Kevin Downard

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Kevin Downard is a British - Australian academic scientist whose research specialises in the improving responses to infectious disease through the application and development of mass spectrometry and other molecular approaches in the life and medical sciences. Downard has over 35 years of experience in the field and has written over 145 lead-author scientific peer-reviewed journal publications, and two books including a textbook [1] for the Royal Society of Chemistry and the first book to be published on the role of mass spectrometry in the study of protein interactions. [2]

Contents

Education

Downard was awarded his Ph.D. degree from the University of Adelaide in South Australia where he received the inaugural Donald Stranks fellowship.

Career

A major focus of his research is to arrest the impact of infectious disease causing viruses. For some 25 years, he has led the development of new mass spectrometry, bioinformatics and computer-aided approaches to characterise respiratory viruses and is an international leader in this field. He has developed approaches to type, subtype, [3] study the lineage, antigenicity, [4] and evolution [5] [6] of the influenza virus [7] and other respiratory biopathogens, [8] including SARS CoV-2, [9] [10] [11] and has identified and investigated the molecular basis of new antiviral enzyme inhibitors, to help arrest the impact of infectious diseases on human health. [12] His laboratory has led Australia's response to the SARS-CoV2 virus with mass spectrometry since 2020.

Downard held a post-doctoral fellowship from 1991 at the Massachusetts Institute of Technology (MIT), working with Klaus Biemann who pioneered protein sequencing by tandem mass spectrometry. He led the laboratory's early implementation of electrospray ionization (ESI) on a high end, four sector mass spectrometer and investigated subtleties of tandem mass spectra to help advance this application [13] He remained at MIT as the Assistant Director of the former National Institutes of Health Mass Spectrometry Research Resource at MIT before leading his own research laboratories in the United States and Australia over the past 25 years. During this time, he has developed new proteotyping approaches to study viruses, viral proteins, [14] and protein structures and interactions more generally to advance the application of MS in biology and medicine. [15] In recent years, he has developed a new mass (i.e. numbers) based molecular phylogenetics approach (referred to as "phylonumerics") that avoids the need for sequence data or sequence alignments [16] and has been applied to a range of evolutionary biology applications. [17]

His laboratory was the first to demonstrate the preservation (in 1999) [18] of large macromolecular complexes on conventional Matrix-assisted laser desorption/ionization (MALDI) targets for their indirect detection, later referred to as Intensity fading MALDI mass spectrometry by others. [19] He also co-developed protein footprinting experiments, in the same year, employing radicals to study protein structures and was the first to apply the technique to study protein complexes. [20]

Honours and other service

Downard has been internationally recognised for his research having received awards from both American (ASMS 1999) and British (2016) mass spectrometry societies. He has received four international fellowships from the Australian Academy of Science and the Japan Society for the Promotion of Science. He convened and chaired the second Sir Mark Oliphant Conference on Proteomics in 2003 and the largest biennial Australian mass spectrometry conference in 2009 [21] after serving on the Executive MS Committee for 7 years (2002-2005 & 2007-2009). He has been active in promoting the importance of research in his field and the history of mass spectrometry and its pioneers [22] [23] for which he received the Moran award from the Australian Academy of Science in 2006. His activities have been highlighted in scientific journals in the analytical sciences, scientific web resources, and in the media including interviews with the Australian Broadcasting Corporation (ABC Australia). He has served on a range of national science, expert panel and professional society committees. He held the role of Biotechnology Program Director for almost a decade and was a founding executive member and advisor to the Sydney Emerging Infectious Disease and Biosecurity Institute. He has collaborated with a range of industry partners in the biotechnology and analytical science sector.

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<span class="mw-page-title-main">Koichi Tanaka</span> Japanese electrical engineer (born 1959)

Koichi Tanaka is a Japanese electrical engineer who shared the Nobel Prize in Chemistry in 2002 for developing a novel method for mass spectrometric analyses of biological macromolecules with John Bennett Fenn and Kurt Wüthrich.

<span class="mw-page-title-main">Peptide mass fingerprinting</span>

Peptide mass fingerprinting (PMF) is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. The method was developed in 1993 by several groups independently. The peptide masses are compared to either a database containing known protein sequences or even the genome. This is achieved by using computer programs that translate the known genome of the organism into proteins, then theoretically cut the proteins into peptides, and calculate the absolute masses of the peptides from each protein. They then compare the masses of the peptides of the unknown protein to the theoretical peptide masses of each protein encoded in the genome. The results are statistically analyzed to find the best match.

