keVChem.com
Downard Laboratory WWW site
The following publications from this laboratory describe novel, new molecular-based, mass spectrometry approaches to detect and characterise the SARS-CoV2, influenza and other viruses, chart their evolutionary history, characterise viral antigenicity and identify new therapeutics. They offer new advantages over conventional molecular and non-molecular approaches currently employed in surveillance and responses to viruses.
Surveillance (with proteotyping)
Lanyon HE, Todd BP, Downard KM (2023) Distinguishing Common SARS-CoV2 Omicron and Recombinant Variants with High Resolution Mass Spectrometry, Analyst, 148: 6306-6314. https://doi.org/10.1039/D3AN01376F
Hoyle JS, Downard KM (2023) High Resolution Mass Spectrometry of Respiratory Viruses. Next Generation Viral Typing, Subtyping, Variant and Sub-Variant Identification, Analyst, 148: 4263-4273. https://doi.org/10.1039/d3an00953j
Lanyon H, Hoyle JS, Downard KM (2023) Resolving Omicron Sub-Variants of SARS CoV-2 Coronavirus with MALDI Mass Spectrometry, Analyst, 148: 966-972. https://doi.org/10.1039/D2AN01843H
Downard KM (2023) Rapid Detection and Evolution of SARS-CoV-2 and other Viruses with High Resolution Mass Spectrometry, in Detection and Analysis of Microorganisms by Mass Spectrometry - New Developments in Mass Spectrometry, Ch.9, pp 188-214. Eds. L. Qiao, J. Li, Royal Society of Chemistry, Cambridge UK. https://books.rsc.org/books/edited-volume/2122/Detection-and-Analysis-of-Microorganisms-by-Mass
Mann C, Hoyle JS, Downard KM (2022) Detection of SARS-CoV2 Coronavirus Omicron Variant with Mass Spectrometry, Analyst, 147: 1181-1190. http://dx.doi.org/10.1039/d2an00028h
Mann C, Griffin JH, Downard KM (2021) Detection and Evolution of SARS-CoV2 Coronavirus Variants of Concern with Mass Spectrometry, Anal. Bioanal. Chem., 413: 7241-7249. http://dx.doi.org/10.1007/s00216-021-03649-1
Griffin JH, Downard KM (2021) Mass Spectrometry Analytical Responses to the SARS-CoV2 Coronavirus in Review, Trends Anal. Chem. 142: 116328. https://doi.org/10.1016/j.trac.2021.116328
Dollman NL, Griffin JH, Downard KM (2020) Detection, Mapping and Proteotyping of SARS CoV-2 Coronavirus with High Resolution Mass Spectrometry, ACS Infect. Dis., 6: 3269-3276. https://dx.doi.org/10.1021/acsinfecdis.0c00664
Uddin R, Downard KM (2017) Subtyping of Hepatitis C Virus with High Resolution Mass Spectrometry, Clin. Mass Spectrom. 4-5: 19-24.
Fernandes ND, Downard KM (2014) Incorporation of a Proteotyping Approach using Mass Spectrometry for the Surveillance of the Influenza Virus in Cell Culture, J. Clin. Microbio. 52: 725-735.
Fernandes ND, Downard KM (2014) Origins of the Reassortant H1N1 2009 Pandemic Influenza Virus by Proteotyping with Mass Spectrometry, J. Mass Spectrom. 49: 93-102.
Downard KM (2013) Proteotyping for the Rapid Identification of Pandemic Influenza Virus and other Biopathogens, Chem. Soc. Rev. 42: 8584-8595.
Nguyen AP, Downard KM (2013) Subtyping of Influenza Neuraminidase using Mass Spectrometry, Analyst 138: 1787- 1793.
Nguyen AP, Downard KM (2013) Proteotyping of the Parainfluenza Virus with High Resolution Mass Spectrometry, Anal. Chem. 85: 1097-1105.
Lun ATL, Wong JWH, Downard KM (2012) FluShuffle and FluResort - New Algorithms to Identify Reassorted Strains of the Influenza Virus by Mass Spectrometry, BMC Bioinformatics 13: 208.
Schwahn AB, Downard KM (2011) Proteotyping to establish the lineage of type A H1N1 and type B human influenza virus, J. Virol. Methods 171: 117-122.
Schwahn AB, Wong JWH, Downard KM (2010) Rapid Differentiation of Seasonal and Pandemic H1N1 Influenza through Proteotyping of Viral Neuraminidase with Mass Spectrometry, Anal. Chem. 82: 4584-4590.
