All Publications

  • TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets NATURE BIOTECHNOLOGY Devabhaktuni, A., Lin, S., Zhang, L., Swaminathan, K., Gonzalez, C., Olsson, N., Pearlman, S. M., Rawson, K., Elias, J. E. 2019; 37 (4): 469-+
  • TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. Nature biotechnology Devabhaktuni, A., Lin, S., Zhang, L., Swaminathan, K., Gonzalez, C. G., Olsson, N., Pearlman, S. M., Rawson, K., Elias, J. E. 2019; 37 (4): 469–79


    Although mass spectrometry is well suited to identifying thousands of potential protein post-translational modifications (PTMs), it has historically been biased towards just a few. To measure the entire set of PTMs across diverse proteomes, software must overcome the dual challenges of covering enormous search spaces and distinguishing correct from incorrect spectrum interpretations. Here, we describe TagGraph, a computational tool that overcomes both challenges with an unrestricted string-based search method that is as much as 350-fold faster than existing approaches, and a probabilistic validation model that we optimized for PTM assignments. We applied TagGraph to a published human proteomic dataset of 25million mass spectra and tripled confident spectrum identifications compared to its original analysis. We identified thousands of modification types on almost 1million sites in the proteome. We show alternative contexts for highly abundant yet understudied PTMs such as proline hydroxylation, and its unexpected association with cancer mutations. By enabling broad characterization of PTMs, TagGraph informs as to how their functions and regulation intersect.

    View details for PubMedID 30936560

  • Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens NATURE Khodadoust, M. S., Olsson, N., Wagar, L. E., Haabeth, O. A., Chen, B., Swaminathan, K., Rawson, K., Liu, C. L., Steiner, D., Lund, P., Rao, S., Zhang, L., Marceau, C., Stehr, H., Newman, A. M., Czerwinski, D. K., Carlton, V. E., Moorhead, M., Faham, M., Kohrt, H. E., Carette, J., Green, M. R., Davis, M. M., Levy, R., Elias, J. E., Alizadeh, A. A. 2017; 543 (7647): 723-?


    Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4(+) T cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification, and exome sequencing is an effective platform to uncover tumour neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

    View details for DOI 10.1038/nature21433

    View details for PubMedID 28329770

  • Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens NATURE Marceau, C. D., Puschnik, A. S., Majzoub, K., Ooi, Y. S., Brewer, S. M., Fuchs, G., Swaminathan, K., Mata, M. A., Elias, J. E., Sarnow, P., Carette, J. E. 2016; 535 (7610): 159-?


    The Flaviviridae are a family of viruses that cause severe human diseases. For example, dengue virus (DENV) is a rapidly emerging pathogen causing an estimated 100 million symptomatic infections annually worldwide. No approved antivirals are available to date and clinical trials with a tetravalent dengue vaccine showed disappointingly low protection rates. Hepatitis C virus (HCV) also remains a major medical problem, with 160 million chronically infected patients worldwide and only expensive treatments available. Despite distinct differences in their pathogenesis and modes of transmission, the two viruses share common replication strategies. A detailed understanding of the host functions that determine viral infection is lacking. Here we use a pooled CRISPR genetic screening strategy to comprehensively dissect host factors required for these two highly important Flaviviridae members. For DENV, we identified endoplasmic-reticulum (ER)-associated multi-protein complexes involved in signal sequence recognition, N-linked glycosylation and ER-associated degradation. DENV replication was nearly completely abrogated in cells deficient in the oligosaccharyltransferase (OST) complex. Mechanistic studies pinpointed viral RNA replication and not entry or translation as the crucial step requiring the OST complex. Moreover, we show that viral non-structural proteins bind to the OST complex. The identified ER-associated protein complexes were also important for infection by other mosquito-borne flaviviruses including Zika virus, an emerging pathogen causing severe birth defects. By contrast, the most significant genes identified in the HCV screen were distinct and included viral receptors, RNA-binding proteins and enzymes involved in metabolism. We found an unexpected link between intracellular flavin adenine dinucleotide (FAD) levels and HCV replication. This study shows notable divergence in host-depenency factors between DENV and HCV, and illuminates new host targets for antiviral therapy.

    View details for DOI 10.1038/nature18631

    View details for Web of Science ID 000379015600044

    View details for PubMedID 27383987

    View details for PubMedCentralID PMC4964798

  • Substituent effects on the binding of natural product anthocyanidin inhibitors to influenza neuraminidase with mass spectrometry ANALYTICA CHIMICA ACTA Swaminathan, K., Mueller, P., Downard, K. M. 2014; 828: 61-69


    The binding of three closely related anthocyanins within the 430-cavity of influenza neuraminidase is studied using a combination of mass spectrometry and molecular docking. Despite their similar structures, which differ only in the number and position of the hydroxyl substituents on the phenyl group attached to the chromenylium ring, subtle differences in their binding characteristics are revealed by mass spectrometry and molecular docking that are in accord with their inhibitory properties by neuraminidase inhibition assays. The cyanidin and delphinidin, with the greatest number of hydroxyl groups, bind more strongly and are better inhibitors than pelargonidin that contains a lone hydroxyl group at the 4' position. The study demonstrates, for the first time, the sensitivity of the mass spectrometry based approach for investigating the molecular basis and relative affinity of antiviral inhibitors, with subtly different structures, to their target protein. It has broader application for the screening of other protein interactions more generally with reasonable high-throughput.