<span class="mw-page-title-main">Matrix-assisted laser desorption/ionization</span> Ionization technique

In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy-absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of biomolecules and various organic molecules, which tend to be fragile and fragment when ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft ways of obtaining ions of large molecules in the gas phase, though MALDI typically produces far fewer multi-charged ions.

Surface-enhanced laser desorption/ionization (SELDI) is a soft ionization method in mass spectrometry (MS) used for the analysis of protein mixtures. It is a variation of matrix-assisted laser desorption/ionization (MALDI). In MALDI, the sample is mixed with a matrix material and applied to a metal plate before irradiation by a laser, whereas in SELDI, proteins of interest in a sample become bound to a surface before MS analysis. The sample surface is a key component in the purification, desorption, and ionization of the sample. SELDI is typically used with time-of-flight (TOF) mass spectrometers and is used to detect proteins in tissue samples, blood, urine, or other clinical samples, however, SELDI technology can potentially be used in any application by simply modifying the sample surface.

Soft laser desorption (SLD) is laser desorption of large molecules that results in ionization without fragmentation. "Soft" in the context of ion formation means forming ions without breaking chemical bonds. "Hard" ionization is the formation of ions with the breaking of bonds and the formation of fragment ions.

<span class="mw-page-title-main">MALDI imaging</span>

MALDI mass spectrometry imaging (MALDI-MSI) is the use of matrix-assisted laser desorption ionization as a mass spectrometry imaging technique in which the sample, often a thin tissue section, is moved in two dimensions while the mass spectrum is recorded. Advantages, like measuring the distribution of a large amount of analytes at one time without destroying the sample, make it a useful method in tissue-based study.

<span class="mw-page-title-main">Protein mass spectrometry</span> Application of mass spectrometry

Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrumentations have been developed for its many uses. Its applications include the identification of proteins and their post-translational modifications, the elucidation of protein complexes, their subunits and functional interactions, as well as the global measurement of proteins in proteomics. It can also be used to localize proteins to the various organelles, and determine the interactions between different proteins as well as with membrane lipids.

Mass spectrometry imaging (MSI) is a technique used in mass spectrometry to visualize the spatial distribution of molecules, as biomarkers, metabolites, peptides or proteins by their molecular masses. After collecting a mass spectrum at one spot, the sample is moved to reach another region, and so on, until the entire sample is scanned. By choosing a peak in the resulting spectra that corresponds to the compound of interest, the MS data is used to map its distribution across the sample. This results in pictures of the spatially resolved distribution of a compound pixel by pixel. Each data set contains a veritable gallery of pictures because any peak in each spectrum can be spatially mapped. Despite the fact that MSI has been generally considered a qualitative method, the signal generated by this technique is proportional to the relative abundance of the analyte. Therefore, quantification is possible, when its challenges are overcome. Although widely used traditional methodologies like radiochemistry and immunohistochemistry achieve the same goal as MSI, they are limited in their abilities to analyze multiple samples at once, and can prove to be lacking if researchers do not have prior knowledge of the samples being studied. Most common ionization technologies in the field of MSI are DESI imaging, MALDI imaging and secondary ion mass spectrometry imaging.

<span class="mw-page-title-main">Top-down proteomics</span>

Top-down proteomics is a method of protein identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS. Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. The name is derived from the similar approach to DNA sequencing. During mass spectrometry intact proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance, quadrupole ion trap or Orbitrap mass spectrometer. Fragmentation for tandem mass spectrometry is accomplished by electron-capture dissociation or electron-transfer dissociation. Effective fractionation is critical for sample handling before mass-spectrometry-based proteomics. Proteome analysis routinely involves digesting intact proteins followed by inferred protein identification using mass spectrometry (MS). Top-down MS (non-gel) proteomics interrogates protein structure through measurement of an intact mass followed by direct ion dissociation in the gas phase.

<span class="mw-page-title-main">Bottom-up proteomics</span>

Bottom-up proteomics is a common method to identify proteins and characterize their amino acid sequences and post-translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry. The major alternative workflow used in proteomics is called top-down proteomics where intact proteins are purified prior to digestion and/or fragmentation either within the mass spectrometer or by 2D electrophoresis. Essentially, bottom-up proteomics is a relatively simple and reliable means of determining the protein make-up of a given sample of cells, tissues, etc.

