Center for Network Systems Biology — Boston University

Databases & Links
Public Data

The CNSB's research has contributed to valuable public datasets used in the fields of proteomic profiling and protein complex characterization. These datasets catalogue such diverse sample classes as mammalian tissues, unicellular organisms, and viral proteins.

Website Urls/Links

Network systems biology – the study of the physical and functional interactions of biomolecules in diverse complex biological systems that are crucial to health and disease – is an emerging strength at Boston University.

Elucidating the biological networks that drive normal development and pathology is fundamental to a deeper mechanistic understanding of biological processes and their causal links to clinical disorders. Network systems biology is expected to drive biological research in the coming decades.

Proteomics & glycoproteomics

Calculating Glycoprotein Similarities From Mass Spectrometric Data.

Hackett, W. E.; Zaia, J. Calculating Glycoprotein Similarities From Mass Spectrometric Data. Mol Cell Proteomics 2021, 20, 100028.

Proteomics, glycomics, and glycoproteomics of matrisome molecules.

Raghunathan, R.; Sethi, M. K.; Klein, J. A.; Zaia, J. Proteomics, glycomics, and glycoproteomics of matrisome molecules. Mol Cell Proteomics 2019, 18, 2138-2148.

Relative Retention Time Estimation Improves N-Glycopeptide Identifications By LC-MS/MS

Klein, J.; Zaia, J. Relative Retention Time Estimation Improves N-Glycopeptide Identifications By LC-MS/MS. J Proteome Res 2020, 19, 2113-2121.

A glycomics and proteomics study of aging and Parkinson’s disease in human brain.

Raghunathan, R.; Hogan, J. D.; Labadorf, A.; Myers, R. H.; Zaia, J. A glycomics and proteomics study of aging and Parkinson's disease in human brain. Sci Rep 2020, 10, 12804.

In-Depth Matrisome and Glycoproteomic Analysis of Human Brain Glioblastoma Versus Control Tissue.

Sethi, M. K.; Downs, M.; Shao, C.; Hackett, W. E.; Phillips, J. J.; Zaia, J. In-Depth Matrisome and Glycoproteomic Analysis of Human Brain Glioblastoma Versus Control Tissue. Mol Cell Proteomics 2022, 21, 100216.

SARS-CoV-2

Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein.

Chang, D.; Klein, J. A.; Nalehua, M. R.; Hackett, W. E.; Zaia, J. Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein. Anal. Bioanal. Chem. 2021, 413, 7305–7318.

Influenza

Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty.

Chang, D.; Hackett, W. E.; Zhong, L.; Wan, X. F.; Zaia, J. Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty. Mol Cell Proteomics 2020, 19, 1533-1545.

Improving statistical certainty of glycosylation similarity between influenza A virus variants using data-independent acquisition mass spectrometry.

Chang, D.; Klein, J.; Hackett, W.; Nalehua, M. R.; Wan, X. F.; Zaia, J. Improving statistical certainty of glycosylation similarity between influenza A virus variants using data-independent acquisition mass spectrometry. Mol Cell Proteomics 2022, , 100412.

Parkinson’s Disease

Matrisome changes in Parkinson’s disease.

Downs, M.; Sethi, M. K.; Raghunathan, R.; Layne, M. D.; Zaia, J. Matrisome changes in Parkinson's disease. Anal Bioanal Chem 2022, 414, 3005-3015.

Alzheimer's disease

Proteomic and biological profiling of extracellular vesicles from Alzheimer’s disease human brain tissues.

Muraoka, S.; DeLeo, A. M.; Sethi, M. K.; Yukawa-Takamatsu, K.; Yang, Z.; Ko, J.; Hogan, J. D.; Ruan, Z.; You, Y.; Wang, Y.; Medalla, M.; Ikezu, S.; Chen, M.; Xia, W.; Gorantla, S.; Gendelman, H. E.; Issadore, D.; Zaia, J.; Ikezu, T. Proteomic and biological profiling of extracellular vesicles from Alzheimer's disease human brain tissues. Alzheimer's & Dementia 2020, doi: 10.1002/alz.12089.

Glycosaminoglycans

Sequencing Heparan Sulfate Using HILIC LC-NETD-MS/MS.

Wu, J.; Wei, J.; Chopra, P.; Boons, G. J.; Lin, C.; Zaia, J. Sequencing Heparan Sulfate Using HILIC LC-NETD-MS/MS. Anal. Chem. 2019, 91, 11738-11746.

Resolving Heparan Sulfate Oligosaccharide Positional Isomers Using Hydrophilic Interaction Liquid Chromatography-Cyclic Ion Mobility Mass Spectrometry.

Cavallero, G. J.; Zaia, J. Resolving Heparan Sulfate Oligosaccharide Positional Isomers Using Hydrophilic Interaction Liquid Chromatography-Cyclic Ion Mobility Mass Spectrometry. Anal. Chem. 2022, 94, 2366-2374.

Project databases

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities. Paul et al. (2021) (pending submission)

Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery. Havugimana & Goel et al (2021): (pending submission)