Schwahn AB, Wong JWH, Downard KM (2010) Typing of Human and Animal Strains of Influenza Virus with Conserved Signature Peptides of Matrix M1 Protein by High Resolution Mass Spectrometry, J. Virol. Methods 165: 178-185.
Schwahn AB, Wong JWH, Downard KM (2009) Signature peptides of influenza nucleoprotein for the typing and subtyping of the virus by high resolution mass spectrometry, Analyst 134: 2253-2261.
Schwahn AB, Wong JWH, Downard KM (2009) Subtyping of the influenza virus by high resolution mass spectrometry, Anal. Chem., 81: 3500-3506.
Downard KM, Morrissey B (2007) Fingerprinting a Killer - Surveillance of the Influenza Virus by Mass Spectrometry, Analyst 132: 611-614.
Evolution
Hoyle JS, Mann C, Akand EH, Downard KM (2023) Charting and Tracking the Evolution of the SARS CoV-2 Coronavirus Variants of Concern with Protein Mass Spectrometry, Analyst, 148, 2834-2843. https://doi.org/10.1039/d3an00614j
Mann C, Downard KM (2022) Evolution of SARS CoV-2 Coronavirus Surface Protein Investigated with Mass Spectrometry Based Phylogenetics, Anal. Lett., 55: 305-317. http://dx.doi.org/10.1080/00032719.2021.1928685
Downard KM (2021) Protein Phylogenetics with Mass Spectrometry. A Comparison of Methods, Anal. Methods 13: 1442-1454. https://doi.org/10.1039/d1ay00153a
Akand EH, Downard KM (2021) Evolution of Type B Influenza Virus using a Mass Spectrometry Based Phylonumerics Approach, Evol. Biol. 48: 259-268. https://dx.doi.org/10.1007/s11692-021-09535-z
Akand EH, Downard KM (2019) Mechanisms of Antiviral Resistance in Influenza Neuraminidase Revealed by a Mass Spectrometry Based Phylonumerics Approach, Mol. Phylogen. Evol., 135: 286-296.
Akand EH, Downard KM (2018) Ancestral and Compensatory Mutations that Promote Antiviral Resistance in Influenza N1 Neuraminidase Revealed by a Phylonumerics Approach, J. Mol. Evol. 86: 546-553.
Akand EH, Downard KM (2018) Identification of Epistatic Mutations and Insights into the Evolution of the Influenza Virus Using a Mass-Based Protein Phylogenetic Approach, Mol. Phylogen. Evol., 121: 132-138.
Akand EH, Downard KM (2017) Mutational Analysis Employing a Phylogenetic Mass Tree Approach in a Study of the Evolution of the Influenza Virus, Mol. Phylogen. Evol. 112: 209-217.
Ma S, Wong JWH, Downard KM (2015) A Novel Algorithm and Approach to Score and Visualize the Phylogeny of the Influenza Virus using Mass Spectrometry, Anal. Chim. Acta 895: 54-61.
Swaminathan K, Downard KM (2014) Evolution of Influenza Neuraminidase and the Detection of Antiviral Resistant Strains Using Mass Trees, Anal. Chem. 86: 629-637.
Lun ATL, Swaminathan K, Wong JWH, Downard KM (2013) Mass Trees – A New Phylogenetic Approach and Algorithm to Chart Evolutionary History with Mass Spectrometry, Anal. Chem. 85: 5475-5482.
Ha J-W, Downard KM (2011) Evolution of H5N1 Influenza Virus through Proteotyping of Hemagglutinin with High Resolution Mass Spectrometry, Analyst 136, 3259-3267.
Vaccines
Schwahn AB, Wong JWH, Downard KM (2010) Rapid typing and subtyping of vaccine strains of the influenza virus with high resolution mass spectrometry, Eur. J. Mass Spectrom. 16: 321-329.
Therapeutics
Uddin R, Downard KM (2018) Molecular Basis of Benzimidazole Inhibitors to Hepatitis C Virus Envelope Glycoprotein, Chem. Biol. Drug Design 92: 1638-1646.
Maleknia SD, Downard KM (2016) New Anthocyanins from Black Elderberry of Inhibitory Potential Revealed by Mass Spectrometry, Nat. Prod. J. 6: 94-102.
Lu R, Muller P, Downard KM (2015) Molecular Basis of Influenza Hemaglutinin Inhibition with an Entry-Blocker Peptide by Computational Docking and Mass Spectrometry, Antiviral Chem. Chemother. 24: 109-117.
Muller P, Downard KM (2015) Catechins Inhibit Influenza Neuraminidase and its Molecular Basis with Mass Spectrometry, J. Pharmaceut. Biomed. Anal. 111: 222-230.