<span class="mw-page-title-main">Laser spray ionization</span>

Laser spray ionization refers to one of several methods for creating ions using a laser interacting with a spray of neutral particles or ablating material to create a plume of charged particles. The ions thus formed can be separated by m/z with mass spectrometry. Laser spray is one of several ion sources that can be coupled with liquid chromatography-mass spectrometry for the detection of larger molecules.

<span class="mw-page-title-main">Capillary electrophoresis–mass spectrometry</span>

Capillary electrophoresis–mass spectrometry (CE–MS) is an analytical chemistry technique formed by the combination of the liquid separation process of capillary electrophoresis with mass spectrometry. CE–MS combines advantages of both CE and MS to provide high separation efficiency and molecular mass information in a single analysis. It has high resolving power and sensitivity, requires minimal volume and can analyze at high speed. Ions are typically formed by electrospray ionization, but they can also be formed by matrix-assisted laser desorption/ionization or other ionization techniques. It has applications in basic research in proteomics and quantitative analysis of biomolecules as well as in clinical medicine. Since its introduction in 1987, new developments and applications have made CE-MS a powerful separation and identification technique. Use of CE–MS has increased for protein and peptides analysis and other biomolecules. However, the development of online CE–MS is not without challenges. Understanding of CE, the interface setup, ionization technique and mass detection system is important to tackle problems while coupling capillary electrophoresis to mass spectrometry.

Protein footprinting is a term used to refer to a method of biochemical analysis that investigates protein structure, assembly, and interactions within a larger macromolecular assembly. It was originally coined in reference to the use of limited proteolysis to investigate contact sites within a monoclonal antibody - protein antigen complex and a year later to examine the protection from hydroxyl radical cleavage conferred by a protein bound to DNA within a DNA-protein complex. In DNA footprinting the protein is envisioned to make an imprint at a particular point of interaction. This latter method was adapted through the direct treatment of proteins and their complexes with hydroxyl radicals and can be generally denoted RP-MS akin to the designation used for Hydrogen-deuterium exchange Mass Spectrometry.

<span class="mw-page-title-main">Surface-assisted laser desorption/ionization</span>

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References

  1. ↑ Downard, Kevin M. (2004). Mass Spectrometry A Foundation Course. Cambridge: Royal Society of Chemistry. doi:10.1039/9781847551306. ISBN   978-0-85404-609-6.
  2. ↑ Downard, Kevin M. (2007). Downard, Kevin M (ed.). Mass Spectrometry of Protein Interactions. Hoboken, N.J.: Wiley-Interscience. doi:10.1002/9780470146330. ISBN   9780470146330.
  3. ↑ Schwahn, Alexander B.; Wong, Jason W. H.; Downard, Kevin M. (May 2009). "Subtyping of the Influenza Virus by High Resolution Mass Spectrometry". Analytical Chemistry. 81 (9): 3500–3506. doi:10.1021/ac900026f. PMID   19402721.
  4. ↑ Morrissey, Bethny; Downard, Kevin M. (April 2006). "A proteomics approach to survey the antigenicity of the influenza virus by mass spectrometry". Proteomics. 6 (7): 2034–2041. doi:10.1002/pmic.200500642. PMID   16502471. S2CID   29117699.
  5. ↑ Lun, Aaron T.; Swaminathan, Kavya; Wong, Jason W.; Downard, Kevin M. (April 2013). "Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry". Analytical Chemistry. 85 (11): 5475–5482. doi:10.1021/ac4005875. PMID   23647083.
  6. ↑ Akand, Elma H.; Downard, Kevin M. (2017). "Mutational Analysis Employing a Phylogenetic Mass Tree Approach in a Study of the Evolution of the Influenza Virus". Mol. Phylogenet. Evol. 112: 209–217. doi:10.1016/j.ympev.2017.04.005. PMID   28400275.
  7. ↑ Akand, Elma H.; Downard, Kevin M. (2018). "Identification of Epistatic Mutations and Insights into the Evolution of the Influenza Virus Using a Mass-Based Protein Phylogenetic Approach". Mol. Phylogenet. Evol. 121: 132–138. doi:10.1016/j.ympev.2018.01.009. PMID   29337273.
  8. ↑ Nyugen, An P.; Downard, Kevin M. (2013). "Proteotyping of the Parainfluenza Virus with High-Resolution Mass Spectrometry". Anal. Chem. 85 (2): 1097–1105. doi:10.1021/ac302962u. PMID   23234308.
  9. ↑ 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 (12): 3269–3276. doi:10.1021/acsinfecdis.0c00664. PMC   7688050 . PMID   33205948.
  10. ↑ Griffin, JH.; Downard, KM. (2021). "Mass Spectrometry Analytical Responses to the SARS-CoV2 Coronavirus in Review". Trends Anal. Chem. 142: 1163286. doi:10.1016/j.trac.2021.116328. ISSN   0165-9936. PMC   8111885 . PMID   33994605.
  11. ↑ Mann, C.; Griffin, JH.; Downard, KM. (2021). "Detection and evolution of SARS-CoV-2 coronavirus variants of concern with mass spectrometry". Anal. Bioanal. Chem. 413 (29): 7241–7249. doi:10.1007/s00216-021-03649-1. PMC   8445501 . PMID   34532764.
  12. ↑ Müller, P.; Downard, KM. (2015). "Catechins Inhibit Influenza Neuraminidase and its Molecular Basis with Mass Spectrometry". J. Pharm. Biomed. Anal. 111: 222–230. doi:10.1016/j.jpba.2015.03.014. PMID   25910046.
  13. ↑ Downard, Kevin M.; Biemann, Klaus (1994). "The effect of charge state and the localization of charge on the collision-induced dissociation of peptide ions". Journal of the American Society for Mass Spectrometry. 5 (11): 966–975. doi:10.1016/1044-0305(94)80015-4. ISSN   1044-0305. PMID   24226386.
  14. ↑ Downard, Kevin M. (2013). "Proteotyping for the rapid identification of influenza virus and other biopathogens". Chemical Society Reviews. 42 (22): 8584–8595. doi:10.1039/c3cs60081e. ISSN   1460-4744. PMID   23632861.
  15. ↑ Downard, Kevin M. (2006). "Ions of the interactome: The role of MS in the study of protein interactions in proteomics and structural biology". Proteomics. 6 (20): 5374–5384. doi:10.1002/pmic.200600247. ISSN   1615-9853. PMID   16991196. S2CID   41482326.
  16. ↑ Downard, Kevin M. (2020). "Sequence-Free Phylogenetics with Mass Spectrometry". Mass Spectrom. Rev. 41 (1): 3–14. doi:10.1002/mas.21658. PMID   33169385. S2CID   226295381.
  17. ↑ Downard, Kevin M. (2020). "Darwin's Tree of Life is Numbered. Resolving the Origins of Species by Mass". Evol. Biol. 47 (4): 325–333. doi:10.1007/s11692-020-09517-7. S2CID   226326027.
  18. ↑ Kiselar, Janna G.; Downard, Kevin M. (1999). "Direct Identification of Protein Epitopes by Mass Spectrometry without Immobilization of Antibody and Isolation of Antibody−Peptide Complexes". Analytical Chemistry. 71 (9): 1792–1801. doi:10.1021/ac9811120. ISSN   0003-2700. PMID   10330909.
  19. ↑ Downard, Kevin M. (2016). "Indirect study of non-covalent protein complexes by MALDI mass spectrometry: Origins, advantages, and applications of the "intensity-fading" approach"". Mass Spectrometry Reviews. 35 (5): 559–573. Bibcode:2016MSRv...35..559D. doi:10.1002/mas.21480. PMID   26250984.
  20. ↑ Maleknia, Simin D.; Downard, Kevin M. (March 2014). "Advances in Radical Probe Mass Spectrometry for Protein Footprinting in Chemical Biology Applications". Chemical Society Reviews. 43 (10): 3244–3258. doi:10.1039/C3CS60432B. PMID   24590115.
  21. ↑ ANZSMS 22: 22nd Biennial Mass Spectrometry Conference in Australia and New Zealand, Sydney, Australia. 2009.
  22. ↑ Downard, Kevin (2007). "Historical Account: Francis William Aston: the man behind the mass spectrograph". European Journal of Mass Spectrometry. 13 (1): 177–90. doi:10.1255/ejms.878. PMID   17881785. S2CID   25747367.
  23. ↑ Downard, Kevin (2022). "Building Australia's first mass spectrometer: Recognising the achievements of J. Roger Bird". Journal of Mass Spectrometry. 57 (10): e4887. doi:10.1002/jms.4887. PMID   36217294.
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