [Internet] [Masters thesis]. Boston University; 2020. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/2144/41277.
Council of Science Editors:
Ke Y. Detection and quantitation of nine fentanyl analogs in urine and oral fluid using QSight Triple Quad LC-MS/MS. [Masters Thesis]. Boston University; 2020. Available from: http://hdl.handle.net/2144/41277
Boston University
16.
Godin, David Andrew.
Development of an UFLC/MS/MS method for the comparative analysis of oxytocin and artesunate-amodiaquine for validation of field detection systems.
Degree: MS, Biomedical Forensic Sciences, 2016, Boston University
URL: http://hdl.handle.net/2144/19190
► Spurious, falsely-labeled, falsified or counterfeit (SFFC) pharmaceuticals are a health concern that claims hundreds of thousands of lives annually1, a violation of intellectual property rights…
(more)
▼ Spurious, falsely-labeled, falsified or counterfeit (SFFC) pharmaceuticals are a health concern that claims hundreds of thousands of lives annually1, a violation of intellectual property rights which cost legitimate companies billions2, and a low-risk high yield revenue stream for organized crime2. While ports of entry and border control points are the primary access control points for SFFC3,4, advances in field portable detection and equipment offers an increasingly effective method for the assessment of pharmaceuticals at regional centers and points of distribution. This is particularly important for less developed countries (LDC) who do not maintain satellite or regional testing facilities.
As part of a proposed protocol to assess field portable detection equipment, an ultrafast liquid chromatography, tandem mass spectrometry (UFLC-MS/MS) method for the quantification of liquid formulation Oxytocin was developed. The six minute method was found to have a within run %bias of +/-16%, a linear dynamic range of 150-1000 nanograms/milliliter (ng/ml), and an accuracy within acceptability criteria for all tested concentrations.
The effectiveness of three identified transition ions, 723.1, 86.2 and 70.1 Daltons, for the analysis of oxytocin by mass spectrometry was assessed across several figures of merit to include signal to noise ratio, %CV, calibration sensitivity, and analytical sensitivity. The 723.1 ion fragment was recommended for quantification, while the 70.1 dalton ion was recommended as a qualifier ion, although 86.2 also performed within acceptability criteria.
A method for the UFLC-MS/MS assessment of degradation products for oxytocin was proposed for specificity testing. Degradation of oxytocin by exposure to highly acidic, basic, and thermal conditions for one hour was attempted. Formation of degraded products was not observed.
Additionally, existing High Performance Liquid Chromatography (HPLC) methods for the simultaneous assessment of Artesunate and Amodiaquine HCl were modified to assess compatibility with UFLC. No method assessed produced sufficient quality signal to continue with method development.
Subjects/Keywords: Chemistry; Oxytocin; Tandem mass spectrometry; Ultra fast liquid chromatography
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APA (6th Edition):
Godin, D. A. (2016). Development of an UFLC/MS/MS method for the comparative analysis of oxytocin and artesunate-amodiaquine for validation of field detection systems. (Masters Thesis). Boston University. Retrieved from http://hdl.handle.net/2144/19190
Chicago Manual of Style (16th Edition):
Godin, David Andrew. “Development of an UFLC/MS/MS method for the comparative analysis of oxytocin and artesunate-amodiaquine for validation of field detection systems.” 2016. Masters Thesis, Boston University. Accessed January 18, 2021.
http://hdl.handle.net/2144/19190.
MLA Handbook (7th Edition):
Godin, David Andrew. “Development of an UFLC/MS/MS method for the comparative analysis of oxytocin and artesunate-amodiaquine for validation of field detection systems.” 2016. Web. 18 Jan 2021.
Vancouver:
Godin DA. Development of an UFLC/MS/MS method for the comparative analysis of oxytocin and artesunate-amodiaquine for validation of field detection systems. [Internet] [Masters thesis]. Boston University; 2016. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/2144/19190.
Council of Science Editors:
Godin DA. Development of an UFLC/MS/MS method for the comparative analysis of oxytocin and artesunate-amodiaquine for validation of field detection systems. [Masters Thesis]. Boston University; 2016. Available from: http://hdl.handle.net/2144/19190
Boston University
17.
Nicholson, Christopher.
Method validation of drugs of abuse using microchip capillary electrophoresis-mass spectrometry.
Degree: MS, Biomedical Forensic Sciences, 2019, Boston University
URL: http://hdl.handle.net/2144/38689
► Drugs of Abuse (DOAs) are among the single largest contributor to crime in the United States and present a high cost to society in terms…
(more)
▼ Drugs of Abuse (DOAs) are among the single largest contributor to crime in the United States and present a high cost to society in terms of financial costs and physical/mental well-being of individuals. The forensic community requires a variety of validated methods to detect and analyze DOAs in a variety of different sample types, and most developed methods utilize a liquid or gas chromatography (GC or LC) separation system paired to a
mass spectrometer (MS) detection detector. Capillary Electrophoresis (CE) based separation techniques have also been experimented with due to this technique’s high efficiency and speed, high resolving power, low sample consumption, and potentially lower cost when compared to GC or LC based techniques, even though the sensitivity of these systems is perceived to be weaker.
The goal of this research to develop a CE-MS/MS method utilizing the ZipChipTM to demonstrate it can accurately and reliably detect and quantify DOAs. The DOAs analyzed for this method were opioids and benzodiazepines, and these were 6-monacetylmorphine, 7-aminoclonazepam, codeine, diazepam, dihydrocodeine, 2-Ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine fentanyl, heroin, hydrocodone, hydromorphone, meperidine, methadone, morphine, norfentanyl, oxycodone, and oxymorphone. Standard Practices for Method Validation in Forensic Toxicology guidelines from the Academy Standards Board (ASB) of Toxicology were used as the template for this validation; samples were prepared and analyzed as neat standards in diluent, blood and urine were assessed for interferences, ionization suppression/enhancement, and extraction recovery.
The total runtime for the method was 3.5 minutes, with the retention time range being 1.4 to 2.9 minutes. All samples were prepared using compound standards diluted in metabolite diluent, which consisted of methanol, ammonium acetate, and water prior to injection. The calibration curves consisted of eight calibrator samples that ranged from 0.5 ng/ml to 200 ng/ml for all analytes, and a linear model was used for each compound. The minimum acceptable 𝑅2 value was set to >0.98, and each curve had a weighing factor of 1𝑥2. Each curve for most of the compounds achieved the minimum requirement apart from two Codeine curves (0.9781 and 0.9785) and 7-aminoclonazepam (0.9791). Bias and precision were assessed at three concentrations- 5, 100, and 150 ng/ml. The minimum requirement for bias and precision for a compound was if the percent bias or coefficient of variation was within +/- 20%. Most compounds in this method exhibit acceptable levels of bias (except for Dihydrocodeine which had a bias of 24.58% at 100 ng/ml), and the only compounds to meet the minimum requirement for precision were 6-MAM, 7-aminoclonazepam, diazepam, fentanyl, methadone, and morphine. The limit of detection and limit of quantitation were both set at the lowest calibrator level of 0.5 ng/ml, and no carryover was observed in this method. No interferences occurred due to both deuterated internal standards and from common compounds such as…
Advisors/Committee Members: Botch-Jones, Sabra (advisor), Miller, Scott (advisor).
