Mass Spectrometry of Glycoproteins

<p>1. Introduction to Glycosylation and Mass Spectrometry</p><p>Steven M. Patrie, Michael J. Roth and Jennifer J. Kohler </p><p> </p><p>Part I – Enrichment and Isolation Methods</p><p> </p><p>2. Tandem Lectin Weak Affinity Chromatography (LWAC) for Glycoprotein Enrichment</p><p>Zhi Yuan Ma, Yuliya Skorobogatko, and Keith Vosseller</p><p> </p><p>3. CSC Technology - Selective Labeling of Glycoproteins by Mild Oxidation to Phenotype Cells</p><p>Andreas Hofmann,Damaris Bausch-Fluck, and Bernd Wollscheid^{<p> </p><p>4. Use of Boronic Acid Nanoparticles in Glycoprotein Enrichment</p><p>Yawei Xu, Lijuan Zhang and Haojie Lu<p> </p><p>5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins</p><p>Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt</p><p></p><p>6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry</p><p>Yashu Liu, Jintang He and David M. Lubman</p><p> </p><p>7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides</p><p>Jonas Nilsson and Göran Larson</p><p> </p><p>Part II – Sample Preparation</p><p> </p><p>8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis</p>Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire</p><p></p><p>9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis</p><p>Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer</p><p> </p><p>Part III – Separation Methods</p><p> </p><p>10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)</p><p>Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen^{<p> </p><p>11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection</p><p>Alina D. Zamfir, Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu</p><p> </p><p>12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics  </p><p>Larissa S. Fenn and John A. McLean </p><p> </p><p>Part IV – Quantitation Methods</p><p> </p><p>13. Quantitative Analysis of Glycoprotein Glycans</p><p>Ron Orlando</p><p> </p><p>14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics</p><p>Hiroyuki Kaji and Toshiaki Isobe</p><p> </p>15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides</p><p>Peng Zhao, Stephanie H. Stalnaker, Lance Wells</p><p> </p><p>16. Glycan Profiling: Label-free Analysis of Glycoproteins</p><p>Yoshinao Wada</p><p> </p><p>Part V – Computational Tools</p><p> </p><p>17. Introduction to Informatics in Glycoprotein Analysis</p><p>Kiyoko F. Aoki-Kinoshita</p><p> </p><p>18. Software Tools for Glycan Profiling</p><p>Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang</p><p> </p><p>Part VI – Case Studies in Mass Spectrometry of Glycoproteins</p><p></p><p>19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ</p><p>Min Shi, Hyejin Hwang and Jing Zhang</p><p> </p>20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid<p>Lei Zhou and Roger W. Beuerman</p><p> </p><p>21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery</p><p>Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher</p><p></p><p>22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins</p><p>Nicole Samuels, David Kates, Jun Liu, Joanne Severs</p>}</p><p> </p><p>11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection</p><p>Alina D. Zamfir, Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu</p><p> </p><p>12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics  </p><p>Larissa S. Fenn and John A. McLean </p><p> </p><p>Part IV – Quantitation Methods</p><p> </p><p>13. Quantitative Analysis of Glycoprotein Glycans</p><p>Ron Orlando</p><p> </p><p>14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics</p><p>Hiroyuki Kaji and Toshiaki Isobe</p><p> </p><p>15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides</p><p>Peng Zhao, Stephanie H. Stalnaker, Lance Wells</p><p> </p><p>16. Glycan Profiling: Label-free Analysis of Glycoproteins</p><p>Yoshinao Wada</p><p> </p><p>Part V – Computational Tools</p><p> </p><p>17. Introduction to Informatics in Glycoprotein Analysis</p><p>Kiyoko F. Aoki-Kinoshita</p><p> </p><p>18. Software Tools for Glycan Profiling</p><p>Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang</p><p> </p><p>Part VI – Case Studies in Mass Spectrometry of Glycoproteins</p><p></p><p>19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ</p><p>Min Shi, Hyejin Hwang and Jing Zhang</p><p> </p>20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid<p>Lei Zhou and Roger W. Beuerman</p><p> </p><p>21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery</p><p>Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher</p><p></p><p>22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins</p><p>Nicole Samuels, David Kates, Jun Liu, Joanne Severs</p></p><p> </p><p>5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins</p><p>Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt</p><p></p><p>6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry</p><p>Yashu Liu, Jintang He and David M. Lubman</p><p> </p><p>7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides</p><p>Jonas Nilsson and Göran Larson</p><p> </p><p>Part II – Sample