%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%T 1912: a titanic year for mass spectrometry.
%B Journal of Mass Spectrometry
%D 2012
%C United Kingdom
%I John Wiley & Sons Ltd.
%V 47
%N 8
%P 1034-1039
%@ 1096-9888
%X The 1912 sinking of the Titanic continues to capture the imagination and fascination of the general public. The year coincides with the birth of mass spectrometry that began with the cathode ray experiments performed by Joseph John (J. J.) Thomson in Cambridge. Modifications made to Thomson''s cathode ray apparatus by Francis William Aston, resulted in an increase in the brightness of the positive rays that aided their detection. This led to the discovery of heavy isotopes for many of the chemical elements in the ensuing decades. As the discovery of (22) Ne was reported in 1913, another of Thomson''s students was taking part in an expedition to help save future ocean liners from the fate of the Titanic. Geoffrey Ingram Taylor took part in the first ice patrol of the North Atlantic in 1913 aboard the SS Scotia to investigate the formation and position of icebergs. This article, 100???years on, describes Taylor''s work and its impact on safe ocean passage across the Atlantic. Copyright ?? 2012 John Wiley & Sons, Ltd.
%Z FOR Codes: 29999


%0 Journal Article
%~ PubMed
%A Swaminathan, Kavya
%A Downard, Kevin M
%T Anti-viral inhibitor binding to influenza neuraminidase by MALDI mass spectrometry.
%B Analytical Chemistry
%D 2012
%C United States
%I American Chemical Society
%V 84
%N 8
%P 3725-3730
%@ 1520-6882
%X A matrix-assisted laser desorption ionization (MALDI) mass spectrometry-based approach is applied to identify active site domains within influenza neuraminidase that bind the antiviral inhibitors zanamivir (ZANA) and 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (DANA). Combined data from the tryptic and Glu-C endoproteinase digests of neuraminidase-inhibitor complexes have identified binding peptides that contain the active site residues Arg118, Glu119, Arg156, Glu276, and Tyr406. The binding of these residues was confirmed from the analysis of available X-ray crystal structures. The ability to identify peptides within the active sites of proteins and likely binding residues provides both a rapid and relatively high throughput approach with which to screen protein-drug interactions by MALDI mass spectrometry.
%Z FOR Codes: 30401 60101 60506


%0 Journal Article
%~ PubMed
%A Lun, Aaron Tl
%A Wong, Jason Wh
%A Downard, Kevin M
%T Flushuffle and Fluresort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry.
%B BMC Bioinformatics
%D 2012
%C United Kingdom
%I BioMed Central Ltd.
%V 13
%N 1
%P 208
%@ 1471-2105
%X ABSTRACT: BACKGROUND: Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics of the past century, with the possible exception of the 1918 pandemic, resulting in tens of millions of deaths. We have developed and tested new computer algorithms, FluShuffle and FluResort, which enable reassorted viruses to be identified by the most rapid and direct means possible. These algorithms enable reassorted influenza, and other, viruses to be rapidly identified to allow prevention strategies and treatments to be more efficiently implemented. RESULTS: The FluShuffle and FluResort algorithms were tested with both experimental and simulated mass spectra of whole virus digests. Flu Shuffle considers different combinations of viral protein identities that match the mass spectral data using a Gibbs sampling algorithm employing a mixed protein Markov chain Monte Carlo (MCMC) method. Flu Resort utilizes those identities to calculate the weighted distance of each across two or more different phylogenetic trees constructed through viral protein sequence alignments. Each weighted mean distance value is normalized by conversion to a Z-score to establish a reassorted strain. CONCLUSIONS: The new Flu Shuffle and Flu Resort algorithms can correctly identify the origins of influenza viral proteins and the number of reassortment events required to produce the strains from the high resolution mass spectral data of whole virus proteolytic digestions. This has been demonstrated in the case of constructed vaccine strains as well as common human seasonal strains of the virus. The algorithms significantly improve the capability of the proteotyping approach to identify reassorted viruses that pose the greatest pandemic risk.
%Z FOR Codes: 60101 60102


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%A Maleknia, Simin D
%A Akashi, Satoko
%T Impact of limited oxidation on protein ion mobility and structure of importance to footprinting by radical probe mass spectrometry.
%B Rapid Communications in Mass Spectrometry
%D 2012
%C United Kingdom
%I John Wiley & Sons Ltd.
%V 26
%N 3
%P 226-230
%@ 1097-0231
%X The effect of hydroxyl radical induced oxidation on the collision cross-sections of hen egg lysozyme and bovine ubiquitin was investigated by travelling wave ion mobility mass spectrometry for the first time. The oxidized ions of lysozyme and ubiquitin share common collision cross-sections with their unoxidized counterparts suggesting that they share common structures that were unaffected by limited oxidation. In the case of bovine ubiquitin, two distinct conformers were detected for the protein in its unoxidized and oxidized states though no change in the levels of each was observed upon oxidation. This supports the validity of Radical Probe Mass Spectrometry (RP-MS) using an electrical discharge source for protein footprinting experiments. Travelling wave ion mobility mass spectrometry has been used for the first time to confirm that limited oxidation does not have an impact on the global structure of proteins.
%Z FOR Codes: 60101