Subjects/Keywords: Chemistry; Capillary electrophoresis; Forensics; Microfluidics; Opiates; Tandem mass spectrometry
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APA (6th Edition):
Nicholson, C. (2019). Method validation of drugs of abuse using microchip capillary electrophoresis-mass spectrometry. (Masters Thesis). Boston University. Retrieved from http://hdl.handle.net/2144/38689
Chicago Manual of Style (16th Edition):
Nicholson, Christopher. “Method validation of drugs of abuse using microchip capillary electrophoresis-mass spectrometry.” 2019. Masters Thesis, Boston University. Accessed January 18, 2021.
http://hdl.handle.net/2144/38689.
MLA Handbook (7th Edition):
Nicholson, Christopher. “Method validation of drugs of abuse using microchip capillary electrophoresis-mass spectrometry.” 2019. Web. 18 Jan 2021.
Vancouver:
Nicholson C. Method validation of drugs of abuse using microchip capillary electrophoresis-mass spectrometry. [Internet] [Masters thesis]. Boston University; 2019. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/2144/38689.
Council of Science Editors:
Nicholson C. Method validation of drugs of abuse using microchip capillary electrophoresis-mass spectrometry. [Masters Thesis]. Boston University; 2019. Available from: http://hdl.handle.net/2144/38689
Hong Kong University of Science and Technology
18.
Leung, Ming Kit CHEM.
Development and application of liquid chromatography tandem mass spectrometric method for detecting DNA/RNA adducts as biomarkers of carcinogen exposure : a case study with aristolochic acids.
Degree: 2016, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-88916
;
https://doi.org/10.14711/thesis-b1585430
;
http://repository.ust.hk/ir/bitstream/1783.1-88916/1/th_redirect.html
► Biomarker is an important indicator that measures the events occurring in a biological system. Apart from being used as a sign to disclose the health…
(more)
▼ Biomarker is an important indicator that measures the events occurring in a biological system. Apart from being used as a sign to disclose the health status of an individual, biomarker is extremely useful in both toxicological research as well as biological monitoring. In addition to the occurrence of natural disease, exposure to toxic or specific environments may lead to fatal alteration of the biological system of a subject. However, if such alteration can be detected in the early stage, life will be spared upon appropriate medication. As a consequence, the evaluation of biomarker is extremely useful in the prevention of mortality. Substances which cause renal damage are defined as nephrotoxic. Aristolochic acid (AA) is one of the examples of nephrotoxic substances. Research studies and literature reveal that AA is strongly associated with the cases of renal fibrosis reported during the late 80s. Evidence has shown that AA will covalently bind to DNA to form stable adducts with remarkable persistence which can be detected after a reasonable long period of time. However, conventional analyses of DNA-AA adducts involve both tedious and invasive DNA isolation procedures in target organ. Herein, we report a non-invasive approach to detect and quantify DNA-AA adducts in rat urine rather than in tissue samples. The developed method entails extraction and enrichment of DNA-AA adducts in urine samples by solid phase extraction, followed by detection with the assistance of liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since the newly developed method is to replace the old and traditional invasive method for adducts detection, method comparison is performed so as to prove that the developed method is of advantageous. Apart from DNA, emerging evidence showed that RNA will be attacked under the influence of carcinogens. The impact is similar to that of DNA where the formation of covalent adducts may be resulted. However, since RNA does not possess proofreading enzyme such as DNA polymerase, there is no repair system for the elimination of the covalent adducts. Instead, RNA relies on enzymatic degradation or decay. Hence, RNA adducts may be released as free ribonucleosides and excreted through urinary system. As a result, we use an approach which is similar to DNA to detect the RNA-AA adducts in urine samples by UPLC-MS/MS. On the other hand, since the synthesis of proteins heavily relies on the integrity of RNA, we have a hypothesis that the deviation in RNA sequence will ultimately lead to mis-folding or truncation of proteins, therefore resulting in AA associated diseases such as kidney fibrosis. Comparing to the traditional detection methods, the advantages of our developed method by utilizing mass spectrometry detection include high sensitivity and good selectivity. Identities of adducts have been made more promising and quantities of adducts are accurately evaluated. Although the traditional methods are interchangeable with our newly developed method, the enzymatic treatment of the old methods is still vital…
Subjects/Keywords: Liquid chromatography
; Tandem mass spectrometry
; Biochemical markers
; DNA adducts
; Analysis
; RNA
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APA (6th Edition):
Leung, M. K. C. (2016). Development and application of liquid chromatography tandem mass spectrometric method for detecting DNA/RNA adducts as biomarkers of carcinogen exposure : a case study with aristolochic acids. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-88916 ; https://doi.org/10.14711/thesis-b1585430 ; http://repository.ust.hk/ir/bitstream/1783.1-88916/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Leung, Ming Kit CHEM. “Development and application of liquid chromatography tandem mass spectrometric method for detecting DNA/RNA adducts as biomarkers of carcinogen exposure : a case study with aristolochic acids.” 2016. Thesis, Hong Kong University of Science and Technology. Accessed January 18, 2021.
http://repository.ust.hk/ir/Record/1783.1-88916 ; https://doi.org/10.14711/thesis-b1585430 ; http://repository.ust.hk/ir/bitstream/1783.1-88916/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Leung, Ming Kit CHEM. “Development and application of liquid chromatography tandem mass spectrometric method for detecting DNA/RNA adducts as biomarkers of carcinogen exposure : a case study with aristolochic acids.” 2016. Web. 18 Jan 2021.
Vancouver:
Leung MKC. Development and application of liquid chromatography tandem mass spectrometric method for detecting DNA/RNA adducts as biomarkers of carcinogen exposure : a case study with aristolochic acids. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2016. [cited 2021 Jan 18].
Available from: http://repository.ust.hk/ir/Record/1783.1-88916 ; https://doi.org/10.14711/thesis-b1585430 ; http://repository.ust.hk/ir/bitstream/1783.1-88916/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Leung MKC. Development and application of liquid chromatography tandem mass spectrometric method for detecting DNA/RNA adducts as biomarkers of carcinogen exposure : a case study with aristolochic acids. [Thesis]. Hong Kong University of Science and Technology; 2016. Available from: http://repository.ust.hk/ir/Record/1783.1-88916 ; https://doi.org/10.14711/thesis-b1585430 ; http://repository.ust.hk/ir/bitstream/1783.1-88916/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Hong Kong University of Science and Technology
19.
Wang, Yinan CHEM.
Development and application of liquid chromatography and tandem mass spectrometry methods to quantitate antibacterial nitrofurans and associated DNA and RNA adducts.
Degree: 2018, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-97209
;
https://doi.org/10.14711/thesis-991012587065103412
;
http://repository.ust.hk/ir/bitstream/1783.1-97209/1/th_redirect.html
► Nitrofuran (NF) is a class of broad-spectrum veterinary drugs for the treatment of microbial infections. They are highly effective in suppressing and killing most kinds…
(more)
▼ Nitrofuran (NF) is a class of broad-spectrum veterinary drugs for the treatment of microbial infections. They are highly effective in suppressing and killing most kinds of bacteria, fungi, and protozoa, which let them to be used extensively in aquaculture and livestock farming as growth promoters until they are observed to be carcinogenic and mutagenic to humans. Currently, the use of NF in food-producing animals has been banned in many countries, including China, U.S.A., and many European countries. However, illegal use of NF exists and the toxicological mechanism of NF is poorly understood. I investigated in this thesis for the first time the genotoxic effect of NF by rigorously quantifying the DNA adducts formed by reacting the hydrazine-containing metabolites of NF with abasic sites in DNA of bacteria and in internal organs of NF-treated rats. Furthermore, I developed a simple and sensitive high-performance liquid chromatography−fluorescence detection (HPLC−FLD) with automated in-injector derivatization method for the determination of NF in food samples. Using my developed HPLC−FLD and high-performance liquid chromatography−tandem mass spectrometry detection method, I further investigated the uptake and metabolism of NF in crops, which is one of the pathways that the genotoxic NFs enter human body after they are discharged into environment. It is my belief that the results in my thesis work have allow better understanding of the genotoxicity of NF and that my developed HPLC−FLD should facilitate regulation and surveillance on illegal use of NF in the food industry.
