Cheng Lin

Cheng LinResearch Assistant Professor

Boston University School of Medicine
Mass Spectrometry Resource
670 Albany St. Rm. 508
Boston, MA 02118

Phone: 617-638-6705
Lab Phone: 617-638-6765
Fax: 617-638-6761




B.Sc. Peking University, Beijing, China
Ph.D. Cornell University, Ithaca, NY


Yiqun Huang (Postdoctoral Associate)     Yuhuan Ji (Graduate Student)     Jiyang Zhang (Visiting Scholar)


Our research focuses on the development of mass spectrometry (MS) methods for the structural characterization of biomolecules. Specifically, we are interested in developing radical driven fragmentation methods that are amenable to the Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry. One such method is electron capture dissociation (ECD). Unlike conventional ergodic fragmentation methods, ECD retains labile modifications in proteins and is well suited for post-translational modification (PTM) analysis. ECD and other electron activated dissociation (ExD) methods have also shown great promises in detailed structural analysis of glycans.

Our present research efforts also include the application of MS techniques to solve biological problems, such as protein deamidation, which is implicated in protein misfolding diseases and aging, and protein S-palmitoylation, which plays an important regulatory role in protein trafficking, membrane localization, and cellular signaling. Other current research projects include the implementation of vacuum ultraviolet photodissociation (VUVPD) in FTICR MS, the development of ion mobility spectrometry (IMS)-ExD-MS/MS method for isomer analysis, theoretical investigation of the glycan ExD mechanisms, and the development of bioinformatics tools for interpretation of complex glycan ExD spectra (collaborative work).

Representative Publications:

  • A Computational Framework for Heparan Sulfate Sequencing Using High-resolution Tandem Mass Spectra. Hu H, Huang Y, Mao Y, Yu X, Xu Y, Liu J, Zong C, Boons GJ, Lin C, Xia Y, Zaia J. Mol Cell Proteomics. 2014 Jun 12. pii: mcp.M114.039560.
  • Detecting O-GlcNAc using in vitro sulfation. Wu ZL, Robey MT, Tatge T, Lin C, Leymarie N, Zou Y, Zaia J. Glycobiology. 2014 Aug;24(8):740-7.
  • Mechanistic Study on Electron Capture Dissociation of the Oligosaccharide-Mg2+ Complex. Huang Y, Pu Y, Yu X, Costello CE, Lin C. J Am Soc Mass Spectrom. 2014 May 21.
  • Direct Detection of S-Palmitoylation by Mass Spectrometry. Y. Ji, N. Leymarie, D. J. Haeussler, M. M. Bachschmid, C. E. Costello, C. Lin, Anal. Chem. 2013, DOI: 10.1021/ac402850s.
  • De Novo Sequencing of Heparan Sulfate Oligosaccharides by Electron-Activated Dissociation. Y. Huang, X. Yu, Y. Mao, C. E. Costello, J. Zaia, C. Lin Anal. Chem. 2013, DOI: 10.1021/ac402931j.
  • Detailed Glycan Structural Characterization by Electronic Excitation Dissociation. X. Yu, Y. Jiang, Y. Chen, Y. Huang, C. E. Costello, C. Lin, Anal. Chem. 2013, 85 (21), 10017-10021.
  • Absorption-Mode Fourier Transform Mass Spectrometry: the Effects of Apodization and Phasing on Modified Protein Spectra. Y. Qi, H. Li, R. H. Wills, P. Perez-Hurtado, X. Yu, D. P. A. Kilgour, M. P. Barrow, C. Lin, P. B. O’Connor, J. Am. Soc. Mass. Spectrom. 2013, 24, 828-834.
  • Top-Down Study of β2-Microglobulin Deamidation. X. Li, X. Yu, C. E. Costello, C. Lin*, P. B. O’Connor*, Anal. Chem. 2012, 84 (14), 6150-6157. *Corresponding authors.
  • Energy-Dependent Electron Activated Dissociation of Metal-Adducted Permethylated Oligosaccharides. X. Yu, Y. Huang, C. Lin*, C. E. Costello*, Anal. Chem. 2012, 84 (12), 7487-7494. *Corresponding authors.
  • Oxidation of HRas Cysteine Thiols by Metabolic Stress Prevents Palmitoylation in Vivo and Contributes to Endothelial Cell Apoptosis. J. R. Burgoyne, D. J. Haeussler, V Kumar, Y. Ji, D. R. Pimental, R. S. Zee, C. E. Costello, C. Lin, M. E. McComb, R. A. Cohen, and M. M. Bachschmid, FASEB J. 2012, 26(2), 832-841.
  • Differentiating N-Terminal Aspartic and Isoaspartic Acid Residues in Peptides. N. P. Sargaeva, C. Lin, and P. B. O’Connor, Anal. Chem. 2011, 83(17), 6675-6682.
  • Unusual Fragmentation of β-Linked Peptides by ExD Tandem Mass Spectrometry. N. P. Sargaeva, C. Lin, and P. B. O’Connor, J. Am. Soc. Mass Spectrom. 2011, 22, 480.
  • Structural Heterogeneity of Doubly-Charged Peptide b-Ions. X. Li, Y. Huang, P. B. O’Connor, and C. Lin, J. Am. Soc. Mass Spectrom. 2011, 22, 245.
  • Glutamine Deamidation: Differentiation of Glutamic Acid and g-Glutamic Acid in Peptides by Electron Capture Dissociation. X. Li, C. Lin, and P. B. O’Connor, Anal. Chem. 2010, 82, 3606.
  • Charge Remote Fragmentation in Electron Capture and Electron Transfer Dissociations. X. Li, C. Lin, L. Han, C. E. Costello, and P. B. O’Connor, J. Am. Soc. Mass Spectrom. 2010, 21, 646.
  • Identification of Aspartic and Isoaspartic Acid Residues in Amyloid-β Peptides, Including Aβ 1−42, Using Electron−Ion Reactions. N. P. Sargaeva, C. Lin, and P. B. O’Connor, Anal. Chem. 2009, 81, 9778.
  • Probing the Gas Phase Folding Kinetics of Peptide Ions by IR Activated DR-ECD. C. Lin, J. J. Cournoyer, and P. B. O’Connor, J. Am. Soc. Mass Spectrom. 2008, 19, 780.
  • First Signal on the Cryogenic Fourier-Transform Ion Cyclotron Resonance Mass Spectrometer. C. Lin, R. Mathur, K. Aizikov, and P. B. O’Connor, J. Am. Soc. Mass Spectrom. 2007, 18, 2090 (Cover Feature).
  • Use of a Double Resonance Electron Capture Dissociation Experiment to Probe Fragment Intermediate Lifetimes. C. Lin, J. J. Cournoyer, and P. B. O’Connor, J. Am. Soc. Mass Spectrom. 2006, 17, 1605.
  • Infrared Photodissociation Spectroscopy of Electrosprayed Ions in a Fourier-Transform Mass Spectrometer. H.-B. Oh, C. Lin, H. Y. Hwang, H. Zhai, K. Breuker, V. Zabrouskov, B. K. Carpenter, and F. W. McLafferty, J. Am. Chem. Soc. 2005, 127, 4076.
  • Nonergodic and Conformational Control of the Electron Capture Dissociation of Protein Cations. K Breuker, H.-B. Oh, C. Lin, B. K. Carpenter, and F. W. McLafferty, Proc. Nat. Acad. Sci. USA 2004, 101, 14011.
  • Oxygen Atom Rydberg Time-of-Flight Spectroscopy. C. Lin, M. F. Witinski, and H. F. Davis, J. Chem. Phys. 2003, 119, 251.
  • Vibrationally Inelastic Scattering of High-n Rydberg H Atoms from N2 and O2. B. R. Strasizar, C. Lin, and H. F. Davis, Phys. Rev. Lett. 2001, 86, 3997.
  • Mode Specific Energy Disposal in the 4-Atom Reaction OH + D2 à HOD + D. B. R. Strasizar, C. Lin and H. F. Davis, Science 2000, 290, 958.