Mass Spectrometry of Glycoproteins: Methods and Protocols

ISBN-13: 9781493962037 / Angielski / Miękka / 2016 / 339 str.

Jennifer J. Kohler; Steven M. Patrie

Opis

This comprehensive new resource in Springer's Methods in Molecular Biology series features contributions from leading researchers who provide expert advice and reproducible, cutting-edge protocols for examining glycoproteins through mass spectrometry.

Spis treści

1. Introduction to Glycosylation and Mass Spectrometry

Steven M. Patrie, Michael J. Roth and Jennifer J. Kohler

 

Part I – Enrichment and Isolation Methods

 

2. Tandem Lectin Weak Affinity Chromatography (LWAC) for Glycoprotein Enrichment

Zhi Yuan Ma, Yuliya Skorobogatko, and Keith Vosseller

 

3. CSC Technology - Selective Labeling of Glycoproteins by Mild Oxidation to Phenotype Cells

Andreas Hofmann,Damaris Bausch-Fluck, and Bernd Wollscheid

 

4. Use of Boronic Acid Nanoparticles in Glycoprotein Enrichment

Yawei Xu, Lijuan Zhang and Haojie Lu

 

5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins

Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt

 

6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry

Yashu Liu, Jintang He and David M. Lubman

 

7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides

Jonas Nilsson and Göran Larson

 

Part II – Sample Preparation

 

8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis

Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire

 

9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis

Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer

 

Part III – Separation Methods

 

10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)

Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen

 

11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection

Alina D. Zamfir , Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu

 

12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics 

Larissa S. Fenn and John A. McLean

 

Part IV – Quantitation Methods

 

13. Quantitative Analysis of Glycoprotein Glycans

Ron Orlando

 

14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics

Hiroyuki Kaji and Toshiaki Isobe

 

15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides

Peng Zhao, Stephanie H. Stalnaker, Lance Wells

 

16. Glycan Profiling: Label-free Analysis of Glycoproteins

Yoshinao Wada

 

Part V – Computational Tools

 

17. Introduction to Informatics in Glycoprotein Analysis

Kiyoko F. Aoki-Kinoshita

 

18. Software Tools for Glycan Profiling

Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang

 

Part VI – Case Studies in Mass Spectrometry of Glycoproteins

 

19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ

Min Shi, Hyejin Hwang and Jing Zhang

 

20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid

Lei Zhou and Roger W. Beuerman

 

21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery

Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher

 

22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins

Nicole Samuels, David Kates, Jun Liu, Joanne Severs

 

11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection

Alina D. Zamfir , Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu

 

12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics 

Larissa S. Fenn and John A. McLean

 

Part IV – Quantitation Methods

 

13. Quantitative Analysis of Glycoprotein Glycans

Ron Orlando

 

14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics

Hiroyuki Kaji and Toshiaki Isobe

 

15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides

Peng Zhao, Stephanie H. Stalnaker, Lance Wells

 

16. Glycan Profiling: Label-free Analysis of Glycoproteins

Yoshinao Wada

 

Part V – Computational Tools

 

17. Introduction to Informatics in Glycoprotein Analysis

Kiyoko F. Aoki-Kinoshita

 

18. Software Tools for Glycan Profiling

Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang

 

Part VI – Case Studies in Mass Spectrometry of Glycoproteins

 

19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ

Min Shi, Hyejin Hwang and Jing Zhang

 

20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid

Lei Zhou and Roger W. Beuerman

 

21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery

Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher

 

22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins

Nicole Samuels, David Kates, Jun Liu, Joanne Severs

 

5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins

Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt

 

6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry

Yashu Liu, Jintang He and David M. Lubman

 

7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides

Jonas Nilsson and Göran Larson

 

Part II – Sample Preparation

 

8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis

Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire

 

9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis

Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer

 

Part III – Separation Methods

 

10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)

Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen

 

11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection

Alina D. Zamfir , Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu

 

12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics 

Larissa S. Fenn and John A. McLean

 

Part IV – Quantitation Methods

 

13. Quantitative Analysis of Glycoprotein Glycans

Ron Orlando

 