Subjects/Keywords: DNA adducts
; Nitrofurans
; Liquid chromatography
; Tandem mass spectrometry
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Export
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APA (6th Edition):
Wang, Y. C. (2018). Development and application of liquid chromatography and tandem mass spectrometry methods to quantitate antibacterial nitrofurans and associated DNA and RNA adducts. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-97209 ; https://doi.org/10.14711/thesis-991012587065103412 ; http://repository.ust.hk/ir/bitstream/1783.1-97209/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Yinan CHEM. “Development and application of liquid chromatography and tandem mass spectrometry methods to quantitate antibacterial nitrofurans and associated DNA and RNA adducts.” 2018. Thesis, Hong Kong University of Science and Technology. Accessed January 18, 2021.
http://repository.ust.hk/ir/Record/1783.1-97209 ; https://doi.org/10.14711/thesis-991012587065103412 ; http://repository.ust.hk/ir/bitstream/1783.1-97209/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Yinan CHEM. “Development and application of liquid chromatography and tandem mass spectrometry methods to quantitate antibacterial nitrofurans and associated DNA and RNA adducts.” 2018. Web. 18 Jan 2021.
Vancouver:
Wang YC. Development and application of liquid chromatography and tandem mass spectrometry methods to quantitate antibacterial nitrofurans and associated DNA and RNA adducts. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2018. [cited 2021 Jan 18].
Available from: http://repository.ust.hk/ir/Record/1783.1-97209 ; https://doi.org/10.14711/thesis-991012587065103412 ; http://repository.ust.hk/ir/bitstream/1783.1-97209/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang YC. Development and application of liquid chromatography and tandem mass spectrometry methods to quantitate antibacterial nitrofurans and associated DNA and RNA adducts. [Thesis]. Hong Kong University of Science and Technology; 2018. Available from: http://repository.ust.hk/ir/Record/1783.1-97209 ; https://doi.org/10.14711/thesis-991012587065103412 ; http://repository.ust.hk/ir/bitstream/1783.1-97209/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Hong Kong University of Science and Technology
20.
Lee, Yik Yeung CBE.
Tandem-MS spectral clustering method by DBSCAN for proteomics data.
Degree: 2018, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-97890
;
https://doi.org/10.14711/thesis-991012634968803412
;
http://repository.ust.hk/ir/bitstream/1783.1-97890/1/th_redirect.html
► With the rapid accumulation of proteomics data from laboratories worldwide, opportunities now exist to leverage this data to build high-quality spectral library to assist peptide…
(more)
▼ With the rapid accumulation of proteomics data from laboratories worldwide, opportunities now exist to leverage this data to build high-quality spectral library to assist peptide identification. Traditional library building in proteomics, however, is error-prone and is not amenable for incremental updates, making it unsustainable for today’s data volume. Spectral clustering has been proposed as a more reliable way to build spectral libraries compared to conventional methods because of its capability of retaining unidentified spectra and correcting identification errors. In this study, we propose a novel method designed for spectral clustering using DBSCAN with Euclidean-style distance metrics, which incorporate both spectral similarities and precursor mass-to-charge ratio differences. The newly proposed method can perform refinement of existing clusters, or directly cluster raw data using a GPU-accelerated algorithm. Existing clusters were each subjected to DBSCAN to identify cluster cores and separate loosely connected nodes. For each distance metric, the distance threshold (Eps) was optimized. With this method, higher-quality clusters could be built compared with the original clusters built by only considering pairwise spectral similarity. Both internal and external measurements to assess the quality of our refined resulting clusters. The clusters constructed by DBSCAN method were less likely to consist of spectra of different peptide identifications, and the lower-quality spectra were removed on account of their lower similarity and fewer connections to the cluster cores.
Subjects/Keywords: Proteomics
; Data processing
; Microclusters
; Tandem mass spectrometry
; Cluster analysis
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APA ·
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Export
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APA (6th Edition):
Lee, Y. Y. C. (2018). Tandem-MS spectral clustering method by DBSCAN for proteomics data. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-97890 ; https://doi.org/10.14711/thesis-991012634968803412 ; http://repository.ust.hk/ir/bitstream/1783.1-97890/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lee, Yik Yeung CBE. “Tandem-MS spectral clustering method by DBSCAN for proteomics data.” 2018. Thesis, Hong Kong University of Science and Technology. Accessed January 18, 2021.
http://repository.ust.hk/ir/Record/1783.1-97890 ; https://doi.org/10.14711/thesis-991012634968803412 ; http://repository.ust.hk/ir/bitstream/1783.1-97890/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lee, Yik Yeung CBE. “Tandem-MS spectral clustering method by DBSCAN for proteomics data.” 2018. Web. 18 Jan 2021.
Vancouver:
Lee YYC. Tandem-MS spectral clustering method by DBSCAN for proteomics data. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2018. [cited 2021 Jan 18].
Available from: http://repository.ust.hk/ir/Record/1783.1-97890 ; https://doi.org/10.14711/thesis-991012634968803412 ; http://repository.ust.hk/ir/bitstream/1783.1-97890/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lee YYC. Tandem-MS spectral clustering method by DBSCAN for proteomics data. [Thesis]. Hong Kong University of Science and Technology; 2018. Available from: http://repository.ust.hk/ir/Record/1783.1-97890 ; https://doi.org/10.14711/thesis-991012634968803412 ; http://repository.ust.hk/ir/bitstream/1783.1-97890/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Washington
21.
Viglino, Emilie Aude.
New Tandem Mass Spectrometric Methods of Structure and Sequence Elucidation of Synthetic and Tryptic Peptides.
