2023

Huang, Y., Jonsson, N. N. , McLaughlin, M. , Burchmore, R. , Johnson, P. C.D. , Jones, R. , McGill, S., Brady, N., Weidt, S. and Eckersall, D. (2023) Quantitative TMT-based proteomics revealing host, dietary and microbial proteins in bovine faeces including barley serpin Z4, a prominent component in the head of beer. Journal of Proteomics, 285, 104941. (doi: 10.1016/j.jprot.2023.104941) (PMID:37285906)

McBride, R., Wandy, J. , Weidt, S., Rogers, S. , Davies, V. , Daly, R. and Bryson, K. (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)

Wandy, J. , Mcbride, R., Rogers, S. , Terzis, N., Weidt, S., van der Hooft, J. J.J. , Bryson, K. , Daly, R. and Davies, V. (2023) Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics. Frontiers in Molecular Biosciences, 10, 1130781. (doi: 10.3389/fmolb.2023.1130781) (PMID:36959982) (PMCID:PMC10027714)

Nguyen, T. X. et al. (2023) Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed part I: serum proteomes. Journal of Proteomics, 270, 104740. (doi: 10.1016/j.jprot.2022.104740) (PMID:36191802)

Nguyen, T. X., Agazzo, A., McGill, S., Weidt, S., Han, Q. H., Gelemanović, A., McLaughlin, M. , Savoini, G., Eckersall, P. D. and Burchmore, R. (2023) Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed part II: ileum proteomes. Journal of Proteomics, 270, 104739. (doi: 10.1016/j.jprot.2022.104739) (PMID:36174954)

2022

Alpizar-Sosa, E. A. et al. (2022) Amphotericin B resistance in Leishmania mexicana: Alterations to sterol metabolism and oxidative stress response. PLoS Neglected Tropical Diseases, 16(9), e0010779. (doi: 10.1371/journal.pntd.0010779) (PMID:36170238) (PMCID:PMC9581426)

Nguyen, T. X. et al. (2022) Abundance of plasma proteins in response to divergent ratios of dietary ω6:ω3 fatty acids in gestating and lactating sows using a quantitative proteomics approach. Journal of Proteomics, 260, 104562. (doi: 10.1016/j.jprot.2022.104562) (PMID:35314360)

Wandy, J. , Davies, V. , McBride, R., Weidt, S., Rogers, S. and Daly, R. (2022) ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics. Journal of Open Source Software, 7(71), 3990. (doi: 10.21105/joss.03990)

Meewan, J. et al. (2022) Limited impact of the protein corona on the cellular uptake of PEGylated zein micelles by melanoma cancer cells. Pharmaceutics, 14(2), e439. (doi: 10.3390/pharmaceutics14020439) (PMID:35214171) (PMCID:PMC8877401)

Rubić, I. et al. (2022) Multi platforms strategies and metabolomics approaches for the investigation of comprehensive metabolite profile in dogs with Babesia canis infection. International Journal of Molecular Sciences, 23(3), 1575. (doi: 10.3390/ijms23031575) (PMID:35163517) (PMCID:PMC8835742)

2021

Davies, V. , Wandy, J. , Weidt, S., van der Hooft, J. J.J. , Miller, A. , Daly, R. and Rogers, S. (2021) Rapid development of improved data-dependent acquisition strategies. Analytical Chemistry, 93(14), pp. 5676-5683. (doi: 10.1021/acs.analchem.0c03895) (PMID:33784814) (PMCID:PMC8047769)

2020

Pesko, B. K., Weidt, S., McLaughlin, M. , Wescott, D. J., Torrance, H., Burgess, K. and Burchmore, R. (2020) Post-mortomics: the potential of untargeted metabolomics to highlight markers for time since death. OMICS: A Journal of Integrative Biology, 24(11), pp. 649-659. (doi: 10.1089/omi.2020.0084) (PMID:33095683)

Burgon, J. D. , Vieites, D. R., Jacobs, A. , Weidt, S. K., Gunter, H. M., Steinfartz, S., Burgess, K., Marble, B. K. and Elmer, K. R. (2020) Functional colour genes and signals of selection in colour polymorphic salamanders. Molecular Ecology, 29(7), pp. 1284-1299. (doi: 10.1111/mec.15411) (PMID:32159878)

2019

Wandy, J. , Davies, V. , van der Hooft, J. J.J. , Weidt, S., Daly, R. and Rogers, S. (2019) In silico optimization of mass spectrometry fragmentation strategies in metabolomics. Metabolites, 9(10), 219. (doi: 10.3390/metabo9100219) (PMID:31600991)

