{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/121413"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/121413","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"High-throughput matrix-assisted laser desorption/ionization mass spectrometry for single-cell and single-organelle measurements","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2023-12-04 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2023-12-04 without embargo terms","abstract_has_math":false,"creators":["Castro, Daniel Cruz"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Molecular & Integrative Physi","degree_department":null,"school":null,"contributors":["Sweedler, Jonathan","Grosman, Claudio","Boppart, Marni","Raetzman, Lori"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-08","date_published":"2023-08","updated_at":"2026-07-22T22:24:57Z","subjects":["Maldi","Mass Spectrometry","High-throughput","Single-cell","Single-organelle","Cell","Organelle","Fourier-transform Ion Cyclotron Resonance."],"languages":["en","eng"],"rights":["Copyright 2023 Daniel Castro"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/121413","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Sweedler, Jonathan","Grosman, Claudio","Boppart, Marni","Raetzman, Lori"]},{"key":"dc:creator","label":"Author","values":["Castro, Daniel Cruz"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2023-08","2023-06-22"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Molecular & Integrative Physi"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Maldi","Mass Spectrometry","High-throughput","Single-cell","Single-organelle","Cell","Organelle","Fourier-transform Ion Cyclotron Resonance."]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2023 Daniel Castro"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/121413"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2023-12-04 without embargo terms","The student, Daniel Castro, accepted the attached license on 2023-06-07 at 12:10.","The student, Daniel Castro, submitted this Dissertation for approval on 2023-06-07 at 12:17.","This Dissertation was approved for publication on 2023-06-22 at 15:39.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19411 on 2023-12-04 at 16:59:54","Little is known regarding the molecular heterogeneity of specific classes of individual cells and organelles. However, clear phenotypical differences are seen between cells of same type, which may be attributed to organelle size, shape and composition differences. Organelle heterogeneity is ubiquitous and an indispensable property in biology that shapes cellular architecture and allows for specialized function by influencing the biochemical output of the cell. To understand how emergent properties of networks arise from an ensemble of cells, understanding their chemical differences can be important. Here, we present high-throughput mass spectrometry-based protocols to chemically profile large populations of single cells and individual organelles. Therefore, to address the fundamental heterogeneity present in these different cellular systems, we take on a single-cell approach where we enzymatically digest tissue to remove the extracellular matrix and connective components, releasing the individual cells from the tissue matrix. Single-cell staining and scattered deposition of the single cells onto the microscopy slide allows the relative spatial locations to be mapped across the microscopy slide for translation of pixel coordinates to physical coordinates, such as millimeters or microns. Performing point-based image registration between the optical microscopy image and a matrix-assisted laser desorption/ionization mass spectrometer allows the locations of the single cells to be mapped to physical stage coordinates on the mass spectrometer’s stage. With the single-cell deposition leaving space between the individual cells, the individual cells can be chemically characterized using the matrix-assisted laser desorption/ionization laser for analyte ionization and subsequent detection by mass spectrometry. In a similar manner, this single-cell workflow can be adapted to individual organelles through distinct modifications of the approach to allow targeting of objects that are tenfold smaller in diameter than the single cells. Specifically, modification of the single-cell approach can allow the targeting and chemical analysis of individual dense-core vesicles and mitochondria. Due to the high-throughput nature of the work, the downstream data analysis and interpretation requires the use and development of informatic based data analysis tools for processing and handling the highly dimensional datasets generated. Together, this work allows the high-throughput investigation of single cells and single organelles with a granularity of detail that was no previously possible."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["High-throughput matrix-assisted laser desorption/ionization mass spectrometry for single-cell and single-organelle measurements"]}]}],"canonical_facts":{"dc:contributor":["Sweedler, Jonathan","Grosman, Claudio","Boppart, Marni","Raetzman, Lori"],"dc:creator":["Castro, Daniel Cruz"],"dc:date":["2023-08","2023-06-22"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2023-12-04 without embargo terms","The student, Daniel Castro, accepted the attached license on 2023-06-07 at 12:10.","The student, Daniel Castro, submitted this Dissertation for approval on 2023-06-07 at 12:17.","This Dissertation was approved for publication on 2023-06-22 at 15:39.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19411 on 2023-12-04 at 16:59:54","Little is known regarding the molecular heterogeneity of specific classes of individual cells and organelles. However, clear phenotypical differences are seen between cells of same type, which may be attributed to organelle size, shape and composition differences. Organelle heterogeneity is ubiquitous and an indispensable property in biology that shapes cellular architecture and allows for specialized function by influencing the biochemical output of the cell. To understand how emergent properties of networks arise from an ensemble of cells, understanding their chemical differences can be important. Here, we present high-throughput mass spectrometry-based protocols to chemically profile large populations of single cells and individual organelles. Therefore, to address the fundamental heterogeneity present in these different cellular systems, we take on a single-cell approach where we enzymatically digest tissue to remove the extracellular matrix and connective components, releasing the individual cells from the tissue matrix. Single-cell staining and scattered deposition of the single cells onto the microscopy slide allows the relative spatial locations to be mapped across the microscopy slide for translation of pixel coordinates to physical coordinates, such as millimeters or microns. Performing point-based image registration between the optical microscopy image and a matrix-assisted laser desorption/ionization mass spectrometer allows the locations of the single cells to be mapped to physical stage coordinates on the mass spectrometer’s stage. With the single-cell deposition leaving space between the individual cells, the individual cells can be chemically characterized using the matrix-assisted laser desorption/ionization laser for analyte ionization and subsequent detection by mass spectrometry. In a similar manner, this single-cell workflow can be adapted to individual organelles through distinct modifications of the approach to allow targeting of objects that are tenfold smaller in diameter than the single cells. Specifically, modification of the single-cell approach can allow the targeting and chemical analysis of individual dense-core vesicles and mitochondria. Due to the high-throughput nature of the work, the downstream data analysis and interpretation requires the use and development of informatic based data analysis tools for processing and handling the highly dimensional datasets generated. Together, this work allows the high-throughput investigation of single cells and single organelles with a granularity of detail that was no previously possible."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/121413"],"dc:language":["en","eng"],"dc:rights":["Copyright 2023 Daniel Castro"],"dc:subject":["Maldi","Mass Spectrometry","High-throughput","Single-cell","Single-organelle","Cell","Organelle","Fourier-transform Ion Cyclotron Resonance."],"dc:title":["High-throughput matrix-assisted laser desorption/ionization mass spectrometry for single-cell and single-organelle measurements"],"dc:type":["text"],"thesis:degree_discipline":["Molecular & Integrative Physi"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:57Z"}