Degree: PhD, 2017, University of Washington
URL: http://hdl.handle.net/1773/38592
► Over the last few decades, technological advances in the physical and life sciences have enabled scientists to look at various systems ever so intricately and…
(more)
▼ Over the last few decades, technological advances in the physical and life sciences have enabled scientists to look at various systems ever so intricately and to gather evidence for the mechanisms behind these systems, be they at the biological level or the astrophysical level. One of the many tools that has spurred the collection of large amounts of data for a better understanding of the World around us is
mass spectrometry. Critical advancements in the engineering of
mass spectrometers since their inception over a century ago have secured
mass spectrometry’ position as a robust technology in the field of Chemistry. The versatility of this tool is illustrated by its application to a variety of scientific disciplines and by its predominance in the scientific literature. Currently,
mass spectrometry is utilized routinely in the clinical laboratory as a means to evaluate the potential for certain biomarkers to be disease-causing. Such biomarkers typically are in protein or peptide form, hence the need to develop tools aimed at probing the sequences and structures of these compounds. Gaining insight into the building blocks of proteins and peptides and their overall organization is crucial for determining their functions and biological impact. The body of work presented herein focuses on the development of two separate tools for the study of peptides and proteins in the gas phase; the first tool was aimed at probing the structure of tyrosine-containing peptide cation radicals, which are particularly important in the functioning of redox enzymes, while the second tool was aimed at the synthesis of a unique iodine-containing charge tag in view of increasing the sequence coverage of digested proteins for easier and more reliable identification. In the first instance, a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-deficient and hydrogen-rich types is reported. Hydrogen-rich and hydrogen-deficient peptide cation radicals vary in electronic states and reactivity. Hydrogen-rich cation radicals [M + nH](n-1)+● are produced when an electron attaches to a multiply charged peptide ion, such as in electron transfer dissociation (ETD). Their backbone fragmentation is dominated by N-Cα cleavage and yields valuable sequencing information. Hydrogen-deficient cation radicals [M + (n-1)H]n+● are produced by an atom abstraction from a protonated peptide or via electron loss from a neutral peptide, as in electron ionization. Formation of the latter highly depends on the presence of both a basic amino acid and a tyrosine or tryptophan residue in the peptide and their fragmentation is dominated by C-Cα backbone cleavage. The former are far less studied and their mechanisms less understood. The generation and photodissociation of both hydrogen-rich and hydrogen-deficient cation radicals in tyrosine-containing pentapeptides was investigated in parallel studies. Using
tandem analyses with an LTQ-XL ion-trap equipped…
Advisors/Committee Members: Turecek, Frank (advisor).
Subjects/Keywords: Peptide Cation Radicals; Peptide Tagging; Sequencing; Tandem Mass Spectrometry; Chemistry; Chemistry
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APA (6th Edition):
Viglino, E. A. (2017). New Tandem Mass Spectrometric Methods of Structure and Sequence Elucidation of Synthetic and Tryptic Peptides. (Doctoral Dissertation). University of Washington. Retrieved from http://hdl.handle.net/1773/38592
Chicago Manual of Style (16th Edition):
Viglino, Emilie Aude. “New Tandem Mass Spectrometric Methods of Structure and Sequence Elucidation of Synthetic and Tryptic Peptides.” 2017. Doctoral Dissertation, University of Washington. Accessed January 18, 2021.
http://hdl.handle.net/1773/38592.
MLA Handbook (7th Edition):
Viglino, Emilie Aude. “New Tandem Mass Spectrometric Methods of Structure and Sequence Elucidation of Synthetic and Tryptic Peptides.” 2017. Web. 18 Jan 2021.
Vancouver:
Viglino EA. New Tandem Mass Spectrometric Methods of Structure and Sequence Elucidation of Synthetic and Tryptic Peptides. [Internet] [Doctoral dissertation]. University of Washington; 2017. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1773/38592.
Council of Science Editors:
Viglino EA. New Tandem Mass Spectrometric Methods of Structure and Sequence Elucidation of Synthetic and Tryptic Peptides. [Doctoral Dissertation]. University of Washington; 2017. Available from: http://hdl.handle.net/1773/38592
Duquesne University
22.
Tatosian, Irena.
Using Tandem Mass Spectrometry and IRMPD Spectroscopy to Determine the Intrinsic Reactions of Uranyl-Containing Ions.
Degree: MS, Chemistry and Biochemistry, 2020, Duquesne University
URL: https://dsc.duq.edu/etd/1899
► Developing a comprehensive understanding of the intrinsic reactivity of uranium-containing species remains an important goal, as it may influence future developments in areas ranging…
(more)
▼ Developing a comprehensive understanding of the intrinsic reactivity of uranium-containing species remains an important goal, as it may influence future developments in areas ranging from new approaches to nuclear fuel processing to studies of the migration and fate of the element in the environment. At a more fundamental level, such studies contribute to the understanding of the role that 5-f electrons may play in chemical bonding, the so called “f-electron challenge”. Electrospray ionization (ESI) is an effective way to generate gas-phase complexes containing uranium and uranyl ions for subsequent studies of intrinsic structure and reactivity. Studies in the gas-phase are important and necessary because investigation of reactivity in the condensed phase, in a species-specific fashion, is complicated by the presence of solvent molecules and counter ions and complex equilibria between metallic species in different form.
Recent experiments have demonstrated that state-of-the art linear ion traps (LIT) can provide access to a wide range of fragmentation pathways and reactions for gas-phase uranium species, whether using collision-induced dissociation (CID) and ion-molecule reactions (IMRs), including ones that were masked in previous experiments by high partial pressures of adventitious H
2O present in 3-D ion traps.
The goal was to survey the types of unimolecular (by CID) and bimolecular (IMR) reactions of precursor and product ions. The experiments outlined in this thesis were undertaken to investigate the intrinsic
reactivity of uranium-containing complexes with a variety of ligands including nitrate, perchlorate, acetate, propionate, acrylate, benzoate, and combinations of different halides. However, a general limitation of
mass spectrometry approaches to the study of intrinsic chemistry is that no direct structural information is produced, and determinations of structure rely heavily either on chemical intuition or theoretical calculations - understanding gas-phase reactivity requires a clearer idea of ion structure. Therefore, an addition goals was to use density functional theory (DFT) calculations, and infrared multiple-photon photodissociation (IRMPD) spectroscopy were used to identify the conformations of selected gas-phase uranyl complexes to enhance the understanding of the relationship between structure and reactivity.
Advisors/Committee Members: Michael Van Stipdonk, Ellen Gawalt, Michael Cascio.
Subjects/Keywords: Tandem-Mass Spectrometry; Uranyl Ion; IRMPD Spectroscopy; CID; Analytical Chemistry; Chemistry
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APA (6th Edition):
Tatosian, I. (2020). Using Tandem Mass Spectrometry and IRMPD Spectroscopy to Determine the Intrinsic Reactions of Uranyl-Containing Ions. (Masters Thesis). Duquesne University. Retrieved from https://dsc.duq.edu/etd/1899
Chicago Manual of Style (16th Edition):
Tatosian, Irena. “Using Tandem Mass Spectrometry and IRMPD Spectroscopy to Determine the Intrinsic Reactions of Uranyl-Containing Ions.” 2020. Masters Thesis, Duquesne University. Accessed January 18, 2021.
https://dsc.duq.edu/etd/1899.
MLA Handbook (7th Edition):
Tatosian, Irena. “Using Tandem Mass Spectrometry and IRMPD Spectroscopy to Determine the Intrinsic Reactions of Uranyl-Containing Ions.” 2020. Web. 18 Jan 2021.
Vancouver:
Tatosian I. Using Tandem Mass Spectrometry and IRMPD Spectroscopy to Determine the Intrinsic Reactions of Uranyl-Containing Ions. [Internet] [Masters thesis]. Duquesne University; 2020. [cited 2021 Jan 18].
Available from: https://dsc.duq.edu/etd/1899.
Council of Science Editors:
Tatosian I. Using Tandem Mass Spectrometry and IRMPD Spectroscopy to Determine the Intrinsic Reactions of Uranyl-Containing Ions. [Masters Thesis]. Duquesne University; 2020. Available from: https://dsc.duq.edu/etd/1899
University of Western Ontario
23.
Sun, Weiping.
Algorithms for Glycan Structure Identification with Tandem Mass Spectrometry.