Preparation</p><p> </p><p>8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis</p><p>Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire</p><p></p><p>9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis</p><p>Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer</p><p> </p><p>Part III – Separation Methods</p><p> </p>10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)</p><p>Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen^{<p> </p><p>11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection</p><p>Alina D. Zamfir, Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu</p><p> </p><p>12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics  </p><p>Larissa S. Fenn and John A. McLean </p><p> </p><p>Part IV – Quantitation Methods</p><p> </p><p>13. Quantitative Analysis of Glycoprotein Glycans</p><p>Ron Orlando</p><p> </p><p>14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics</p><p>Hiroyuki Kaji and Toshiaki Isobe</p><p> </p><p>15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides</p><p>Peng Zhao, Stephanie H. Stalnaker, Lance Wells</p><p> </p><p>16. Glycan Profiling: Label-free Analysis of Glycoproteins</p><p>Yoshinao Wada</p><p> </p><p>Part V – Computational Tools</p><p> </p><p>17. Introduction to Informatics in Glycoprotein Analysis</p><p>Kiyoko F. Aoki-Kinoshita</p><p> </p><p>18. Software Tools for Glycan Profiling</p><p>Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang</p><p> </p><p>Part VI – Case Studies in Mass Spectrometry of Glycoproteins</p><p></p><p>19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ</p><p>Min Shi, Hyejin Hwang and Jing Zhang</p><p> </p>20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid<p>Lei Zhou and Roger W. Beuerman</p><p> </p><p>21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery</p><p>Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher</p><p></p><p>22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins</p><p>Nicole Samuels, David Kates, Jun Liu, Joanne Severs</p>}</p>}</p><p> </p><p>4. Use of Boronic Acid Nanoparticles in Glycoprotein Enrichment</p><p>Yawei Xu, Lijuan Zhang and Haojie Lu<p> </p><p>5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins</p><p>Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt</p><p></p><p>6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry</p><p>Yashu Liu, Jintang He and David M. Lubman</p><p> </p><p>7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides</p>Jonas Nilsson and Göran Larson</p><p> </p><p>Part II – Sample Preparation</p><p> </p><p>8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis</p><p>Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire</p><p></p><p>9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis</p><p>Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer</p><p> </p><p>Part III – Separation Methods</p><p> </p><p>10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)</p><p>Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen^{<p> </p><p>11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection</p><p>Alina D. Zamfir, Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu</p><p> </p><p>12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics  </p><p>Larissa S. Fenn and John A. McLean </p><p> </p><p>Part IV – Quantitation Methods</p><p> </p><p>13. Quantitative Analysis of Glycoprotein Glycans</p><p>Ron Orlando</p> </p><p>14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics</p><p>Hiroyuki Kaji and Toshiaki Isobe</p><p> </p><p>15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides</p><p>Peng Zhao, Stephanie H. Stalnaker, Lance Wells</p><p> </p><p>16. Glycan Profiling: Label-free Analysis of Glycoproteins</p><p>Yoshinao Wada</p><p> </p><p>Part V – Computational Tools</p><p> </p><p>17. Introduction to Informatics in Glycoprotein Analysis</p><p>Kiyoko F. Aoki-Kinoshita</p><p> </p><p>18. Software Tools for Glycan Profiling</p><p>Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang</p><p> </p><p>Part VI – Case Studies in Mass Spectrometry of Glycoproteins</p><p></p><p>19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ</p><p>Min Shi, Hyejin Hwang and Jing Zhang</p><p> </p>20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid<p>Lei Zhou and Roger W. Beuerman</p><p> </p><p>21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery</p><p>Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher</p><p></p><p>22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins</p><p>Nicole Samuels, David Kates, Jun Liu, Joanne Severs</p>}</p> </p><p>11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection</p><p>Alina D. Zamfir, Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu</p><p> </p><p>12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics  </p><p>Larissa S. Fenn and John A. McLean </p><p> </p><p>Part IV – Quantitation Methods</p><p> </p><p>13. Quantitative Analysis of Glycoprotein Glycans</p><p>Ron Orlando</p><p> </p><p>14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics</p><p>Hiroyuki Kaji