%0 Journal Article
%~ PubMed
%A Maleknia, Simin D
%A Downard, Kevin M
%T On-plate deposition of oxidized proteins to facilitate protein footprinting studies by radical probe mass spectrometry.
%B Rapid Communications in Mass Spectrometry
%D 2012
%C United Kingdom
%I John Wiley & Sons Ltd.
%V 26
%N 19
%P 2311-2318
%@ 1097-0231
%X The on-plate deposition of oxidized proteins is described to advance footprinting applications by radical probe mass spectrometry (RP-MS). An electrospray ionization (ESI) needle assembly mounted vertically over a 384-target matrix-assisted laser desorption/ionization (MALDI) plate enabled the limited oxidation of proteins as they were released in the charged droplets ahead of their deposition on the plate. This method combined with on-plate proteolytic digestion protocols expedites the analysis of proteins oxidized by RP-MS, and avoids the need to collect and reconstitute samples prior to analysis by MALDI mass spectrometry. Oxidation of peptides from solutions in water as well as an ammonium bicarbonate solution was investigated to test the optimal conditions required for on-plate oxidation of proteins. These comprised of peptides with a wide range of reactive amino acids including Phe, Tyr, Pro, His, Leu, Met and Lys that were previously shown to oxidize in both electrospray discharge and synchrotron radiolysis based footprinting experiments. The on-plate deposition of lysozyme oxidized at electrospray needle voltages of 6 and 9 kV were carried out to demonstrate conditions suitable for footprinting experiments as well as those that induce the onset of protein damage. Copyright ?? 2012 John Wiley & Sons, Ltd.
%Z FOR Codes: 60101 699


%0 Journal Article
%~ PubMed
%A Ha, Ji-Won
%A Downard, Kevin M
%T Evolution of H5N1 influenza virus through proteotyping of hemagglutinin with high resolution mass spectrometry.
%B The Analyst
%D 2011
%C United Kingdom
%I Royal Society of Chemistry
%V 136
%N 16
%P 3259-67
%@ 1364-5528
%X The evolution of the major surface hemagglutinin (HA) antigen of type A H5N1 influenza viruses is explored at the amino acid level using a new proteotyping approach. Alignments of translated hemagglutinin gene sequences of all characterised type A H5N1 strains, or subsets thereof, has enabled the presence of signature peptides of conserved sequence and unique mass to be investigated from the perspective of the host, period and region from which strains were isolated. Consistent with the rapid, cross species transmission of H5N1 strains among migratory birds, poultry and humans throughout south-east Asia, no signatures unique to the host or region were found. Nevertheless, several period-specific signature peptides were identified that enable strains associated with the 1997 H5N1 pandemic to be rapidly differentiated from those in circulation across the subsequent decade.
%Z FOR Codes: 60502 60101 60102


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%A Kokabu, Yuichi
%A Ikeguchi, Mitsunori
%A Akashi, Satoko
%T Homology Modelled Structure of the ??B2B3-Crystallin Heterodimer Studied by Ion Mobility and Radical Probe Mass Spectrometry.
%B The FEBS journal
%D 2011
%C United Kingdom
%I Wiley-Blackwell Publishing Ltd.
%V 278
%N 21
%P 4044-54
%@ 1742-464X
%X Ion mobility MS was employed to study the structure of the ??B2B3-crystallin heterodimer following its detection by ESI-TOF MS. The results demonstrate that the heterodimer has a similar cross-section (3 165 ??(2)) and structure to the ??B2B2-crystallin homodimer. Several homology-modelled structures for the ??B2B3 heterodimer were constructed and assessed in terms of their calculated collision cross-sections and whether the solvent accessibilities of reactive amino acid side chains throughout the ??B3 subunit are in accord with measured oxidation levels in radical probe MS protein footprinting experiments. The ??B2B3 heterodimer AD model provides the best representation of the heterodimer''s structure overall following a consideration of both the ion mobility and radical probe MS data.
%Z FOR Codes: 60112 60101