Degree: 2016, University of Western Ontario
URL: https://ir.lib.uwo.ca/etd/4105
► Glycosylation is a frequently observed post-translational modification (PTM) of proteins. It has been estimated over half of eukaryotic proteins in nature are glycoproteins. Glycoprotein analysis…
(more)
▼ Glycosylation is a frequently observed post-translational modification (PTM) of proteins. It has been estimated over half of eukaryotic proteins in nature are glycoproteins. Glycoprotein analysis plays a vital role in drug preparation. Thus, characterization of glycans that are linked to proteins has become necessary in glycoproteomics. Mass spectrometry has become an effective analytical technique for glycoproteomics analysis because of its high throughput and sensitivity. The large amount of spectral data collected in a mass spectrometry experiment makes manual interpretation impossible and requires effective computational approaches for automated analysis. Different algorithmic solutions have been proposed to address the challenges in glycoproteomics analysis based on mass spectrometry. However, new algorithms that can identify intact glycopeptides are still demanded to improve result accuracy.
In this research, a glycan is represented as a rooted unordered labelled tree and we focus on developing effective algorithms to determine glycan structures from tandem mass spectra. Interpreting the tandem mass spectra of glycopeptides with a de novo sequencing method is essential to identifying novel glycan structures. Thus, we mathematically formulated the glycan de novo sequencing problem and propose a heuristic algorithm for glycan de novo sequencing from HCD tandem mass spectra of glycopeptides.
Characterizing glycans from MS/MS with a de novo sequencing method requires high-quality mass spectra for accurate results. The database search method usually has the ability to obtain more reliable results since it has the assistance of glycan structural information. Thus, we propose a de novo sequencing assisted database search method, GlycoNovoDB, for mass spectra interpretation.
Subjects/Keywords: Glycan Identification; Tandem Mass Spectrometry; Glycopeptide; Algorithms; Bioinformatics; Theory and Algorithms
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APA ·
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APA (6th Edition):
Sun, W. (2016). Algorithms for Glycan Structure Identification with Tandem Mass Spectrometry. (Thesis). University of Western Ontario. Retrieved from https://ir.lib.uwo.ca/etd/4105
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Sun, Weiping. “Algorithms for Glycan Structure Identification with Tandem Mass Spectrometry.” 2016. Thesis, University of Western Ontario. Accessed January 18, 2021.
https://ir.lib.uwo.ca/etd/4105.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Sun, Weiping. “Algorithms for Glycan Structure Identification with Tandem Mass Spectrometry.” 2016. Web. 18 Jan 2021.
Vancouver:
Sun W. Algorithms for Glycan Structure Identification with Tandem Mass Spectrometry. [Internet] [Thesis]. University of Western Ontario; 2016. [cited 2021 Jan 18].
Available from: https://ir.lib.uwo.ca/etd/4105.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Sun W. Algorithms for Glycan Structure Identification with Tandem Mass Spectrometry. [Thesis]. University of Western Ontario; 2016. Available from: https://ir.lib.uwo.ca/etd/4105
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
East Tennessee State University
24.
Carpenter, Skylar.
A Comparison of Standard Denoising Methods for Peptide Identification.
Degree: MS, Mathematical Sciences, 2019, East Tennessee State University
URL: https://dc.etsu.edu/etd/3579
► Peptide identification using tandem mass spectrometry depends on matching the observed spectrum with the theoretical spectrum. The raw data from tandem mass spectrometry, however,…
(more)
▼ Peptide identification using tandem mass spectrometry depends on matching the observed spectrum with the theoretical spectrum. The raw data from tandem mass spectrometry, however, is often not optimal because it may contain noise or measurement errors. Denoising this data can improve alignment between observed and theoretical spectra and reduce the number of peaks. The method used by Lewis et. al (2018) uses a combined constant and moving threshold to denoise spectra. We compare the effects of using the standard preprocessing methods baseline removal, wavelet smoothing, and binning on spectra with Lewis et. al’s threshold method. We consider individual methods and combinations, using measures of distance from Lewis et. al's scoring function for comparison. Our findings showed that no single method provided better results than Lewis et. al's, but combining techniques with that of Lewis et. al's reduced the distance measurements and size of the data set for many peptides.
Subjects/Keywords: Peptide identification; denoising; tandem mass spectrometry; baseline; wavelet; binning; Applied Statistics
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APA ·
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APA (6th Edition):
Carpenter, S. (2019). A Comparison of Standard Denoising Methods for Peptide Identification. (Thesis). East Tennessee State University. Retrieved from https://dc.etsu.edu/etd/3579
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Carpenter, Skylar. “A Comparison of Standard Denoising Methods for Peptide Identification.” 2019. Thesis, East Tennessee State University. Accessed January 18, 2021.
https://dc.etsu.edu/etd/3579.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Carpenter, Skylar. “A Comparison of Standard Denoising Methods for Peptide Identification.” 2019. Web. 18 Jan 2021.
Vancouver:
Carpenter S. A Comparison of Standard Denoising Methods for Peptide Identification. [Internet] [Thesis]. East Tennessee State University; 2019. [cited 2021 Jan 18].
Available from: https://dc.etsu.edu/etd/3579.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Carpenter S. A Comparison of Standard Denoising Methods for Peptide Identification. [Thesis]. East Tennessee State University; 2019. Available from: https://dc.etsu.edu/etd/3579
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Hong Kong University of Science and Technology
25.
Wong, Sum Kok ENVR.
Quantitation of Nε-carboxymethyllysine and Nε-carboxyethyllysine in oxidative stressor exposed cells by liquid chromatography tandem mass spectrometry.
Degree: 2019, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-101607
;
https://doi.org/10.14711/thesis-991012752456703412
;
http://repository.ust.hk/ir/bitstream/1783.1-101607/1/th_redirect.html
► Advanced glycation end-products (AGEs) are a large group of compounds originated from the Maillard reaction. Their formation and accumulation in human body are closely related…
(more)
▼ Advanced glycation end-products (AGEs) are a large group of compounds originated from the Maillard reaction. Their formation and accumulation in human body are closely related to aging and various degenerative diseases. AGEs can be formed by oxidative glycosylation and reaction between lysyl or arginyl residues and dicarbonyl compounds such as glyoxal (GO) and methylglyoxal (MGO). These reactive species are produced endogenously in normal cell process and under conditions of oxidative stress, for example, monosaccharide autoxidation and lipid peroxidation. Although the correlation between oxidative stress and AGEs formation are frequently described, the effects of different extent of oxidative stress on AGEs formation remain unclear. In this study, the tendency of AGEs generation is studied by exposing different dicarbonyls, GO and MGO, and oxidative stressor, Fe-EDTA, to protein and Escherichia coli. Nε-carboxymethyllysine (CML), a well-studied and frequently used biomarker for measuring AGEs content in food and biological systems, was quantitated simultaneously with Nε-carboxyethyllysine (CEL) to account for the oxidative stress-induced damages to E. coli. Hydrophilic interaction chromatography (HILIC) was employed for separating AGEs prior to tandem mass spectrometry (MS/MS) detection in the analysis of CML and CEL. Isotopically labelled internal standards were applied for accounting any analyte loss during sample preparation and correcting errors arisen from instrumental analysis. The data revealed that the CML formation caused by Fe-EDTA was contributed equally by oxidative fragmentation of Amadori products, and the generated GO. Interestingly, the formation of CEL may lead to an alternative pathway for the generation of CEL by glycosylation of Amadori product, which has not been considered before.