14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics

Hiroyuki Kaji and Toshiaki Isobe

 

15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides

Peng Zhao, Stephanie H. Stalnaker, Lance Wells

 

16. Glycan Profiling: Label-free Analysis of Glycoproteins

Yoshinao Wada

 

Part V – Computational Tools

 

17. Introduction to Informatics in Glycoprotein Analysis

Kiyoko F. Aoki-Kinoshita

 

18. Software Tools for Glycan Profiling

Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang

 

Part VI – Case Studies in Mass Spectrometry of Glycoproteins

 

19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ

Min Shi, Hyejin Hwang and Jing Zhang

 

20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid

Lei Zhou and Roger W. Beuerman

 

21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery

Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher

 

22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins

Nicole Samuels, David Kates, Jun Liu, Joanne Severs

 

4. Use of Boronic Acid Nanoparticles in Glycoprotein Enrichment

Yawei Xu, Lijuan Zhang and Haojie Lu

 

5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins

Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt

 

6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry

Yashu Liu, Jintang He and David M. Lubman

 

7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides

Jonas Nilsson and Göran Larson

 

Part II – Sample Preparation

 

8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis

Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire

 

9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis

Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer

 

Part III – Separation Methods

 

10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)

Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen

 

11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection

Alina D. Zamfir , Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu

 

12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics 

Larissa S. Fenn and John A. McLean

 

Part IV – Quantitation Methods

 

13. Quantitative Analysis of Glycoprotein Glycans

Ron Orlando

 

14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics

Hiroyuki Kaji and Toshiaki Isobe

 

15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides

Peng Zhao, Stephanie H. Stalnaker, Lance Wells

 

16. Glycan Profiling: Label-free Analysis of Glycoproteins

Yoshinao Wada

 

Part V – Computational Tools

 

17. Introduction to Informatics in Glycoprotein Analysis

Kiyoko F. Aoki-Kinoshita

 

18. Software Tools for Glycan Profiling

Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang

 

Part VI – Case Studies in Mass Spectrometry of Glycoproteins

 

19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ

Min Shi, Hyejin Hwang and Jing Zhang

 

20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid

Lei Zhou and Roger W. Beuerman

 

21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery

Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher

 

22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins

Nicole Samuels, David Kates, Jun Liu, Joanne Severs

 

11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection

Alina D. Zamfir , Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu

 

12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics 

Larissa S. Fenn and John A. McLean

 

Part IV – Quantitation Methods

 

13. Quantitative Analysis of Glycoprotein Glycans

Ron Orlando

 

14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics

Hiroyuki Kaji and Toshiaki Isobe

 

15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides

Peng Zhao, Stephanie H. Stalnaker, Lance Wells

 

16. Glycan Profiling: Label-free Analysis of Glycoproteins

Yoshinao Wada

 

Part V – Computational Tools

 

17. Introduction to Informatics in Glycoprotein Analysis

Kiyoko F. Aoki-Kinoshita

 

18. Software Tools for Glycan Profiling

Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang

 

Part VI – Case Studies in Mass Spectrometry of Glycoproteins

 

19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ

Min Shi, Hyejin Hwang and Jing Zhang

 

20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid

Lei Zhou and Roger W. Beuerman

 

21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery

Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher

 

22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins

Nicole Samuels, David Kates, Jun Liu, Joanne Severs

 

5. Incorporation of Unnatural Sugars for the Identification of Glycoproteins

Balyn W. Zaro , Howard C. Hang , Matthew R. Pratt

 

6. Characterization of Membrane-associated Glycoproteins using Lectin Affinity Chromatography and Mass Spectrometry

Yashu Liu, Jintang He and David M. Lubman

 

7. Sialic Acid Capture-and-Release and LC-MSⁿ Analysis of Glycopeptides

Jonas Nilsson and Göran Larson

 

Part II – Sample Preparation

 

8.  In-Solution Digestion of Glycoproteins for Glycopeptide-Based Mass Analysis

Eden P. Go, Kathryn R. Rebecchi, and Heather Desaire

 

