Research output per year
Research output per year
Personal profile
Current Research Interests
Biomolecular Mass Spectrometry, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), Top-Down Mass Spectrometry, Protein Chemistry, Enzymology, Structural Biology.
Biography
The core research theme of our group is the application of modern techniques in mass spectrometry (MS) for the functional and structural characterisation of biological systems. The School of Chemistry houses an excellent array of MS instrumentation - including FT-ICR, an ion mobility equipped Q-Tof, an extended mass range ESI Q-tof, and a MALDI ToF-ToF.
Our research utilises a range of MS-based techniques including - top-down and middle down fragmentation, ion-mobility mass spectrometry, native mass spectrometry, and hydrogen/deuterium exchange. In addition, MS-based studies are supported by complementary biochemical analysis and structural biology approaches.
Websites
www.clarkelab.co.uk
Qualifications
MChem, PhD
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Probing TDP-43 condensation using an in silico designed aptamer
Zacco, E., Kantelberg, O., Milanetti, E., Armaos, A., Panei, F. P., Gregory, J., Jeacock, K., Clarke, D. J., Chandran, S., Ruocco, G., Gustincich, S., Horrocks, M. H., Pastore, A. & Tartaglia, G. G., 23 Jun 2022, (E-pub ahead of print) In: Nature Communications. 13, 1, p. 3306Research output: Contribution to journal › Article › peer-review
Open AccessFile -
Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment
Ross, J., McIver, Z., Lambert, T., Piergentili, C., Bird, J. E., Gallagher, K. J., Cruickshank, F. L., James, P., Zarazúa-Arvizu, E., Horsfall, L. E., Waldron, K. J., Wilson, M. D., Logan Mackay, C., Baslé, A., Clarke, D. J. & Marles-Wright, J., 26 Jan 2022, (E-pub ahead of print) In: Science Advances. 8, 4, eabj4461.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
A native mass spectrometry platform identifies HOP inhibitors that modulate the HSP90–HOP protein–protein interaction
Veale, C. G. L., Mateos-jiménez, M., Vaaltyn, M. C., Müller, R., Makhubu, M. P., Alhassan, M., De La Torre, B. G., Albericio, F., Mackay, C. L., Edkins, A. L. & Clarke, D. J., 27 Sep 2021, (E-pub ahead of print) In: Chemical Communications.Research output: Contribution to journal › Article › peer-review
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Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins
Piergentili, C., Ross, J., He, D., Gallagher, K. J., Stanley, W. A., Adam, L., Mackay, C. L., Baslé, A., Waldron, K. J., Clarke, D. J. & Marles-Wright, J., 2 Sep 2020, (E-pub ahead of print) In: Journal of Biological Chemistry.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
Mass spectrometry reveals the assembly pathway of encapsulated ferritins and highlights a dynamic ferroxidase interface
Ross, J., Lambert, T., Piergentili, C., He, D., Waldron, K. J., Mackay, C. L., Marles-wright, J. & Clarke, D. J., 13 Feb 2020, (E-pub ahead of print) In: Chemical Communications.Research output: Contribution to journal › Article › peer-review
Open AccessFile
Activities
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Chemical Science (Journal)
David Clarke (Peer reviewer)
2 Apr 2019Activity: Publication peer-review and editorial work types › Publication peer-review
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Invited Talk
David Clarke (Assessor)
12 Feb 2019 → 14 Feb 2019Activity: Academic talk or presentation types › Oral presentation
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Analytical Chemistry (Journal)
David Clarke (Peer reviewer)
14 Mar 2019Activity: Publication peer-review and editorial work types › Publication peer-review
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Analyst (Journal)
David Clarke (Peer reviewer)
6 Aug 2018Activity: Publication peer-review and editorial work types › Publication peer-review
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Isotope Depletion Mass Spectrometry for Improved Top-Down Fragmentation
David Clarke (Assessor)
17 Jul 2018Activity: Academic talk or presentation types › Invited talk
Projects
- 11 Finished
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Native Mass Spectrometry analysis of the P2X7 membrane protein complex
Menzies, R. & Clarke, D.
1/01/17 → 31/12/17
Project: University Awarded Project Funding
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Engineering a novel industrial bio-transformation pathway for surfactant manufacture
1/10/16 → 1/11/17
Project: Research
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Inhibiting the HOP-Hsp90 interaction through fragment based drug discovery
1/09/16 → 30/09/19
Project: Research
Datasets
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Native MS Analysis of Encapsulated Ferritin from Rhodospirillum rubrum
Clarke, D. (Creator), University of Edinburgh, 22 Jul 2016
DOI: 10.7488/ds/1449
Dataset
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Optimization of sprayer for matrix application in MALDI mass spectrometry imaging
Tucker, L. (Creator) & Clarke, D. (Depositor), Edinburgh DataShare, 6 Feb 2018
DOI: 10.7488/ds/2300
Dataset
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Untargeted Metabolite Mapping in 3D Cell Culture Models using High Spectral Resolution FT-ICR Mass Spectrometry Imaging - Datasets
Clarke, D. (Creator) & Tucker, L. (Creator), Edinburgh DataShare, 29 Jan 2019
DOI: 10.7488/ds/2490
Dataset
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Native MS Analysis of Encapsulated Ferritins from Rhodospirillum rubrum, Haliangium ochraceum and Pyrococcus furiosus
Ross, J. (Creator), Marles-Wright, J. (Creator) & Clarke, D. (Creator), Edinburgh DataShare, 21 Sep 2018
DOI: 10.7488/ds/2443
Dataset
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The Implementation and Impact of Isotope Depletion for Improved Protein Mass Spectrometry.
Mackay, C. L. (Creator), Syka, J. (Creator), Clarke, D. (Creator), Kilgour, D. (Creator), Gallagher, K. (Creator) & Ross, J. (Creator), Edinburgh DataShare, 19 Aug 2020
DOI: 10.7488/ds/2902
Dataset