Subjects/Keywords: Glycosylation
; Oxidative stress
; Liquid chromatography
; Tandem mass spectrometry
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APA ·
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Export
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APA (6th Edition):
Wong, S. K. E. (2019). Quantitation of Nε-carboxymethyllysine and Nε-carboxyethyllysine in oxidative stressor exposed cells by liquid chromatography tandem mass spectrometry. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-101607 ; https://doi.org/10.14711/thesis-991012752456703412 ; http://repository.ust.hk/ir/bitstream/1783.1-101607/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wong, Sum Kok ENVR. “Quantitation of Nε-carboxymethyllysine and Nε-carboxyethyllysine in oxidative stressor exposed cells by liquid chromatography tandem mass spectrometry.” 2019. Thesis, Hong Kong University of Science and Technology. Accessed January 18, 2021.
http://repository.ust.hk/ir/Record/1783.1-101607 ; https://doi.org/10.14711/thesis-991012752456703412 ; http://repository.ust.hk/ir/bitstream/1783.1-101607/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wong, Sum Kok ENVR. “Quantitation of Nε-carboxymethyllysine and Nε-carboxyethyllysine in oxidative stressor exposed cells by liquid chromatography tandem mass spectrometry.” 2019. Web. 18 Jan 2021.
Vancouver:
Wong SKE. Quantitation of Nε-carboxymethyllysine and Nε-carboxyethyllysine in oxidative stressor exposed cells by liquid chromatography tandem mass spectrometry. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2019. [cited 2021 Jan 18].
Available from: http://repository.ust.hk/ir/Record/1783.1-101607 ; https://doi.org/10.14711/thesis-991012752456703412 ; http://repository.ust.hk/ir/bitstream/1783.1-101607/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wong SKE. Quantitation of Nε-carboxymethyllysine and Nε-carboxyethyllysine in oxidative stressor exposed cells by liquid chromatography tandem mass spectrometry. [Thesis]. Hong Kong University of Science and Technology; 2019. Available from: http://repository.ust.hk/ir/Record/1783.1-101607 ; https://doi.org/10.14711/thesis-991012752456703412 ; http://repository.ust.hk/ir/bitstream/1783.1-101607/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Michigan
26.
Crellin, John.
Protein Analysis by Liquid Chromatography-Tandem Mass Spectrometry: Detecting and Profiling Protein S-Palmitoylation and Host Cell Protein Characterization.
Degree: PhD, Chemical Biology, 2020, University of Michigan
URL: http://hdl.handle.net/2027.42/163145
► Proteins perform many biological functions and characterizing their role in the cellular environment is critical in understanding a protein’s role in disease. ‘Bottom-up’ liquid chromatography-tandem…
(more)
▼ Proteins perform many biological functions and characterizing their role in the cellular environment is critical in understanding a protein’s role in disease. ‘Bottom-up’ liquid chromatography-
tandem mass spectrometry (LC-MS/MS) offers the most effective strategy for large-scale global analysis of highly complex protein mixtures, i.e., proteomics. However, LC-MS/MS workflow strategies must be carefully adapted to maintain experimental reproducibility and overcome inherent limitations in detecting low abundance proteins in concentrated mixtures and labile posttranslational modifications (PTMs). This dissertation presents LC-MS/MS based analytical strategies for the direct detection and site-specific profiling of S-palmitoylated peptides, and for characterizing low abundance host cell proteins (HCPs) in purified biopharmaceutical drug substances (DS).
Chapter 1 presents an introduction to quantitative LC-MS/MS-based protein analysis, including instrumentation and techniques relevant to the work presented in Chapters 2 and 3.
Chapter 2 discusses S-palmitoylation, the reversible and dynamic modification of a cysteine sulfhydryl with a 16-carbon fatty acid. The dynamic cycling between a protein’s palmitoylated and depalmitoylated states regulates several intracellular events such as protein activity, localization, and protein-protein interactions. N-Ras, a well-known driver of many cancers, is S-palmitoylated near its C-terminus, and despite the therapeutic potential of targeting this modification, direct detection of this modified peptide by LC-MS/MS has not previously been successful. In fact, robust methods for direct LC-MS/MS-based analysis of S-palmitoylated proteins have been lacking. We addressed this issue by developing an LC-MS/MS “bottom-up” workflow that mitigates sample processing issues associated with S-palmitoylation, including peptide solubility, stability, LC column retention, and MS/MS-based sequence analysis. We successfully applied this workflow to directly detect and annotate endogenous acylation sites on recombinant N-Ras.
Chapter 3 discusses the adaptation of an LC-MS/MS workflow for HCP characterization in biopharmaceutical drug substances. HCPs are native proteins derived from a host organism used to express biotherapeutic proteins and may be co-purified with a drug substance as process related impurities. The presence of these impurities in drug formulations may present problems in product performance and affect the health of patients. Therefore, effective monitoring of HCP levels in drug substances is essential. Common procedures for quantifying HCP content are limited to immunocapture detection methods, but serious efforts are underway in developing LC-MS/MS strategies for characterizing HCPs. Problematically, HCPs can be 106-fold less concentrated than the biotherapeutic protein in downstream products presenting a dynamic range challenge for electrospray ionization-MS. We developed a generalized, semi-automated, and plate-based hydrophilic interaction liquid chromatography (HILIC)…
Advisors/Committee Members: Hakansson, Kristina I (committee member), Martin, Brent Randall (committee member), Kennedy, Robert T (committee member), Marsh, E Neil G (committee member), Ruotolo, Brandon Thomas (committee member).
Subjects/Keywords: tandem mass spectrometry; Host Cell Protein; S-palmitoylation; Biological Chemistry; Science
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APA ·
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Export
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APA (6th Edition):
Crellin, J. (2020). Protein Analysis by Liquid Chromatography-Tandem Mass Spectrometry: Detecting and Profiling Protein S-Palmitoylation and Host Cell Protein Characterization. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/163145
Chicago Manual of Style (16th Edition):
Crellin, John. “Protein Analysis by Liquid Chromatography-Tandem Mass Spectrometry: Detecting and Profiling Protein S-Palmitoylation and Host Cell Protein Characterization.” 2020. Doctoral Dissertation, University of Michigan. Accessed January 18, 2021.
http://hdl.handle.net/2027.42/163145.
MLA Handbook (7th Edition):
Crellin, John. “Protein Analysis by Liquid Chromatography-Tandem Mass Spectrometry: Detecting and Profiling Protein S-Palmitoylation and Host Cell Protein Characterization.” 2020. Web. 18 Jan 2021.
Vancouver:
Crellin J. Protein Analysis by Liquid Chromatography-Tandem Mass Spectrometry: Detecting and Profiling Protein S-Palmitoylation and Host Cell Protein Characterization. [Internet] [Doctoral dissertation]. University of Michigan; 2020. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/2027.42/163145.
Council of Science Editors:
Crellin J. Protein Analysis by Liquid Chromatography-Tandem Mass Spectrometry: Detecting and Profiling Protein S-Palmitoylation and Host Cell Protein Characterization. [Doctoral Dissertation]. University of Michigan; 2020. Available from: http://hdl.handle.net/2027.42/163145
University of New South Wales
27.
Wang, Huixin.
Fundamentals and Applications of Tandem Mass Spectrometry in Top-down and Bottom-up Protein Analysis.