Rankin, N. J. , Burgess, K., Weidt, S., Wannamethee, G., Sattar, N. and Welsh, P. (2019) High-throughput quantification of carboxymethyl lysine in serum and plasma using high-resolution accurate mass Orbitrap mass spectrometry. Annals of Clinical Biochemistry, 56(3), pp. 397-407. (doi: 10.1177/0004563219830432) (PMID:30832481) (PMCID:PMC6498755)

Pountain, A. W. , Weidt, S. K., Regnault, C., Bates, P. A., Donachie, A. M., Dickens, N. J. and Barrett, M. P. (2019) Genomic instability at the locus of sterol C24-methyltransferase promotes amphotericin B resistance in Leishmania parasites. PLoS Neglected Tropical Diseases, 13(2), e0007052. (doi: 10.1371/journal.pntd.0007052) (PMID:30716073) (PMCID:PMC6375703)

2018

Kovarova, J., Pountain, A. W. , Wildridge, D., Weidt, S., Bringaud, F., Burchmore, R. J.S. , Achcar, F. and Barrett, M. P. (2018) Deletion of transketolase triggers a stringent metabolic response in promastigotes and loss of virulence in amastigotes of Leishmania mexicana. PLoS Pathogens, 14(3), e1006953. (doi: 10.1371/journal.ppat.1006953) (PMID:29554142) (PMCID:PMC5882173)

2017

Mwenechanya, R. et al. (2017) Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana. PLoS Neglected Tropical Diseases, 11(6), e0005649. (doi: 10.1371/journal.pntd.0005649) (PMID:28622334) (PMCID:PMC5498063)

Akpunarlieva, S., Weidt, S., Lamasudin, D., Naula, C. , Henderson, D., Barrett, M. , Burgess, K. and Burchmore, R. (2017) Integration of proteomics and metabolomics to elucidate metabolic adaptation in Leishmania. Journal of Proteomics, 155, pp. 85-98. (doi: 10.1016/j.jprot.2016.12.009) (PMID:28040509)

2016

Weidt, S., Haggarty, J., Kean, R., Cojocariu, C. I., Silcock, P. J., Rajendran, R., Ramage, G. and Burgess, K. E. V. (2016) A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms. Metabolomics, 12, 189. (doi: 10.1007/s11306-016-1134-2) (PMID:28003796) (PMCID:PMC5097782)

Mudaliar, M. et al. (2016) Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics. Molecular BioSystems, 12(9), pp. 2748-2761. (doi: 10.1039/C6MB00290K) (PMID:27412694) (PMCID:PMC5048399)

Meek, S. et al. (2016) Reduced levels of dopamine and altered metabolism in brains of HPRT knock-out rats: a new rodent model of Lesch-Nyhan Disease. Scientific Reports, 6, 25592. (doi: 10.1038/srep25592) (PMID:27185277) (PMCID:PMC4869022)

2015

Haggarty, J., Oppermann, M., Dalby, M. J. , Burchmore, R. J. , Cook, K., Weidt, S. and Burgess, K. E.V. (2015) Serially coupling hydrophobic interaction and reversed-phase chromatography with simultaneous gradients provides greater coverage of the metabolome. Metabolomics, 11(5), pp. 1465-1470. (doi: 10.1007/s11306-014-0770-7) (PMID:26366140) (PMCID:PMC4559102)

Creek, D. J. et al. (2015) Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose. PLoS Pathogens, 11(3), e1004689. (doi: 10.1371/journal.ppat.1004689) (PMID:25775470) (PMCID:PMC4361558)

2014

Vincent, I. M. , Weidt, S., Rivas, L., Burgess, K., Smith, T. K. and Ouellette, M. (2014) Untargeted metabolomic analysis of miltefosine action in Leishmania infantum reveals changes to the internal lipid metabolism. International Journal for Parasitology: Drugs and Drug Resistance, 4(1), pp. 20-27. (doi: 10.1016/j.ijpddr.2013.11.002) (PMID:24596665) (PMCID:PMC3940234)

Burgess, K., Rankin, N. and Weidt, S. (2014) Metabolomics. In: Padmanabhan, S. (ed.) Handbook of Pharmacogenomics and Stratified Medicine. Academic Press: London, pp. 181-205. ISBN 9780123868824 (doi: 10.1016/B978-0-12-386882-4.00010-4)