and Toshiaki Isobe</p><p> </p><p>15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides</p><p>Peng Zhao, Stephanie H. Stalnaker, Lance Wells</p><p> </p><p>16. Glycan Profiling: Label-free Analysis of Glycoproteins</p><p>Yoshinao Wada</p><p> </p><p>Part V – Computational Tools</p><p> </p><p>17. Introduction to Informatics in Glycoprotein Analysis</p><p>Kiyoko F. Aoki-Kinoshita</p><p> </p><p>18. Software Tools for Glycan Profiling</p><p>Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang</p><p> </p><p>Part VI – Case Studies in Mass Spectrometry of Glycoproteins</p><p></p><p>19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ</p>Min Shi, Hyejin Hwang and Jing Zhang</p><p> </p>20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid<p>Lei Zhou and Roger W. Beuerman</p><p> </p><p>21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery</p><p>Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher</p><p></p><p>22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins</p><p>Nicole Samuels, David Kates, Jun Liu, Joanne Severs</p></p><p> </p><p>5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins</p><p>Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt</p><p></p><p>6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry</p><p>Yashu Liu, Jintang He and David M. Lubman</p><p> </p><p>7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides</p><p>Jonas Nilsson and Göran Larson</p><p> </p><p>Part II – Sample Preparation</p><p> </p><p>8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis</p><p>Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire</p><p></p><p>9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis</p>Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer</p><p> </p><p>Part III – Separation Methods</p><p> </p><p>10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)</p><p>Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen^{<p> </p><p>11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection</p><p>Alina D. Zamfir, Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu</p><p> </p><p>12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics  </p><p>Larissa S. Fenn and John A. McLean </p><p> </p><p>Part IV – Quantitation Methods</p><p> </p><p>13. Quantitative Analysis of Glycoprotein Glycans</p><p>Ron Orlando</p><p> </p><p>14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics</p><p>Hiroyuki Kaji and Toshiaki Isobe</p><p> </p><p>15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides</p><p>Peng Zhao, Stephanie H. Stalnaker, Lance Wells</p><p> </p><p>16. Glycan Profiling: Label-free Analysis of Glycoproteins</p><p>Yoshinao Wada</p><p> </p><p>Part V – Computational Tools</p><p> </p><p>17. Introduction to Informatics in Glycoprotein Analysis</p><p>Kiyoko F. Aoki-Kinoshita</p><p> </p><p>18. Software Tools for Glycan Profiling</p><p>Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang</p><p> </p><p>Part VI – Case Studies in Mass Spectrometry of Glycoproteins</p><p></p><p>19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ</p><p>Min Shi, Hyejin Hwang and Jing Zhang</p><p> </p>20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid<p>Lei Zhou and Roger W. Beuerman</p><p> </p><p>21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery</p><p>Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher</p><p></p><p>22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins</p><p>Nicole Samuels, David Kates, Jun Liu, Joanne Severs</p>}</p><p> </p><p>11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection</p><p>Alina D. Zamfir, Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu</p><p> </p><p>12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics  </p>Larissa S. Fenn and John A. McLean </p><p> </p><p>Part IV – Quantitation Methods</p><p> </p><p>13. Quantitative Analysis of Glycoprotein Glycans</p><p>Ron Orlando</p><p> </p><p>14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics</p><p>Hiroyuki Kaji and Toshiaki Isobe</p><p> </p><p>15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides</p><p>Peng Zhao, Stephanie H. Stalnaker, Lance Wells</p><p> </p><p>16. Glycan Profiling: Label-free Analysis of Glycoproteins</p><p>Yoshinao Wada</p><p> </p><p>Part V – Computational Tools</p><p> </p><p>17. Introduction to Informatics in Glycoprotein Analysis</p><p>Kiyoko F. Aoki-Kinoshita</p><p> </p><p>18. Software Tools for Glycan Profiling</p><p>Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang</p><p> </p><p>Part VI – Case Studies in Mass Spectrometry of Glycoproteins</p><p></p><p>19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ</p><p>Min Shi, Hyejin Hwang and Jing Zhang</p><p> </p>20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid<p>Lei Zhou and Roger W. Beuerman</p><p> </p><p>21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery</p>Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher</p><p></p><p>22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins</p><p>Nicole Samuels, David Kates, Jun Liu, Joanne Severs</p>