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Standing in the Way of Profiling Depth : = How the Selection of Chromatography and Mass Spectrometry Data Acquisition Limit Our View of the Proteome.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Standing in the Way of Profiling Depth :/
Reminder of title:	How the Selection of Chromatography and Mass Spectrometry Data Acquisition Limit Our View of the Proteome.
Author:	Delafield, Daniel Graham.
Description:	1 online resource (493 pages)
Notes:	Source: Dissertations Abstracts International, Volume: 84-10, Section: B.
Contained By:	Dissertations Abstracts International84-10B.
Subject:	Chemistry. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=30425876click for full text (PQDT)
ISBN:	9798379440046

Standing in the Way of Profiling Depth : = How the Selection of Chromatography and Mass Spectrometry Data Acquisition Limit Our View of the Proteome.
Delafield, Daniel Graham.

Standing in the Way of Profiling Depth :How the Selection of Chromatography and Mass Spectrometry Data Acquisition Limit Our View of the Proteome. - 1 online resource (493 pages)

Source: Dissertations Abstracts International, Volume: 84-10, Section: B.

Thesis (Ph.D.)--The University of Wisconsin - Madison, 2023.

Includes bibliographical references

This thesis outlines research focusing on the development and application of chromatography separation and mass spectrometry data acquisition methods aimed at improving profiling depth in proteomic analyses. This work is briefly outlined and explained in Chapter 1, highlighting how reliance on common analytical methodologies inherently limits our view of the proteome. Chapter 2 details the initial reports of utilizing porous graphitic carbon (PGC) chromatography as an alternative to reversed-phase liquid chromatography (RPLC). This report describes demonstrable improvements in peptide, glycopeptide, and protein identifications while highlighting the various analytical advantages seen over traditional separations. In this preliminary work, we observed elevated column temperatures imparted potentially detrimental effects of various glycopeptides, a phenomenon explored in Chapter 3. This following report provides heuristic guidance in PGC-based glycoproteomic analyses and details how column temperature must be optimized to suit the given analytical need. Chapter 4 provides a topical overview of quantitative approaches in glycan and glycopeptide analyses, providing meaningful consideration and comparison of methodologies most appropriate for use in future glycoproteomic analyses. In Chapter 5, we return to PGC separations with a specific focus on further detailing the benefits found in proteomic analyses. This report highlights substantial improvements in the number of peptide and protein identifications compared to what was seen previously and highlights the breadth of information lost during routine RPLC analyses. Chapter 6 departs from chromatographic separation and turns attention towards quantitative mass spectrometry (MS) methods useful for biological discovery. The knowledge and information garnered from this report informed the experimental design used in Chapter 7, which describes the employment of data independent acquisition (DIA)-MS to study a novel, progressive prostate cancer cell model. Here we quantified 6,614 proteins across 9 biological samples, finding 1,242 to be significantly dysregulated in malignant cancer phenotypes. These proteins demonstrate potential for disease diagnosis, phenotypic stratification, and therapeutic targeting. In Chapter 8 we expand on the utility of DIA-MS, detailing the ability to reuse and repurpose prior proteomic measurements for enhanced biomolecular identification. We apply this workflow to the analysis of neurological disorder patient cohorts, revealing 1,642 dysregulated proteins that speak to the biomolecular organization related to Alzheimer's Disease. Chapter 9 describes new and emerging ion mobility (IM)-based analytical modalities and discuss their capacity for biomolecular interrogation and structural analysis. Given instrumentation of this kind is not utilized in the works preceding, this report explains potential advantages and necessary considerations, should this technology become of interest. Finally, we conclude with Chapter 10, briefly discussing the various investigations that may follow this body of work.

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2023

Mode of access: World Wide Web

ISBN: 9798379440046Subjects--Topical Terms:

516420
Chemistry.
Subjects--Index Terms:

GlycoproteomicsIndex Terms--Genre/Form:

542853
Electronic books.

Standing in the Way of Profiling Depth : = How the Selection of Chromatography and Mass Spectrometry Data Acquisition Limit Our View of the Proteome.
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520 $a This thesis outlines research focusing on the development and application of chromatography separation and mass spectrometry data acquisition methods aimed at improving profiling depth in proteomic analyses. This work is briefly outlined and explained in Chapter 1, highlighting how reliance on common analytical methodologies inherently limits our view of the proteome. Chapter 2 details the initial reports of utilizing porous graphitic carbon (PGC) chromatography as an alternative to reversed-phase liquid chromatography (RPLC). This report describes demonstrable improvements in peptide, glycopeptide, and protein identifications while highlighting the various analytical advantages seen over traditional separations. In this preliminary work, we observed elevated column temperatures imparted potentially detrimental effects of various glycopeptides, a phenomenon explored in Chapter 3. This following report provides heuristic guidance in PGC-based glycoproteomic analyses and details how column temperature must be optimized to suit the given analytical need. Chapter 4 provides a topical overview of quantitative approaches in glycan and glycopeptide analyses, providing meaningful consideration and comparison of methodologies most appropriate for use in future glycoproteomic analyses. In Chapter 5, we return to PGC separations with a specific focus on further detailing the benefits found in proteomic analyses. This report highlights substantial improvements in the number of peptide and protein identifications compared to what was seen previously and highlights the breadth of information lost during routine RPLC analyses. Chapter 6 departs from chromatographic separation and turns attention towards quantitative mass spectrometry (MS) methods useful for biological discovery. The knowledge and information garnered from this report informed the experimental design used in Chapter 7, which describes the employment of data independent acquisition (DIA)-MS to study a novel, progressive prostate cancer cell model. Here we quantified 6,614 proteins across 9 biological samples, finding 1,242 to be significantly dysregulated in malignant cancer phenotypes. These proteins demonstrate potential for disease diagnosis, phenotypic stratification, and therapeutic targeting. In Chapter 8 we expand on the utility of DIA-MS, detailing the ability to reuse and repurpose prior proteomic measurements for enhanced biomolecular identification. We apply this workflow to the analysis of neurological disorder patient cohorts, revealing 1,642 dysregulated proteins that speak to the biomolecular organization related to Alzheimer's Disease. Chapter 9 describes new and emerging ion mobility (IM)-based analytical modalities and discuss their capacity for biomolecular interrogation and structural analysis. Given instrumentation of this kind is not utilized in the works preceding, this report explains potential advantages and necessary considerations, should this technology become of interest. Finally, we conclude with Chapter 10, briefly discussing the various investigations that may follow this body of work.
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538 $a Mode of access: World Wide Web
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653 $a Liquid chromatography
653 $a Mass spectrometry
653 $a Proteomics
653 $a Data independent acquisition
653 $a Porous graphitic carbon
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