Articles

Huang, Y., Jonsson, N. N. , McLaughlin, M. , Burchmore, R. , Johnson, P. C.D. , Jones, R. , McGill, S., Brady, N., Weidt, S. and Eckersall, D. (2023) Quantitative TMT-based proteomics revealing host, dietary and microbial proteins in bovine faeces including barley serpin Z4, a prominent component in the head of beer. Journal of Proteomics, 285, 104941. (doi: 10.1016/j.jprot.2023.104941) (PMID:37285906)

McBride, R., Wandy, J. , Weidt, S., Rogers, S. , Davies, V. , Daly, R. and Bryson, K. (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)

Wandy, J. , Mcbride, R., Rogers, S. , Terzis, N., Weidt, S., van der Hooft, J. J.J. , Bryson, K. , Daly, R. and Davies, V. (2023) Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics. Frontiers in Molecular Biosciences, 10, 1130781. (doi: 10.3389/fmolb.2023.1130781) (PMID:36959982) (PMCID:PMC10027714)

Nguyen, T. X. et al. (2023) Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed part I: serum proteomes. Journal of Proteomics, 270, 104740. (doi: 10.1016/j.jprot.2022.104740) (PMID:36191802)

Nguyen, T. X., Agazzo, A., McGill, S., Weidt, S., Han, Q. H., Gelemanović, A., McLaughlin, M. , Savoini, G., Eckersall, P. D. and Burchmore, R. (2023) Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed part II: ileum proteomes. Journal of Proteomics, 270, 104739. (doi: 10.1016/j.jprot.2022.104739) (PMID:36174954)

Alpizar-Sosa, E. A. et al. (2022) Amphotericin B resistance in Leishmania mexicana: Alterations to sterol metabolism and oxidative stress response. PLoS Neglected Tropical Diseases, 16(9), e0010779. (doi: 10.1371/journal.pntd.0010779) (PMID:36170238) (PMCID:PMC9581426)

Nguyen, T. X. et al. (2022) Abundance of plasma proteins in response to divergent ratios of dietary ω6:ω3 fatty acids in gestating and lactating sows using a quantitative proteomics approach. Journal of Proteomics, 260, 104562. (doi: 10.1016/j.jprot.2022.104562) (PMID:35314360)

Wandy, J. , Davies, V. , McBride, R., Weidt, S., Rogers, S. and Daly, R. (2022) ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics. Journal of Open Source Software, 7(71), 3990. (doi: 10.21105/joss.03990)

Meewan, J. et al. (2022) Limited impact of the protein corona on the cellular uptake of PEGylated zein micelles by melanoma cancer cells. Pharmaceutics, 14(2), e439. (doi: 10.3390/pharmaceutics14020439) (PMID:35214171) (PMCID:PMC8877401)

Rubić, I. et al. (2022) Multi platforms strategies and metabolomics approaches for the investigation of comprehensive metabolite profile in dogs with Babesia canis infection. International Journal of Molecular Sciences, 23(3), 1575. (doi: 10.3390/ijms23031575) (PMID:35163517) (PMCID:PMC8835742)

Davies, V. , Wandy, J. , Weidt, S., van der Hooft, J. J.J. , Miller, A. , Daly, R. and Rogers, S. (2021) Rapid development of improved data-dependent acquisition strategies. Analytical Chemistry, 93(14), pp. 5676-5683. (doi: 10.1021/acs.analchem.0c03895) (PMID:33784814) (PMCID:PMC8047769)

Pesko, B. K., Weidt, S., McLaughlin, M. , Wescott, D. J., Torrance, H., Burgess, K. and Burchmore, R. (2020) Post-mortomics: the potential of untargeted metabolomics to highlight markers for time since death. OMICS: A Journal of Integrative Biology, 24(11), pp. 649-659. (doi: 10.1089/omi.2020.0084) (PMID:33095683)

Burgon, J. D. , Vieites, D. R., Jacobs, A. , Weidt, S. K., Gunter, H. M., Steinfartz, S., Burgess, K., Marble, B. K. and Elmer, K. R. (2020) Functional colour genes and signals of selection in colour polymorphic salamanders. Molecular Ecology, 29(7), pp. 1284-1299. (doi: 10.1111/mec.15411) (PMID:32159878)

Wandy, J. , Davies, V. , van der Hooft, J. J.J. , Weidt, S., Daly, R. and Rogers, S. (2019) In silico optimization of mass spectrometry fragmentation strategies in metabolomics. Metabolites, 9(10), 219. (doi: 10.3390/metabo9100219) (PMID:31600991)