    View details for DOI 10.1016/j.aca.2014.04.021

    View details for Web of Science ID 000336336900008

    View details for PubMedID 24845816

  • Evolution of Influenza Neuraminidase and the Detection of Antiviral Resistant Strains Using Mass Trees ANALYTICAL CHEMISTRY Swaminathan, K., Downard, K. M. 2014; 86 (1): 629-637


    A new approach employing mass trees is described and implemented which enables the evolution of influenza neuraminidase across all subtypes (N1-N9) in human and animal hosts to be monitored and charted without gene or protein sequencing. These mass trees are shown to be congruent with sequence based trees. Such trees can be built solely from the masses of the proteolytic peptide ions of viral proteins recorded by a mass spectrometer. They are shown to be able to correctly chart the evolutionary history of human pandemic influenza viruses, which originated in animal hosts, and can also resolve antiviral resistant from sensitive strains. Furthermore, experimental mass map data recorded for a circulating strain is correctly positioned onto a mass tree so as to quickly establish its evolutionary history and identify whether it is resistant or sensitive to the antiviral inhibitor oseltamivir. This new computational approach is expected to find wider application for evolutionary studies of organisms more generally.

    View details for DOI 10.1021/ac402892m

    View details for Web of Science ID 000329548700066

    View details for PubMedID 24224726

  • Inhibition of influenza hemagglutinin with the antiviral inhibitor arbidol using a proteomics based approach and mass spectrometry. Antiviral research Nasser, Z. H., Swaminathan, K., Müller, P., Downard, K. M. 2013; 100 (2): 399-406


    A proteomics gel electrophoresis based approach has been applied to study the effect of arbidol on the proliferation of influenza virus in vitro through quantitation of hemagglutinin levels. An arbidol concentration of 20μg/ml was required to achieve a 50% reduction in virus proliferation and hemagglutinin levels. The use of a MALDI mass spectrometry approach to study the binding of arbidol to influenza hemagglutinin revealed it bound solely to residues 104-120 of the HA2 subunit, a region known to contain an arbidol resistance mutation. Parallel molecular docking results revealed that this binding site was favoured in which the arbidol molecule binds in two possible orientations approximately 180° to one another at HA2 residues 118-123. The combined studies support the recognized potential of arbidol as an effective and targeted antiviral agent against the influenza virus.

    View details for DOI 10.1016/j.antiviral.2013.08.021

    View details for PubMedID 24012882

  • Binding of a natural anthocyanin inhibitor to influenza neuraminidase by mass spectrometry ANALYTICAL AND BIOANALYTICAL CHEMISTRY Swaminathan, K., Dyason, J. C., Maggioni, A., von Itzstein, M., Downard, K. M. 2013; 405 (20): 6563-6572


    The binding of a natural anthocyanin to influenza neuraminidase has been studied employing mass spectrometry and molecular docking. Derived from a black elderberry extract, cyanidin-3-sambubiocide has been found to be a potent inhibitor of sialidase activity. This study reveals the molecular basis for its activity for the first time. The anthocyanin is shown by parallel experimental and computational approaches to bind in the so-called 430-cavity in the vicinity of neuraminidase residues 356-364 and 395-432. Since this antiviral compound binds remote from Asp 151 and Glu 119, two residues known to regulate neuraminidase resistance, it provides the potential for the development of a new class of antivirals against the influenza virus without this susceptibility.

    View details for DOI 10.1007/s00216-013-7068-x

    View details for Web of Science ID 000321911800019

    View details for PubMedID 23748498

  • Mass Trees: A New Phylogenetic Approach and Algorithm to Chart Evolutionary History with Mass Spectrometry ANALYTICAL CHEMISTRY Lun, A. T., Swaminathan, K., Wong, J. W., Downard, K. M. 2013; 85 (11): 5475-5482


    A new phylogenetics approach and algorithm with which to chart the evolutionary history of organisms is presented. It utilizes mass spectral data produced from the proteolytic digestion of proteins, rather than partial or complete gene or translated gene sequences. The concept and validity of the approach is demonstrated herein using both theoretical and experimental mass data, together with the translated gene sequences of the hemagglutinin protein of the influenza virus. A comparison of the mass trees with conventional sequenced-based phylogenetic trees, using two separate tree comparison algorithms, reveals a high degree of similarity and congruence among the trees. Given that the mass map data can be generated more rapidly than gene sequences, even when next generation parallel sequencing is employed, mass trees offer new opportunities and advantages for phylogenetic analysis.

    View details for DOI 10.1021/ac4005875

    View details for Web of Science ID 000320096900029

    View details for PubMedID 23647083

  • Anti-Viral Inhibitor Binding to Influenza Neuraminidase by MALDI Mass Spectrometry ANALYTICAL CHEMISTRY Swaminathan, K., Downard, K. M. 2012; 84 (8): 3725-3730


    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.

    View details for DOI 10.1021/ac300291c

    View details for Web of Science ID 000302838500036

    View details for PubMedID 22409142