Degree: Chemistry, 2019, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/62225
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:58312/SOURCE02?view=true
► Owing to the development of electrospray ionization (ESI), various ion dissociation techniques and software algorithms, mass spectrometry has become an indispensable tool for protein analysis.…
(more)
▼ Owing to the development of electrospray ionization (ESI), various ion dissociation techniques and software algorithms, mass spectrometry has become an indispensable tool for protein analysis. However, new approaches are needed to overcome some of the challenges in protein sequencing, including in the identification of post-translational modifications (PTMs), and in the analysis of protein complexes and protein-protein interaction networks. For PTM identification, commonly used database search algorithms for bottom-up proteomics often fail to identify peptides with unexpected PTMs due to their relatively low abundances and the absence of such modifications in the PTM databases. However, such unexpected PTMs can have important roles in biological functions. Here, we report a novel mass spectrometry method to identify the proteins targets of organophosphate (OP) insecticides in a non-targeted fashion. This method integrates a high-resolution twin-ion metabolite extraction program with Mascot database searching. Using this method, transmethylation was identified as a new reaction pathway for OP insecticides, in addition to the well-known phosphorylation modification that causes acute toxicity. Our results show that this method can be used for the reliable identification of unknown PTMs in complicated biomatrices which may ultimately benefit the discovery of protein biomarkers for a variety of conditions. For protein sequence identification, collision induced dissociation (CID) is the most widely used dissociation technique. In the CID of intact proteins, the fragmentation patterns of the protein ion depend strongly on the protein charge state. An optimal charge state can generate selective fragmentation resulting in a limited number of sequence ions in high abundances which can be useful for protein identification with high sensitivity. However, an accurate model to predict the fragmentation patterns of particular charge states is needed. Here, we report an approach to predict the specific cleavage sites of intact protein ions upon CID by use of an improved electrostatic model for calculating the proton configurations of protein ions at different charge states. The origin of highly selective cleavage sites in the CID of highly charged proteins ions is investigated using an improved electrostatic model, molecular dynamics and hybrid ONIOM simulations. The ONIOM results indicate that the protons located at low-basicity amino acid residues can dramatically reduce the reaction barrier to the cleavages at such amide bonds. The results from our electrostatic model suggest that unlike peptide ions at relatively high charge states, protons at low-basicity amino acid residue sites are electrostatically confined within a relatively narrow range of amino acid residues. Such confined protons can ‘trigger’ the fragmentation at the specific peptide bonds. Our model can potentially be used to predict the specific charge states that yield either specific sequence ions in high abundances, or fragment extensively for optimal protein…
Subjects/Keywords: Top - down protein analysis; Tandem mass spectrometry; Bottom - up protein analysis
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APA ·
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Export
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APA (6th Edition):
Wang, H. (2019). Fundamentals and Applications of Tandem Mass Spectrometry in Top-down and Bottom-up Protein Analysis. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/62225 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:58312/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Wang, Huixin. “Fundamentals and Applications of Tandem Mass Spectrometry in Top-down and Bottom-up Protein Analysis.” 2019. Doctoral Dissertation, University of New South Wales. Accessed January 18, 2021.
http://handle.unsw.edu.au/1959.4/62225 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:58312/SOURCE02?view=true.
MLA Handbook (7th Edition):
Wang, Huixin. “Fundamentals and Applications of Tandem Mass Spectrometry in Top-down and Bottom-up Protein Analysis.” 2019. Web. 18 Jan 2021.
Vancouver:
Wang H. Fundamentals and Applications of Tandem Mass Spectrometry in Top-down and Bottom-up Protein Analysis. [Internet] [Doctoral dissertation]. University of New South Wales; 2019. [cited 2021 Jan 18].
Available from: http://handle.unsw.edu.au/1959.4/62225 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:58312/SOURCE02?view=true.
Council of Science Editors:
Wang H. Fundamentals and Applications of Tandem Mass Spectrometry in Top-down and Bottom-up Protein Analysis. [Doctoral Dissertation]. University of New South Wales; 2019. Available from: http://handle.unsw.edu.au/1959.4/62225 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:58312/SOURCE02?view=true
Purdue University
28.
Pilo, Alice Lindsay.
The Gas-Phase Oxidation of Cationic Bioanalytes via Ion/Ion Reactions.
Degree: PhD, Chemistry, 2016, Purdue University
URL: https://docs.lib.purdue.edu/open_access_dissertations/1394
► Several solution-phase derivatizations have recently been implemented in the gas-phase through the interaction between oppositely charged ions, viz., ion/ion reactions. The work presented here primarily…
(more)
▼ Several solution-phase derivatizations have recently been implemented in the gas-phase through the interaction between oppositely charged ions, viz., ion/ion reactions. The work presented here primarily focuses on the oxidation of bioanalytes via ion/ion reactions with periodate and persulfate anions. Methionine and tryptophan residues in simple polypeptides are selectively oxidized upon ion/ion reactions with periodate anion. The oxidative labeling of disulfide bonds is performed via ion/ion reactions and is used to identify intermolecularly disulfide-linked peptides and further probe their primary structure. Non-modified, non-disulfide linked peptides lacking easily oxidized residues (i.e., methionine and tryptophan) can also undergo oxidation. Peptides containing neutral basic sites undergo oxidation upon ion/ion reactions with periodate anion to various forms, including the [M+H+O]+,[M-H]+, and [M-H-NH3]+ species. Furthermore, persulfate anion is a stronger oxidizing reagent than periodate and increases the amount of oxidation observed with these less-readily oxidized residues. Persulfate anion and its derivatives, sulfate radical anion and peroxymonosulfate anion are capable of generating a variety of oxidation products, including the [M+H+O]+, [M-H]+, and M+• species.
Advisors/Committee Members: Scott A McLuckey, Mary J Wirth, Marcy H Towns, Paul Wenthold.
Subjects/Keywords: Dehydroalanine; Ion/Ion Reactions; Oxidation; Radical Cations; Tandem Mass Spectrometry
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APA (6th Edition):
Pilo, A. L. (2016). The Gas-Phase Oxidation of Cationic Bioanalytes via Ion/Ion Reactions. (Doctoral Dissertation). Purdue University. Retrieved from https://docs.lib.purdue.edu/open_access_dissertations/1394
Chicago Manual of Style (16th Edition):
Pilo, Alice Lindsay. “The Gas-Phase Oxidation of Cationic Bioanalytes via Ion/Ion Reactions.” 2016. Doctoral Dissertation, Purdue University. Accessed January 18, 2021.
https://docs.lib.purdue.edu/open_access_dissertations/1394.
MLA Handbook (7th Edition):
Pilo, Alice Lindsay. “The Gas-Phase Oxidation of Cationic Bioanalytes via Ion/Ion Reactions.” 2016. Web. 18 Jan 2021.
Vancouver:
Pilo AL. The Gas-Phase Oxidation of Cationic Bioanalytes via Ion/Ion Reactions. [Internet] [Doctoral dissertation]. Purdue University; 2016. [cited 2021 Jan 18].
Available from: https://docs.lib.purdue.edu/open_access_dissertations/1394.
Council of Science Editors:
Pilo AL. The Gas-Phase Oxidation of Cationic Bioanalytes via Ion/Ion Reactions. [Doctoral Dissertation]. Purdue University; 2016. Available from: https://docs.lib.purdue.edu/open_access_dissertations/1394
McMaster University
29.