%0 Journal Article
%~ PubMed
%A Schwahn, Alexander B
%A Downard, Kevin M
%T Proteotyping to Establish the Lineage of Type A H1N1 and Type B Human Influenza Virus.
%B Journal of virological methods
%D 2011
%C Netherlands
%I Elsevier BV
%V 171
%N 1
%P 117-22
%@ 1879-0984
%X The ability to establish the lineage of type A H1N1 and type B human influenza virus strains using a new proteotyping approach is demonstrated. Lineage-specific signature peptides have been determined for the hemagglutinin antigen of type A H1N1 and type B influenza viruses. The detection of these peptides alone within the high resolution mass spectra of whole antigen digests enables the lineage of the strain to be rapidly and unequivocally assigned. This proteotyping approach complements conventional PCR approaches and should aid in the monitoring of the evolution of the influenza virus in both humans and animals.
%Z FOR Codes: 60506 60101 60102


%0 Journal Article
%~ PubMed
%A Ha, Ji-won
%A Schwahn, Alexander B
%A Downard, Kevin M
%T Proteotyping to establish gene origin within reassortant influenza viruses.
%B PLoS One
%D 2011
%C United States
%I Public Library of Science
%V 6
%N 1
%P e15771
%@ 1932-6203
%X The application of a rapid and direct proteotyping approach with which to identify the gene origin of viral antigens in a reassortant influenza strain is demonstrated. The reassortant strain, constructed for a vaccine against type A 2009 H1N1 pandemic influenza, contains genes derived from a wild-type pandemic strain (A/California/7/2009) and an egg adapted high-growth strain (denoted NYMC X-157) derived from an earlier A/Puerto Rico/8/34 strain. The proteotyping approach employs modern proteomics methods and high resolution mass spectrometry to correctly establish that the genes of the surface antigens, hemagglutinin and neuraminidase, are derived from the A/California/7/2009 strain while those for nucleoprotein and matrix protein M1 antigens are derived from the NYMC X-157 strain. This is achieved for both gel-separated antigens and those from a whole vaccine digest. Furthermore, signature peptides detected in the mass spectra of the digested antigens enable the engineered reassortant strain to be identified as a type A virus of the H1N1 subtype in accord with earlier studies. The results demonstrate that proteotyping approach provides a more direct and rapid approach over RT-PCR with which to characterize reassortant strains of the influenza virus at the molecular protein level. Given that these strains pose the greatest risk to human and animal health and have been responsible for all human pandemics of the 20th and 21st centuries, there is a vital need for the origins and evolutionary history of these strains to be rapidly established.
%Z FOR Codes: 60502 60506 60101


%0 Journal Article
%~ PubMed
%A Ha, Ji-Won
%A Schwahn, Alexander B
%A Downard, Kevin M
%T Ability of N-acetylcarnosine to protect lens crystallins from oxidation and oxidative damage by radical probe mass spectrometry (RP-MS).
%B Rapid communications in mass spectrometry : RCM
%D 2010
%C United Kingdom
%I John Wiley & Sons Ltd.
%V 24
%N 19
%P 2900-8
%@ 1097-0231
%X The application of Radical Probe Mass Spectrometry based on protein footprinting studies is described to investigate the effectiveness of the antioxidant N-acetylcarnosine (NAC) in preventing oxidative damage to lens crystallins present in the eye of mammals. Despite separate clinical trials which have reported the benefit of administering NAC to the eye as a 1% topical solution for the treatment of human cataract, no evidence was found to suggest that the antioxidant had any significant direct effect on reducing the levels of oxidation within the most abundant lens crystallins, ?? and ??-crystallin, at the molecular level at increasing concentrations of NAC. The results of this laboratory study suggest that the therapeutic benefit demonstrated in clinical trials is associated with the nature or formulation of the topical solution and/or that the mode of action of NAC as an antioxidant is not a direct one.
%Z FOR Codes: 60101


%0 Journal Article
%~ PubMed
%A Wong, Jason Wh
%A Schwahn, Alexander B
%A Downard, Kevin M
%T FluTyper - an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data.
%B BMC bioinformatics
%D 2010
%C United Kingdom
%I BioMed Central Ltd.
%V 11
%N 1
%P 266
%@ 1471-2105
%X High resolution mass spectrometry has been employed to rapidly and accurately type and subtype influenza viruses. The detection of signature peptides with unique theoretical masses enables the unequivocal assignment of the type and subtype of a given strain. This analysis has, to date, required the manual inspection of mass spectra of whole virus and antigen digests.
%Z FOR Codes: 69999