9. Nano-HPLC-MS of Glycopeptides Obtained After Non-specific Proteolysis

Gerhild Zauner, Carolien A. M. Koeleman, André M. Deelder and Manfred Wuhrer

 

Part III – Separation Methods

 

10. Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE)

Pia Hønnerup Jensen, Simon Mysling, Peter Højrup and Ole Nørregaard Jensen

 

11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection

Alina D. Zamfir , Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu

 

12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics 

Larissa S. Fenn and John A. McLean

 

Part IV – Quantitation Methods

 

13. Quantitative Analysis of Glycoprotein Glycans

Ron Orlando

 

14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics

Hiroyuki Kaji and Toshiaki Isobe

 

15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides

Peng Zhao, Stephanie H. Stalnaker, Lance Wells

 

16. Glycan Profiling: Label-free Analysis of Glycoproteins

Yoshinao Wada

 

Part V – Computational Tools

 

17. Introduction to Informatics in Glycoprotein Analysis

Kiyoko F. Aoki-Kinoshita

 

18. Software Tools for Glycan Profiling

Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang

 

Part VI – Case Studies in Mass Spectrometry of Glycoproteins

 

19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ

Min Shi, Hyejin Hwang and Jing Zhang

 

20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid

Lei Zhou and Roger W. Beuerman

 

21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery

Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher

 

22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins

Nicole Samuels, David Kates, Jun Liu, Joanne Severs

 

11. Separation and Identification of Glycoforms by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometric Detection

Alina D. Zamfir , Corina Flangea, Alina Serb³, Ana-Maria Zagrean⁴, Andreas M. Rizzi⁵ and Eugen Sisu

 

12. Structural Separations by Ion Mobility-MS for Glycomics and Glycoproteomics 

Larissa S. Fenn and John A. McLean

 

Part IV – Quantitation Methods

 

13. Quantitative Analysis of Glycoprotein Glycans

Ron Orlando

 

14. Stable Isotope Labeling of N-glycosylated Peptides by Enzymatic Deglycosylation for Mass Spectrometry-based Glycoproteomics

Hiroyuki Kaji and Toshiaki Isobe

 

15. Approaches for Site Mapping and Quantification of O-linked Glycopeptides

Peng Zhao, Stephanie H. Stalnaker, Lance Wells

 

16. Glycan Profiling: Label-free Analysis of Glycoproteins

Yoshinao Wada

 

Part V – Computational Tools

 

17. Introduction to Informatics in Glycoprotein Analysis

Kiyoko F. Aoki-Kinoshita

 

18. Software Tools for Glycan Profiling

Chuan-Yih Yu, Anoop Mayampurath, Haixu Tang

 

Part VI – Case Studies in Mass Spectrometry of Glycoproteins

 

19. Quantitative Characterization of Glycoproteins in Neurodegenerative Disorders using iTRAQ

Min Shi, Hyejin Hwang and Jing Zhang

 

20. Quantitative Proteomic Analysis of N-linked Glycoproteins in Human Tear Fluid

Lei Zhou and Roger W. Beuerman

 

21. Elucidation of N-glycosites Within Human Plasma Glycoproteins for Cancer Biomarker Discovery

Penelope Drake, Birgit Schilling, Brad Gibson and Susan Fisher

 

22. Characterizing the Glycosylation State of Therapeutic Recombinant Glycoproteins

Nicole Samuels, David Kates, Jun Liu, Joanne Severs

Blurb

 Glycosylation is the most abundant post-translational modification of proteins.  Estimates vary widely, but a common assessment is that upwards of 50% of eukaryotic proteins are modified by some type of glycan. In Mass Spectrometry of Glycoproteins: Methods and Protocols, expert researchers in the field detail many of the methods that are now commonly used for glycoproteomics.  These methods and techniques include robust sample preparation techniques; advanced chromatographic strategies for improving dynamic range; state-of-the-art mass spectrometry instrumentation and associated ionization and fragmentation methods; and informatics tools used for identifying glycoproteins and characterizing the associated glycans. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and practical, Mass Spectrometry of Glycoproteins: Methods and Protocol  is  an essential resource for those who work at the interface of glycobiology and mass spectrometry.