{"id":{"repo_id":"uwo","oai_identifier":"oai:uwo.scholaris.ca:20.500.14721/35888"},"canonical_url":"https://search.dev.ndltd.org/etd/uwo/oai:uwo.scholaris.ca:20.500.14721/35888","repository":{"repo_id":"uwo","name":"Western University","base_url":"https://uwo.scholaris.ca/server/oai/request"},"display":{"title":"From Solution Into the Gas Phase: Studying Protein Hydrogen Exchange and Electrospray Ionization Using Molecular Dynamics Simulation","abstract":"Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting in the production of gaseous protein ions. The mechanism of ion formation from nanometer sized droplets is unclear. We apply a trajectory stitching MD approach to simulate protein-containing nanodroplets, finding that natively‑folded proteins remain solvated as droplets shrink. Residual charge carriers remain following desolvation, consistent with Dole’s charged residue model.","abstract_html":"Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting in the production of gaseous protein ions. The mechanism of ion formation from nanometer sized droplets is unclear. We apply a trajectory stitching MD approach to simulate protein-containing nanodroplets, finding that natively‑folded proteins remain solvated as droplets shrink. Residual charge carriers remain following desolvation, consistent with Dole’s charged residue model.","abstract_has_math":false,"creators":["McAllister, Robert G"],"institution":"The University of Western Ontario","degree_name":"M Sc","degree_level":null,"degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":[],"advisors":["Lars Konermann"],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-07-08","date_published":"2015-07-08","updated_at":"2026-07-27T21:56:13Z","subjects":["Proteins","Molecular Dynamics","Mass Spectrometry","Electrospray Ionization","Hydrogen Deuterium Exchange"],"languages":["en_ca"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/20.500.14721/35888","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Lars Konermann"]},{"key":"dc:creator","label":"Author","values":["McAllister, Robert G"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-07-10T20:43:21Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2025-07-10T20:43:21Z"]},{"key":"dc:date.issued","label":"Date","values":["2015-07-08"]},{"key":"dc:publisher","label":"Institution","values":["The University of Western Ontario"]},{"key":"dc:type","label":"Dc Type","values":["thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemistry"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M Sc"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Proteins","Molecular Dynamics","Mass Spectrometry","Electrospray Ionization","Hydrogen Deuterium Exchange"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_ca"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/20.500.14721/35888"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The thesis cover page in the PDF document includes references to Western University’s previous institutional repository platform, known as Scholarship@Western, and links to that platform (beginning with ir.lib.uwo.ca). In citing or referring to this thesis, use the DOI or handle from this page instead. Sample citation: Author name, \"Thesis title.\" (Year). Western University Open Repository. https://doi.org/10.71858/123456."]},{"key":"dc:description.abstract","label":"Abstract","values":["Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting in the production of gaseous protein ions. The mechanism of ion formation from nanometer sized droplets is unclear. We apply a trajectory stitching MD approach to simulate protein-containing nanodroplets, finding that natively‑folded proteins remain solvated as droplets shrink. Residual charge carriers remain following desolvation, consistent with Dole’s charged residue model."]},{"key":"dc:title","label":"Title","values":["From Solution Into the Gas Phase: Studying Protein Hydrogen Exchange and Electrospray Ionization Using Molecular Dynamics Simulation"]}]}],"canonical_facts":{"dc:contributor.advisor":["Lars Konermann"],"dc:creator":["McAllister, Robert G"],"dc:date.accessioned":["2025-07-10T20:43:21Z"],"dc:date.available":["2025-07-10T20:43:21Z"],"dc:date.issued":["2015-07-08"],"dc:description":["The thesis cover page in the PDF document includes references to Western University’s previous institutional repository platform, known as Scholarship@Western, and links to that platform (beginning with ir.lib.uwo.ca). In citing or referring to this thesis, use the DOI or handle from this page instead. Sample citation: Author name, \"Thesis title.\" (Year). Western University Open Repository. https://doi.org/10.71858/123456."],"dc:description.abstract":["Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting in the production of gaseous protein ions. The mechanism of ion formation from nanometer sized droplets is unclear. We apply a trajectory stitching MD approach to simulate protein-containing nanodroplets, finding that natively‑folded proteins remain solvated as droplets shrink. Residual charge carriers remain following desolvation, consistent with Dole’s charged residue model."],"dc:identifier.uri":["https://hdl.handle.net/20.500.14721/35888"],"dc:language.iso":["en_ca"],"dc:publisher":["The University of Western Ontario"],"dc:subject":["Proteins","Molecular Dynamics","Mass Spectrometry","Electrospray Ionization","Hydrogen Deuterium Exchange"],"dc:title":["From Solution Into the Gas Phase: Studying Protein Hydrogen Exchange and Electrospray Ionization Using Molecular Dynamics Simulation"],"dc:type":["thesis"],"thesis:degree_discipline":["Chemistry"],"thesis:degree_name":["M Sc"]},"updated_at":"2026-07-27T21:56:13Z"}