%0 Journal Article
%~ PubMed
%A Schwahn, Alexander B
%A Wong, Jason W H
%A Downard, Kevin M
%T Rapid Differentiation of Seasonal and Pandemic H1N1 Influenza through Proteotyping of Viral Neuraminidase with Mass Spectrometry.
%B Analytical chemistry
%D 2010
%C United States
%I American Chemical Society
%V 82
%N 11
%P 4584-90
%@ 1520-6882
%X Signature peptides of the neuraminidase antigen across all common circulating human subtypes of type A and B influenza are identified through the bioinformatic alignment of translated gene sequences. The detection of these peptides within the high-resolution mass spectra of whole antigen, virus, and vaccine digests enables the strains to be rapidly and directly typed and subtyped. Importantly, unique signature peptides for pandemic (H1N1) 2009 influenza are identified and detected that enable pandemic strains to be rapidly and directly differentiated from seasonal type A (H1N1) influenza strains. The detection of these peptides can enable the origins of the neuraminidase gene to be monitored in the case of reassorted strains.
%Z FOR Codes: 60506 69999


%0 Journal Article
%~ PubMed
%A Schwahn, Alexander B
%A Wong, Jason W H
%A Downard, Kevin M
%T Rapid typing and subtyping of vaccine strains of the influenza virus with high resolution mass spectrometry.
%B European Journal of Mass Spectrometry
%D 2010
%C United Kingdom
%I IM Publications
%V 16
%N 3
%P 321-329
%@ 1469-0667
%X The application of high-resolution mass spectrometry to type and subtype strains of the influenza virus within recent recommended vaccine formulations is described. Proteolytic digests of whole virus or separated hemagglutinin antigen generate conserved signature peptides of unique mass that can be used to characterise each component virus in a rapid and direct manner by the detection of their ions alone. The approach is demonstrated for two type A strains and one type B strain of human influenza viruses present in recommended seasonal vaccines in the northern and southern hemispheres from 2007 through 2010.
%Z FOR Codes: 60502


%0 Journal Article
%~ PubMed
%A Schwahn, Alexander B
%A Wong, Jason W H
%A Downard, Kevin M
%T Typing of human and animal strains of influenza virus with conserved signature peptides of matrix M1 protein by high resolution mass spectrometry.
%B Journal of Virological Methods
%D 2010
%C Netherlands
%I Elsevier BV
%V 165
%N 2
%P 178-185
%@ 1879-0984
%X The use of high resolution mass spectrometry to detect signature peptides within proteolytic digests of the isolated matrix M1 protein, and whole virus digests, for both human and animal strains of influenza is shown to be able to rapidly and reliably type the virus. Conserved sequences for predicted tryptic peptides were identified through alignments of matrix M1 protein sequences across all human, avian and swine strains of the influenza virus. Peptides with unique masses, when compared with those from the in silico digestion of all influenza antigens and those proteins known to contaminate egg grown strains, were identified using the purpose built FluGest algorithm. Their frequency of occurrence within the matrix M1 protein across all type A and type B strains was established with the FluAlign algorithm. The subsequent detection of the signature peptides of matrix M1 protein within proteolytic digests of type A and type B human and avian strains has been demonstrated.
%Z FOR Codes: 60506 69999


%0 Journal Article
%~ PubMed
%A Schwahn, Alexander B
%A Downard, Kevin M
%T Antigenicity of a type A influenza virus through comparison of hemagglutination inhibition and mass spectrometry immunoassays.
%B Journal of immunoassay & immunochemistry
%D 2009
%C United States
%I Taylor & Francis Inc.
%V 30
%N 3
%P 245-261
%@ 1532-4230
%X The antigenicity of a type A (H1N1) influenza strain has been characterised through the application of mass spectrometry (MS) and hemagglutination-inhibition immunoassays performed in parallel. Two monoclonal antibodies were found to be highly and equally specific in HI assays against influenza strain A/New Caledonia/20/99 while the MS immunoassay demonstrated that both antibodies recognise the same epitopic peptide localised to residues 225-232 of the hemagglutinin HA1 subunit whose C-terminal residues reside in close proximity to the receptor binding site. Both immunoassays showed no binding of a monoclonal antibody that recognizes the hemagglutinin antigen of type B strains.
%Z FOR Codes: 60506 60502


%0 Journal Article
%~ PubMed
%A Diemer, Hélène
%A Atmanene, Cédric
%A Sanglier, Sarah
%A Morrissey, Bethny
%A Van Dorsselaer, Alain
%A Downard, Kevin M
%T Detection and structural features of the betaB2-B3-crystallin heterodimer by radical probe mass spectrometry (RP-MS).
%B Journal of mass spectrometry
%D 2009
%C United Kingdom
%I John Wiley & Sons Ltd
%V 44
%N 5
%P 803-812
%@ 1096-9888
%X The predilection of the beta-crystallin B2 subunit to interact with the betaB3 subunit rather than self associate is evident by the detection of the betaB2-B3-crystallin heterodimer by native gel electrophoresis and electrospray ionisation time-of-flight (ESI-TOF) mass spectrometry under non denaturing conditions. The complex has been detected for the first time and its molecular mass is measured to be 47,450 +/- 1 Da. Radical probe mass spectrometry (RP-MS) was subsequently applied to investigate the nature of the heterodimer through the limited oxidation of the subunits in the complex. Two peptide segments of the betaB2 subunit and six of the betaB3 subunit were found to oxidise, with far greater oxidation observed within the betaB3 versus the betaB2 subunit. This, and the observation that the oxidation data of betaB2 subunit is inconsistent with the structure of the betaB2 monomer, demonstrates that the protection of betaB2 is conferred by its association with betaB3 subunit within the heterodimer where only the residues of, and towards, its N-terminal domain remain exposed to solvent. The results suggest that the betaB2 subunit adopts a more compacted form than in its monomeric form in order for much of its structure to be enveloped by the betaB3 subunit within the heterodimer.
%Z FOR Codes: 60101