McFarlane, Nicole.
Global Evaluation of the Escherichia coli Proteome during Stationary Phase.
Degree: MSc, 2019, McMaster University
URL: http://hdl.handle.net/11375/25302
► Escherichia coli survives in both nutrient rich nutrient-limited environments. As such, understanding the gene and protein level activity that occurs during stationary phase is considered…
(more)
▼ Escherichia coli survives in both nutrient rich nutrient-limited environments. As such, understanding the gene and protein level activity that occurs during stationary phase is considered an important aspect of bacterial survival. Escherichia coli has been studied for decades providing substantial insight into gene expression profiles in exponential phase and recently, during adaptation to stationary phase. This led to the discovery of RpoS as a growth phase-dependent sigma factor. Further studies indicated that there are many genes that are expressed in an RpoS-independent but stationary phase-specific manner. However, proteins represent the functional molecules of the cell. Additionally, protein expression does not always correlate with the corresponding gene expression patterns. Therefore, to obtain an in depth understanding of the proteins that play a role in long-term growth in E. coli, TMT- (Tandem Mass Tags) based quantitative proteomic analysis was performed to identify proteins that are preferentially expressed during prolonged starvation. We identified proteins that were both positively and negatively regulated by RpoS during stationary phase, such as GadA and TnaA, respectively. RpoS levels peaked during early stationary phase and declined thereafter. However, proteins that were RpoS-dependent continued to increase during prolonged stationary phase. Additionally, we identified proteins that were expressed in an RpoS-independent manner during stationary phase. This suggests that protein expression during early stationary phase is distinct from prolonged stationary phase. Furthermore, RpoS-independent proteins may also play an important role during long-term growth.
Thesis
Master of Science (MSc)
Escherichia coli adapts to shifts in nutrient availability using the alternative sigma factor RpoS which controls morphological and physiological changes. Although gene expression during growth has been extensively studied, comparable information regarding changes in protein abundance during prolonged incubation is not available. We employed a quantitative proteomics approach to identify proteins that are preferentially expressed during stationary phase in E. coli. We identified classes of proteins that are upregulated and downregulated by RpoS in addition to proteins regulated independently of RpoS. Global analysis of protein expression during growth can aid in understanding the adaptation of E. coli under starvation conditions.
Advisors/Committee Members: Schellhorn, Herb, Biology.
Subjects/Keywords: E. coli; Proteomics; Stationary Phase; Long-term growth; Differential Expression; Tandem Mass Tags; Mass Spectrometry
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APA (6th Edition):
McFarlane, N. (2019). Global Evaluation of the Escherichia coli Proteome during Stationary Phase. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/25302
Chicago Manual of Style (16th Edition):
McFarlane, Nicole. “Global Evaluation of the Escherichia coli Proteome during Stationary Phase.” 2019. Masters Thesis, McMaster University. Accessed January 18, 2021.
http://hdl.handle.net/11375/25302.
MLA Handbook (7th Edition):
McFarlane, Nicole. “Global Evaluation of the Escherichia coli Proteome during Stationary Phase.” 2019. Web. 18 Jan 2021.
Vancouver:
McFarlane N. Global Evaluation of the Escherichia coli Proteome during Stationary Phase. [Internet] [Masters thesis]. McMaster University; 2019. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/11375/25302.
Council of Science Editors:
McFarlane N. Global Evaluation of the Escherichia coli Proteome during Stationary Phase. [Masters Thesis]. McMaster University; 2019. Available from: http://hdl.handle.net/11375/25302
University of Alberta
30.
Stanislaus, Avalyn E.
Metabolite Identification and Quantification in Biofluids
Using Liquid Chromatography Mass Spectrometry.
Degree: PhD, Department of Chemistry, 2012, University of Alberta
URL: https://era.library.ualberta.ca/files/w0892b834
► Metabolomics, one of the branches of systems biology, is the comprehensive measurement of all the endogenous metabolites in a biological system. It can be applied…
(more)
▼ Metabolomics, one of the branches of systems biology,
is the comprehensive measurement of all the endogenous metabolites
in a biological system. It can be applied in the areas of biomarker
discovery and diagnosis of critical diseases and disorders, and can
significantly increase our understanding of the pathophysiology
involved in development of acute diseases. For metabolomics to
reach its true potential, there are many key areas that need to be
addressed. This thesis focuses on the development and application
of new mass spectrometric techniques aimed at improving several
areas in metabolomics research: 1) detection and identification of
compound classes, 2) enhancing the electrospray response and
improving the chromatographic behavior of metabolites, 3)
increasing sample throughput, 4) accurate quantification of
endogenous metabolites and 5) expanding current databases used in
metabolite identification. The initial work, the comprehensive
analysis of acylglycines in human urine, illustrates the analytical
challenges of detection and identification of trace levels of
metabolites in urine. Mass spectrometric methods were optimized
using fragmentation patterns and breakdown graphs, and putative
identifications were made using a combination of diagnostic neutral
losses. This method was successful in detecting and putatively
identifying 43 new acylglycines. Quantification of these
metabolites in human urine and plasma was performed using a new
labeling strategy. Chemical modification was advantageous as it
enhanced the electrospray response of these polar metabolites and
provided a way to incorporate a stable isotope onto the molecule.
Quantification using a new “surrogate matrix” strategy was also
developed. A new fast LC method was developed for the analysis of
several analytes in the vitamin B12 pathway in less than 36
seconds. This method was very useful in improving high-throughput
and in the discovery of the role of ABC protein transporters in B12
metabolism. Finally, a web-based software called MyCompoundID was
developed to expand the metabolome coverage of an existing database
(HMBD) by generating metabolic products derived from 76 common
biotransformations. This served to increase the number of entries
from 8000 to more than 10 million.
Subjects/Keywords: Metabolomics, Metabolite identification, Quantification,
Acylglycines, Methylmalonic acid, MycompoundID, Ultra-High
Performance Liquid Chromatography, Mass spectrometry, Tandem mass
spectrometry
Record Details
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Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Stanislaus, A. E. (2012). Metabolite Identification and Quantification in Biofluids
Using Liquid Chromatography Mass Spectrometry. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/w0892b834
Chicago Manual of Style (16th Edition):
Stanislaus, Avalyn E. “Metabolite Identification and Quantification in Biofluids
Using Liquid Chromatography Mass Spectrometry.” 2012. Doctoral Dissertation, University of Alberta. Accessed January 18, 2021.
https://era.library.ualberta.ca/files/w0892b834.
MLA Handbook (7th Edition):
Stanislaus, Avalyn E. “Metabolite Identification and Quantification in Biofluids
Using Liquid Chromatography Mass Spectrometry.” 2012. Web. 18 Jan 2021.
Vancouver:
Stanislaus AE. Metabolite Identification and Quantification in Biofluids
Using Liquid Chromatography Mass Spectrometry. [Internet] [Doctoral dissertation]. University of Alberta; 2012. [cited 2021 Jan 18].
Available from: https://era.library.ualberta.ca/files/w0892b834.
Council of Science Editors:
Stanislaus AE. Metabolite Identification and Quantification in Biofluids
Using Liquid Chromatography Mass Spectrometry. [Doctoral Dissertation]. University of Alberta; 2012. Available from: https://era.library.ualberta.ca/files/w0892b834
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Open Access Theses and Dissertations