Rankin, N. J. , Burgess, K., Weidt, S., Wannamethee, G., Sattar, N. and Welsh, P. (2019) High-throughput quantification of carboxymethyl lysine in serum and plasma using high-resolution accurate mass Orbitrap mass spectrometry. Annals of Clinical Biochemistry, 56(3), pp. 397-407. (doi: 10.1177/0004563219830432) (PMID:30832481) (PMCID:PMC6498755)

Pountain, A. W. , Weidt, S. K., Regnault, C., Bates, P. A., Donachie, A. M., Dickens, N. J. and Barrett, M. P. (2019) Genomic instability at the locus of sterol C24-methyltransferase promotes amphotericin B resistance in Leishmania parasites. PLoS Neglected Tropical Diseases, 13(2), e0007052. (doi: 10.1371/journal.pntd.0007052) (PMID:30716073) (PMCID:PMC6375703)

Kovarova, J., Pountain, A. W. , Wildridge, D., Weidt, S., Bringaud, F., Burchmore, R. J.S. , Achcar, F. and Barrett, M. P. (2018) Deletion of transketolase triggers a stringent metabolic response in promastigotes and loss of virulence in amastigotes of Leishmania mexicana. PLoS Pathogens, 14(3), e1006953. (doi: 10.1371/journal.ppat.1006953) (PMID:29554142) (PMCID:PMC5882173)

Mwenechanya, R. et al. (2017) Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana. PLoS Neglected Tropical Diseases, 11(6), e0005649. (doi: 10.1371/journal.pntd.0005649) (PMID:28622334) (PMCID:PMC5498063)

Akpunarlieva, S., Weidt, S., Lamasudin, D., Naula, C. , Henderson, D., Barrett, M. , Burgess, K. and Burchmore, R. (2017) Integration of proteomics and metabolomics to elucidate metabolic adaptation in Leishmania. Journal of Proteomics, 155, pp. 85-98. (doi: 10.1016/j.jprot.2016.12.009) (PMID:28040509)

Weidt, S., Haggarty, J., Kean, R., Cojocariu, C. I., Silcock, P. J., Rajendran, R., Ramage, G. and Burgess, K. E. V. (2016) A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms. Metabolomics, 12, 189. (doi: 10.1007/s11306-016-1134-2) (PMID:28003796) (PMCID:PMC5097782)

Mudaliar, M. et al. (2016) Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics. Molecular BioSystems, 12(9), pp. 2748-2761. (doi: 10.1039/C6MB00290K) (PMID:27412694) (PMCID:PMC5048399)

Meek, S. et al. (2016) Reduced levels of dopamine and altered metabolism in brains of HPRT knock-out rats: a new rodent model of Lesch-Nyhan Disease. Scientific Reports, 6, 25592. (doi: 10.1038/srep25592) (PMID:27185277) (PMCID:PMC4869022)

Haggarty, J., Oppermann, M., Dalby, M. J. , Burchmore, R. J. , Cook, K., Weidt, S. and Burgess, K. E.V. (2015) Serially coupling hydrophobic interaction and reversed-phase chromatography with simultaneous gradients provides greater coverage of the metabolome. Metabolomics, 11(5), pp. 1465-1470. (doi: 10.1007/s11306-014-0770-7) (PMID:26366140) (PMCID:PMC4559102)

Creek, D. J. et al. (2015) Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose. PLoS Pathogens, 11(3), e1004689. (doi: 10.1371/journal.ppat.1004689) (PMID:25775470) (PMCID:PMC4361558)

Vincent, I. M. , Weidt, S., Rivas, L., Burgess, K., Smith, T. K. and Ouellette, M. (2014) Untargeted metabolomic analysis of miltefosine action in Leishmania infantum reveals changes to the internal lipid metabolism. International Journal for Parasitology: Drugs and Drug Resistance, 4(1), pp. 20-27. (doi: 10.1016/j.ijpddr.2013.11.002) (PMID:24596665) (PMCID:PMC3940234)

Book Sections

Burgess, K., Rankin, N. and Weidt, S. (2014) Metabolomics. In: Padmanabhan, S. (ed.) Handbook of Pharmacogenomics and Stratified Medicine. Academic Press: London, pp. 181-205. ISBN 9780123868824 (doi: 10.1016/B978-0-12-386882-4.00010-4)