%0 Journal Article
%~ PubMed
%A Wong, Jason W H
%A Schwahn, Alexander B
%A Downard, Kevin M
%T ETISEQ - an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics.
%B BMC Vioinformatics
%D 2009
%C United Kingdom
%I BioMed Central Ltd.
%V 10
%N 10
%P 244
%@ 1471-2105
%X BACKGROUND: Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or MSE) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. RESULTS: An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. CONCLUSION: The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories.
%Z FOR Codes: 110106


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%T J. J. Thomson Goes to America.
%B Journal of the American Society for Mass Spectrometry
%D 2009
%C United States
%I Elsevier Inc.
%V 20
%N 
%P 1964-73
%@ 1044-0305
%X Joseph John (J. J.) Thomson was an accomplished scientist who helped lay the foundations of nuclear physics. A humble man of working class roots, Thomson went on to become one of the most influential physicists of the late 19th century. He is credited with the discovery of the electron, received a Nobel Prize in physics in 1906 for investigations into the conduction of electricity by gases, was knighted in 1908, and served as a Cavendish Professor and Director of the laboratory for over 35 years from 1884. His laboratory attracted some of the world''s brightest minds; Francis W. Aston, Niels H. D. Bohr, Hugh L. Callendar, Charles T. R. Wilson, Ernest Rutherford, George F. C. Searle, Geoffrey I. Taylor, and John S. E. Townsend all worked under him. This article recounts J. J. Thomson''s visits to North America in 1896, 1903, 1909, and finally 1923. It presents his activities and his personal impressions of the people and society of the U.S.A. and Canada, and the science of atomic physics and chemistry in the late 1800s and early 1900s.
%Z FOR Codes: 1004


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%A Morrissey, Bethny
%A Schwahn, Alex B
%T Mass spectrometry analysis of the influenza virus.
%B Mass spectrometry reviews
%D 2009
%C United States
%I John Wiley & Sons, Inc.
%V 28
%N 0
%P 35-49
%@ 1098-2787
%X The role of mass spectrometry to probe characteristics of the influenza virus, and vaccine and antiviral drugs that target the virus, are reviewed. Genetic and proteomic approaches have been applied which incorporate high resolution mass spectrometry and mass mapping to genotype the virus and establish its evolution in terms of the primary structure of the surface protein antigens. A mass spectrometric immunoassay has been developed and applied to assess the structure and antigenicity of the virus in terms of the hemagglutinin antigen. The quantitation of the hemagglutinin antigen in vaccine preparations has also been conducted that is of importance to their efficacy. Finally, the characterization and quantitation of antiviral drugs against the virus, and their metabolites, have been monitored in blood, serum, and urine. The combined approaches demonstrate the strengths of modern mass spectrometric methods for the characterization of this killer virus. [This article was published online 10 September 2008. An error was subsequently identified. This notice is included in the online and print versions to indicate that both have been corrected 7 November 2008.]
%Z FOR Codes: 110106


%0 Journal Article
%~ PubMed
%A Schwahn, Alexander B
%A Wong, Jason W H
%A Downard, Kevin M
%T Signature peptides of influenza nucleoprotein for the typing and subtyping of the virus by high resolution mass spectrometry.
%B The Analyst
%D 2009
%C United Kingdom
%I Royal Society of Chemistry
%V 134
%N 11
%P 2253-2261
%@ 1364-5528
%X The use of high resolution mass spectrometry to record the accurate mass of signature peptides within proteolytic digests of the nucleoprotein antigen, and whole influenza virus, is shown to be able to rapidly type and subtype the virus. Conserved sequences for predicted tryptic peptides were identified through alignments of those for the nucleoprotein across all influenza types and subtypes. Peptides with unique theoretical masses from those generated in silico for all influenza antigen sequences, and from those proteins known to contaminate virus preparations in laboratory grown samples, were identified using a purpose built algorithm (FluGest). The frequency of occurrence of such conserved peptide signatures was assessed across all nucleoprotein sequences to subsequently type and subtype human strains of the virus. The application of the approach is illustrated for both type A H1N1 and H3N2, and type B strains of human influenza virus.
%Z FOR Codes: 60502 60101 60502 60101


