Joseph Zaia, PhD

Professor, Biochemistry

Joseph Zaia
670 Albany St Biosquare III


The manner in which a cell responds to many growth factor stimuli depends on interactions between glycosaminoglycans (GAGs), growth factors, and growth factor receptors. Extracellular matrix GAGs binds growth factors, creating morphogens gradients essential to tissue patterning. Because these events depend on the fine structure of the GAG chains present, regulation of GAG biosynthesis is a key factor for understanding normal and disease related cellular growth
The key to exploiting an understanding of GAG structure-function relationships for human disease therapy is to winnow oligosaccharide-protein binding patterns from heterogeneous biological preparations. Toward this end, we have developed mass spectral methods for GAGs that enable comparison of structures as a function of biological variables.

The long term research aims are (1) to develop a fundamental understanding of the manner in which glycosaminoglycan expression is varied according to the cellular growth environment related to human disease and (2) to identify HS chain structures useful as therapeutic targets.

New bioinformatics methods are essential to realizing these goals. The data produced using our methods are information rich and not amenable to manual interpretation. Further, the methods needed are distinct from those used in genomics and proteomics. We are developing bioinformatics methods appropriate for interpretation of structural data on glycosaminoglycans and other carbohydrates to identify targets for disease therapy.

Other Positions

  • Graduate Faculty (Primary Mentor of Grad Students), Boston University School of Medicine, Graduate Medical Sciences
  • Member, Bioinformatics Graduate Program, Boston University
  • Center Faculty Member, Mass Spectrometry, Boston University School of Medicine


  • Massachusetts Institute of Technology, PhD
  • Bates College, BS


  • Published on 12/18/2018

    Klein JA, Zaia J. psims - A declarative writer for mzML and mzIdentML for Python. Mol Cell Proteomics. 2018 Dec 18. PMID: 30563850.

    Read at: PubMed
  • Published on 10/15/2018

    Klein J, Carvalho L, Zaia J. Application of network smoothing to glycan LC-MS profiling. Bioinformatics. 2018 Oct 15; 34(20):3511-3518. PMID: 29790907.

    Read at: PubMed
  • Published on 6/18/2018

    Raghunathan R, Polinski NK, Klein JA, Hogan JD, Shao C, Khatri K, Leon D, McComb ME, Manfredsson FP, Sortwell CE, Zaia J. Glycomic and Proteomic Changes in Aging Brain Nigrostriatal Pathway. Mol Cell Proteomics. 2018 Sep; 17(9):1778-1787. PMID: 29915149.

    Read at: PubMed
  • Published on 6/1/2018

    Zaia J, Bierbaum VM. Focus on Mass Spectrometry in Glycobiology and Related Fields, Honoring Catherine E. Costello, Recipient of the 2017 ASMS Award for a Distinguished Contribution in Mass Spectrometry. J Am Soc Mass Spectrom. 2018 Jun; 29(6):1061-1064. PMID: 29855889.

    Read at: PubMed
  • Published on 5/17/2018

    Klein JA, Meng L, Zaia J. Deep Sequencing of Complex Proteoglycans: A Novel Strategy for High Coverage and Site-specific Identification of Glycosaminoglycan-linked Peptides. Mol Cell Proteomics. 2018 Aug; 17(8):1578-1590. PMID: 29773674.

    Read at: PubMed
  • Published on 5/16/2018

    van Eijk M, Rynkiewicz MJ, Khatri K, Leymarie N, Zaia J, White MR, Hartshorn KL, Cafarella TR, van Die I, Hessing M, Seaton BA, Haagsman HP. Lectin-mediated binding and sialoglycans of porcine surfactant protein D synergistically neutralize influenza A virus. J Biol Chem. 2018 07 06; 293(27):10646-10662. PMID: 29769321.

    Read at: PubMed
  • Published on 4/16/2018

    Khatri K, Pu Y, Klein JA, Wei J, Costello CE, Lin C, Zaia J. Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides. J Am Soc Mass Spectrom. 2018 Jun; 29(6):1075-1085. PMID: 29663256.

    Read at: PubMed
  • Published on 4/3/2018

    Hogan JD, Klein JA, Wu J, Chopra P, Boons GJ, Carvalho L, Lin C, Zaia J. Software for Peak Finding and Elemental Composition Assignment for Glycosaminoglycan Tandem Mass Spectra. Mol Cell Proteomics. 2018 Jul; 17(7):1448-1456. PMID: 29615495.

    Read at: PubMed
  • Published on 3/21/2018

    Wu J, Wei J, Hogan JD, Chopra P, Joshi A, Lu W, Klein J, Boons GJ, Lin C, Zaia J. Negative Electron Transfer Dissociation Sequencing of 3-O-Sulfation-Containing Heparan Sulfate Oligosaccharides. J Am Soc Mass Spectrom. 2018 Jun; 29(6):1262-1272. PMID: 29564812.

    Read at: PubMed
  • Published on 2/25/2018

    Turiák L, Tóth G, Ozohanics O, Révész Á, Ács A, Vékey K, Zaia J, Drahos L. Sensitive method for glycosaminoglycan analysis of tissue sections. J Chromatogr A. 2018 Apr 06; 1544:41-48. PMID: 29506752.

    Read at: PubMed

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