Swaminathan K, Muller P, Downard KM (2014) Substituent Effects on the Binding of Natural Product Anthocyanidin Inhibitors to Influenza Neuraminidase with Mass Spectrometry, Anal. Chim. Acta 828: 61-69.
Nasser Z, Swaminathan K, Muller P, Downard KM (2013) in-vitro Inhibition of the Influenza virus with the Anti-Viral Inhibitor Arbidol by a Proteomics based Approach with Mass Spectrometry, Antiviral Res. 100: 399-406.
Swaminathan K, Dyason JC, Maggioni A, von Itzstein M, Downard KM (2013) Binding of a Natural Anthocyanin Inhibitor to Influenza Neuraminidase by Mass Spectrometry, Anal. Bio. Chem. 405: 6563-6572.
Swaminathan K, Downard KM (2012) Anti-Viral Inhibitor Binding to Influenza Neuraminidase by MALDI Mass Spectrometry, Anal. Chem. 84: 3725-3730.
Viral Antigenicity
Downard KM (2019) A Molecular Immunoproteomics Approach to Assess the Viral Antigenicity of Influenza, in Methods in Molecular Biology: Immunoproteomics: Methods and Protocols (Ed. S. Twine & K. Fulton), Second Edition, Vol. 2024, Ch. 24, pp. 353-369.
Downard KM (2013) An Immunoproteomics Approach to Screen the Antigenicity of the Influenza Virus, in Methods in Molecular Biology: Immunoproteomics (Ed. S. Twine & K. Fulton), Vol. 1061, Ch. 8, pg 141-153.
Schwahn AB, Downard KM (2009) Antigenicity of a type A influenza virus through a comparison of hemagglutination inhibition and mass spectrometry immunoassays, J. Immunoassay Immunochem. 30: 245-261.
Morrissey B, Downard KM (2008) Kinetics of Antigen-Antibody Interactions Employing a MALDI Mass Spectrometry Immunoassay, Anal. Chem. 80: 7720-7726.
Morrissey B, Streamer M, Downard KM (2007) Antigenic Characterisation of H3N2 subtypes of the Influenza Virus by Mass Spectrometry, J. Virol. Methods 145: 106-114.
Morrissey B, Downard KM (2006) A Proteomics Approach to Survey the Antigenicity of the Influenza Virus by Mass Spectrometry, Proteomics 6: 2034-2041.
Kiselar JG, Downard KM (1999) Antigenic Surveillance of the Influenza Virus by Mass Spectrometry, Biochemistry 43: 14185-14191.
Software (for Viral Antigenicity and Inhibitor Binding Studies)
Ho JWK, Morrissey B, Downard KM (2007) A Computer Algorithm for the Identification of Protein Interactions from the Spectra of Masses (PRISM), J. Am. Soc. Mass Spectrom., 18, 563– 566.
Additional Reviews
Downard KM (2023) 25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry, Mass Spectrom. (Tokyo), in press.
Downard KM, Morrissey B, Schwahn AB (2009) Mass Spectrometry Analysis of the Influenza Virus, Mass Spectrom. Rev. 28: 35-49.
Downard K.M. (2000) Contributions of Mass Spectrometry to Structural Immunology, J. Mass Spectrom. 35: 493-503.
Related Methodology Development (and Reviews thereof)
Downard KM (2023) 25 years Responding to Respiratory and Other Viruses with Mass Spectrometry, Mass Spectrom (Tokyo), 12: A0136.
Downard KM (2016) Indirect Study of Non-Covalent Protein Complexes by MALDI Mass Spectrometry. Origins, Advantages and Applications of the "Intensity-Fading" Approach, Mass Spectrom. Rev. 35: 559-573.
Downard KM (2007) Softly. Softly. Detection of Protein Complexes by Matrix-assisted Laser Desorption Ionization Mass Spectrometry, in Mass Spectrometry of Protein Interactions, Downard KM (ed.), John Wiley & Sons, New Jersey U.S.A., pp. 25-43.
Mackun K., Downard KM (2003) Strategy for the Study of Protein-Protein Interactions of Gel- Separated Proteins by Mass Spectrometry, Anal. Biochem. 318: 60-70.
Kiselar JG, Downard KM (2001) Preservation of Specific Immune Complexes by Matrix-assisted Laser Desorption Ionization Mass Spectrometry, in Advances in Mass Spectrometry, Volume 15, E. Gelphi (ed.) John Wiley & Sons, Chichester, UK.
Kiselar JG, Downard KM (1999) Direct Identification of Protein Epitopes by Mass Spectrometry without Immobilization of Antibody and Isolation of Antibody-Peptide Complexes, Anal. Chem. 17: 1792-1801.