%0 Journal Article
%~ PubMed
%A Schwahn, Alexander B
%A Wong, Jason W H
%A Downard, Kevin M
%T Subtyping of the influenza virus by high resolution mass spectrometry.
%B Analytical chemistry
%D 2009
%C United States
%I American Chemical Society
%V 81
%N 9
%P 3500-3506
%@ 1520-6882
%X High resolution, high mass accuracy mass spectra of hemagglutinin and whole virus digests of influenza are shown to be able to be used to type and subtype the major circulating forms of the virus in humans. Conserved residues and peptide segments of the hemagglutinin antigen have been identified across type A and B strains, and for type B strains of the Yamagata 16/88 and Victoria 2/87 lineages. The theoretical masses for the protonated peptide ions for tryptic peptides of conserved sequence were subsequently shown to be unique in mass when compared to in silico generated peptides from all influenza viral protein sequences and those proteins known to contaminate virus preparations. The approach represents a more rapid and direct approach with which to type and subtype the virus that is of critical need to prepare strategies and treatments in the event of a local epidemic or global pandemic.
%Z FOR Codes: 69999


%0 Journal Article
%~ PubMed
%A Downard, Kevin
%T Editorial: Australia contributors' issue.
%B Mass spectrometry reviews
%D 2008
%C United States
%I John Wiley & Sons, Inc.
%V 28
%N 1
%P 1
%@ 1098-2787
%X 
%Z FOR Codes: 30499


%0 Journal Article
%~ PubMed
%A Morrissey, Bethny
%A Downard, Kevin M
%T Kinetics of antigen-antibody interactions employing a MALDI mass spectrometry immunoassay.
%B Analytical chemistry
%D 2008
%C United States
%I American Chemical Society
%V 80
%N 20
%P 7720-6
%@ 1520-6882
%X Time-course MALDI mass spectrometry immunoassays have been shown to be able to detect differences in the relative rates of binding of peptides, both from within and across epitopic domains, with antibodies in non-competitive and competitive experiments. A monoclonal antibody raised to target the HA1 subunit of the hemagglutinin antigen of type A H3N2 influenza strains is found to recognize two epitopic peptides comprising residues 109-125 and 158-166 that likely form part of an extended discontinuous domain. Time-course experiments show the smaller peptide binds antibody at a rate that is 5-fold faster than that for the larger peptide. A shorter segment of this larger peptide, comprised of residues 119-125, is also found to bind at twice the rate of the extended peptide. Studies of modified peptide variants and synthetic variants of HA peptide 119-125 has enabled important contact residues to be identified whose accessibilities in the native protein are in accord with the mass spectrometry results.
%Z FOR Codes: 110704


%0 Journal Article
%~ PubMed
%A Morrissey, Bethny
%A Streamer, Margaret
%A Downard, Kevin M
%T Antigenic characterisation of H3N2 subtypes of the influenza virus by mass spectrometry.
%B Journal of virological methods
%D 2007
%C Netherlands
%I Elsevier/North-Holland Biomedical Press
%V 145
%N 
%P 106-14
%@ 0166-0934
%X The antigenic characterisation of three H3N2 type A influenza strains by mass spectrometry is described. The approach, developed in this laboratory, employs matrix-assisted laser desorption ionisation (MALDI) mass spectrometry to analyse gel-resolved antigens, post their proteolysis and treatment with monoclonal antibodies. The primary structure and antigenicity of the component antigens of the virus can be determined in a single step. Four antigenic domains of hemagglutinin have been identified and these are localised at residues 109-125, 158-170 and 316-326 of the HA1 subunit and to residues 159-183 of the HA2 subunit. The results demonstrate the applicability of the approach for identifying antigenic determinants across various H3N2 strains with high throughput and at low sample levels. Comparative rates of antibody binding between two of the antigenic peptides have also been reported.
%Z FOR Codes: 110705


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%T Cavendish's crocodile and dark horse: The lives of Rutherford and Aston in parallel.
%B Mass spectrometry reviews
%D 2007
%C United States
%I John Wiley & Sons, Inc.
%V 26
%N 
%P 713-23
%@ 0277-7037
%X Ernest Rutherford and Francis Aston were born a world apart but both would become two of the most influential physicists of their time. Their separate training, under the direction of J.J. Thomson at the Cavendish Laboratory, shaped their future and allowed both men to develop and apply their considerable skills in experimental physics. It also catalyzed their careers and ultimately led to each receiving a Nobel Prize. Although they had very different characters, Rutherford and Aston became close colleagues and confidants who spent considerable time together within the confines of the Cavendish Laboratory, at Trinity College, and elsewhere in Cambridge. They also traveled the world in company, usually as part of a group or British delegation of scientists attending conferences and meetings overseas. This article parallels the lives of the two men. It describes how they came to work at the Cavendish, their scientific accomplishments and accolades, and their activities and interactions away from the laboratory.
%Z FOR Codes:


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%A Morrissey, Bethny
%T Fingerprinting a killer: surveillance of the influenza virus by mass spectrometry.
%B The Analyst
%D 2007
%C England
%I Royal Society of Chemistry
%V 132
%N 7
%P 611-614
%@ 0003-2654
%X Influenza is a deadly virus that continues to kill and inflict illness and suffering the world over. Despite a global surveillance strategy, an annual response to vaccine preparation and the development of new anti-viral drugs to treat the virus ahead of, or after, infection, no cure exists. Future pandemics are a very real threat and countries have mobilised efforts to stockpile treatments and prepare for outbreaks. A new surveillance approach in which the structure and antigenicity of the virus can be rapidly screened by mass spectrometry is expected to have a greater role in the characterisation of emerging influenza strains, even at the site of an outbreak.
%Z FOR Codes: 110705


%0 Book Section
%A Maleknia, Simin D
%A Downard, Kevin
%T Genesis and Application of Radical Probe 
Mass Spectrometry (RP-MS) to Study Protein Interactions, in/ Mass 
Spectrometry of Protein Interactions
%B Mass Spectrometry of Protein Interactions
%D 2007
%C New Jersey, USA
%I John Wiley & Sons, Inc.
%V 
%N 
%P 109-133
%@ 978-0-471-79373-1
%E Downard, Kevin
%X 
%Z FOR Codes:


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%T Historical Account: Francis William Aston: the man behind the mass spectrograph.
%B European journal of mass spectrometry
%D 2007
%C United Kingdom
%I IM Publications
%V 13
%N 3
%P 177-190
%@ 1469-0667
%X Francis William Aston was among the most accomplished physicists of the 20th century. A Nobel laureate and Fellow of the Royal Society, his research career spanned four decades. During this time, he provided experimental proof for the existence of isotopes of many of the chemical elements and recorded their masses using several, hand-built mass spectrographs. A rather private man who lived alone in Trinity College for much of his adult life, Aston remains a somewhat elusive and mysterious figure. This biography attempts to shed some more light on the man, including his character and his personal life, and particularly how his life was shaped by his childhood, environment and education. It contains previously unpublished material and photographs and complements the biographies of Hevesy and Thomson, following Aston''s death, and that by Squires detailing the construction and performance of his mass spectrographs at the Cavendish Laboratory. It is published at a timely juncture, some 100 years after Aston''s first arrival at Cambridge.
%Z FOR Codes: 110705


%0 Book Section
%A Downard, Kevin
%T Softly softly - detection of protein complexes by matrix-assisted laser desorption ionization mass spectrometry
%B Mass Spectrometry of Protein Interactions
%D 2007
%C New Jersey, USA
%I John Wiley & Sons
%V 
%N 
%P 25-43
%@ 978-0-471-79373-1
%X 
%Z FOR Codes: 30406


%0 Journal Article
%~ PubMed
%A Ho, Joshua W K
%A Morrissey, Bethny
%A Downard, Kevin M
%T A Computer Algorithm for the Identification of Protein Interactions from the Spectra of Masses (PRISM).
%B Journal of the American Society for Mass Spectrometry
%D 2006
%C NEW YORK, USA, NY
%I ELSEVIER SCIENCE INC
%V 18
%N 0
%P 563-6
%@ 1044-0305
%X A new algorithm is reported to assist with the identification of protein interaction domains by comparing pairs of MALDI mass spectra recorded for protein digests treated with a binding partner versus an untreated control. Known as PRISM, for protein interactions from the spectra of masses, the algorithm imports m/z versus peak area data directly from a pair of MALDI mass spectra recorded for the control and reaction sample. The algorithm is shown to be able to successfully identify antigenic determinants for protein antigens within mixed protein digests. The algorithm has general utility for the comparative analysis of differences within any two mass spectra of any type and is easily implemented using a simple, intuitive graphical user interface (GUI).
%Z FOR Codes:


%0 Journal Article
%~ PubMed
%A Morrissey, Bethny
%A Downard, Kevin M
%T A proteomics approach to survey the antigenicity of the influenza virus by mass spectrometry.
%B Proteomics
%D 2006
%C Germany
%I Wiley - VCH Verlag GmbH & Co. KGaA
%V 6
%N 7
%P 2034-41
%@ 1615-9853
%X A proteomics-based approach is described that combines gel electrophoresis and MS in order to identify protein interactions and the nature of the interaction interface with high-sample throughput and sensitivity. Results for protein antigens of the influenza virus have demonstrated that the approach can be successfully employed to detect determinants within the hemagglutinin antigen of two divergent type A forms of the virus in present circulation. The determinants are localised to residues 206-224 following tryptic digestion of the hemagglutinin antigen. Specific peptide-antibody complexes formed after treatment of gel-recovered antigen are shown to be able to be preserved on the MALDI target array as has been previously demonstrated in this laboratory for whole virus. The approach has broad applicability for the analysis of a wide array of protein complexes with identification of the interaction interface in a single step with high-sample throughput and at low sample levels.
%Z FOR Codes: 110705 110705


%0 Journal Article
%~ PubMed
%A Issa, Samah
%A Downard, Kevin M
%T Interaction between alpha and upsilon-crystallin, common to the eye of the Australian platypus, by radical probe mass spectrometry.
%B Journal of mass spectrometry : JMS
%D 2006
%C United Kingdom
%I John Wiley & Sons Ltd
%V 41
%N 
%P 1298-303
%@ 1076-5174
%X The interaction between alpha-crystallin and upsilon-crystallin, a class recently discovered in the eye of the Australian platypus, has been shown by native shift gel assay and examined by radical probe mass spectrometry in the context of the ability of alpha-crystallin to protect upsilon-crystallin from oxidation and oxidative damage through radical-based oxidative stress mechanisms. Residues 22-41, 132-148, 212-227 and 245-264 of upsilon-crystallin display the greatest protection when interacted with alpha-crystallin at a ratio of 2 : 1 observed for the complex, which is commensurate with their levels measured in the eye of the platypus. Across each domain, a delay in the onset of oxidative damage is observed as the time of exposure to radicals is increased. The results are discussed in the context of the structure of the porcine homologue of upsilon-crystallin.
%Z FOR Codes:


%0 Journal Article
%~ PubMed
%A Downard, Kevin M
%T Ions of the interactome: The role of MS in the study of protein interactions in proteomics and structural biology.
%B Proteomics
%D 2006
%C WEINHEIM, GERMANY
%I Wiley - VCH Verlag GmbH & Co. KGaA
%V 6
%N 
%P 5374-84
%@ 1615-9853
%X The role of MS in the study of protein-protein interactions in solution is described from a proteomics perspective, in terms of high-throughput analyses of protein complexes in vivo, through to chemical and biochemical treatments ahead of MS analysis in the context of complementary experimental approaches in structural biology. The use of MS to characterise protein-protein interactions is described following the single and tandem affinity purification of protein complexes and assemblies of expressed proteins in host cells, the isolation and preservation of protein complexes on surfaces and microarrays, and their prior treatment with chemical and biochemical probes by hydrogen exchange, radical probe, chemical cross-linking, and limited proteolysis. The advantages and disadvantages of each of the approaches are presented. These new and emerging applications, which further demonstrate the power of MS, continue to ensure that the mass spectrometer will remain at the heart of discoveries in proteomics in the foreseeable future.
%Z FOR Codes:


%0 Journal Article
%~ PubMed
%A Gerega, Sebastien K
%A Downard, Kevin M
%T PROXIMO - a new algorithm to model protein complexes using data from Radical Probe Mass Spectrometry (RP-MS).
%B Bioinformatics (Oxford, England)
%D 2006
%C United Kingdom
%I Oxford University Press
%V 22
%N 14
%P 1702-9
%@ 1367-4803
%X The design and implementation of a new algorithm, known as PROXIMO for protein oxidation interface modeller, is described to predict the structure of protein complexes using data generated in radical probe mass spectrometry (RP-MS) experiments. Photochemical radiolysis and discharge sources can be used to effect RP-MS in which hydroxyl radicals are formed directly from the bulk solvent on millisecond timescales and react with surface accessible residues in footprinting-like experiments. The algorithm utilizes a geometric surface fitting routine to predict likely structures for protein complexes. These structures are scored based on a correlation between the measured solvent accessibility of oxidizable residue side chains and oxidation shielding data obtained by RP-MS. The algorithm has been implemented to predict structures for the ribonuclease S-protein-peptide and calmodulin-melittin complexes using RP-MS data generated in this laboratory. The former is in close agreement with the high-resolution experimental structure available.
%Z FOR Codes:


%0 Journal Article
%A Downard, Kevin
%T The Life and Travels to Australia of Francis Aston - Inventor of the Mass Spectrograph
%B Chemistry in Australia
%D 2006
%C Australia
%I Royal Australian Chemical Institute
%V 73
%N 1
%P 17-20
%@ 0314-4240
%X 
%Z FOR Codes: