ORCID Profile
0000-0003-3188-1472
Current Organisations
Macquarie University Australian Proteome Analysis Facility
,
Acadia University
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Publisher: Wiley
Date: 04-05-2017
Publisher: Wiley
Date: 08-06-2017
Publisher: Springer Science and Business Media LLC
Date: 26-04-2022
Publisher: Springer Science and Business Media LLC
Date: 06-02-2008
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5AY00710K
Abstract: Extreme supercharging of proteins yields significant performance gains for the direct characterization of protein sequences by electron capture dissociation mass spectrometry.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4AN02338B
Abstract: High-performance solutions for supercharging proteins in electrospray ionization were optimized and the origin of the strong dependence of supercharging on acid strength was investigated.
Publisher: American Chemical Society (ACS)
Date: 27-02-2020
DOI: 10.26434/CHEMRXIV.11573337.V2
Abstract: Top-down proteomics by mass spectrometry (MS) involves the mass measurement of an intact protein followed by subsequent activation of the protein to generate product ions. Electron-based fragmentation methods like electron capture dissociation (ECD) and electron transfer dissociation (ETD) are widely used for these types of analysis, however these fragmentation methods can be inefficient due to the low energy electrons fragmenting the protein without the dissociation products that is no detection of fragments formed. Recently, electron ionization dissociation (EID), which utilizes higher energy electrons ( 20 eV) has been shown to be more efficient for top-down protein fragmentation compared to other electron-based dissociation methods. Here we demonstrate that the use of EID enhances protein fragmentation and subsequent detection of protein fragments. Protein product ions can form by either single cleavage events, resulting in terminal fragments containing the C-terminus or N-terminus of the protein, or by multiple cleavage events to give rise to internal fragments that do not contain the C-terminus or N-terminus of the protein. Conventionally, internal fragments have been disregarded as reliable assignments of these fragments were limited. Here, we demonstrate that internal fragments generated by EID can account for ~20-40% of the mass spectral signals detected by top-down EID-MS experiments. By including internal fragments, the extent of the protein sequence that can be explained from a single tandem mass spectrum increases from ~50% to ~99% for 29 kDa carbonic anhydrase II and 8.6 kDa ubiquitin. By including internal fragments in the data analysis, previously unassigned peaks can be readily and accurately assigned to enhance the efficiencies of top-down protein sequencing experiments.
Publisher: American Chemical Society (ACS)
Date: 13-01-2020
DOI: 10.26434/CHEMRXIV.11573337.V1
Abstract: Top-down proteomics by mass spectrometry (MS) involves the mass measurement of an intact protein followed by subsequent activation of the protein to generate product ions. Electron-based fragmentation methods like electron capture dissociation (ECD) and electron transfer dissociation (ETD) are widely used for these types of analysis, however these fragmentation methods can be inefficient due to the low energy electrons fragmenting the protein without the dissociation products that is no detection of fragments formed. Recently, electron ionization dissociation (EID), which utilizes higher energy electrons ( 20 eV) has been shown to be more efficient for top-down protein fragmentation compared to other electron-based dissociation methods. Here we demonstrate that the use of EID enhances protein fragmentation and subsequent detection of protein fragments. Protein product ions can form by either single cleavage events, resulting in terminal fragments containing the C-terminus or N-terminus of the protein, or by multiple cleavage events to give rise to internal fragments that do not contain the C-terminus or N-terminus of the protein. Conventionally, internal fragments have been disregarded as reliable assignments of these fragments were limited. Here, we demonstrate that internal fragments generated by EID can account for ~20-40% of the mass spectral signals detected by top-down EID-MS experiments. By including internal fragments, the extent of the protein sequence that can be explained from a single tandem mass spectrum increases from ~50% to ~99% for 29 kDa carbonic anhydrase II and 8.6 kDa ubiquitin. By including internal fragments in the data analysis, previously unassigned peaks can be readily and accurately assigned to enhance the efficiencies of top-down protein sequencing experiments.
Publisher: Elsevier BV
Date: 03-2018
Publisher: American Chemical Society (ACS)
Date: 15-04-2022
DOI: 10.26434/CHEMRXIV-2022-LVPTC
Abstract: Theta capillary nanoelectrospray ionization (θ-nanoESI) can be used to ‘supercharge’ protein ions directly from solution for detection by mass spectrometry (MS). In native top-down MS, the extent of protein charging is low. Given that ions with more charge fragment more readily, increasing charge can enhance the extent of sequence information obtained by top-down MS. For θ-nanoESI, dual-channelled nanoESI emitters are used to mix two solutions in low to sub-μs prior to MS. The mechanism for θ-nanoESI mixing has been reported to occur in the Taylor cone prior to ESI-droplet formation, or by the fusion of droplets formed from separate Taylor cones. Using θ-nanoESI-ion mobility-MS, native protein solutions were rapidly mixed with denaturing supercharging solutions to form protein ions in significantly higher charge states and with more elongated structures than those formed by pre-mixing the solutions prior to nanoESI-MS. If θ-nanoESI mixing occurred in the Taylor cone, then the extent of protein charging and unfolding should be comparable or less than that obtained by pre-mixing solutions. Thus, these data are consistent with mixing occurring via droplet fusion rather than in the Taylor cone prior to ESI droplet formation. The presence of supercharging additives in pre-mixed solutions can suppress volatile electrolyte evaporation, limiting the extent of protein charging compared to when the additive is delivered via one channel of a θ-nanoESI emitter. In θ-nanoESI, the formation of two Taylor cones can presumably result in substantial electrolyte evaporation from the ESI droplets containing native-like proteins prior to droplet fusion, thereby enhancing ion charging.
Publisher: Wiley
Date: 15-12-2021
DOI: 10.1002/PRO.4252
Abstract: The enzyme enoyl‐ACP reductase (also called FabI in bacteria) is an essential member of the fatty acid synthase II pathway in plants and bacteria. This enzyme is the target of the antibacterial drug triclosan and has been the subject of extensive studies for the past 20 years. Despite the large number of reports describing the biochemistry of this enzyme, there have been no studies that provided direct observation of the protein and its various ligands. Here we describe the use of native MS to characterize the protein–ligand interactions of FabI with its coenzymes NAD + and NADH and with the inhibitor triclosan. Measurements of the gas‐phase affinities of the enzyme for these ligands yielded values that are in close agreement with solution‐phase affinity measurements. Additionally, FabI is a homotetramer and we were able to measure the affinity of each subunit for each coenzyme, which revealed that both coenzymes exhibit a positive homotropic allosteric effect. An allosteric effect was also observed in association with the inhibitor triclosan. These observations provide new insights into this well‐studied enzyme and suggest that there may still be gaps in the existing mechanistic models that explain FabI inhibition.
Publisher: Elsevier BV
Date: 02-2022
Publisher: American Chemical Society (ACS)
Date: 19-07-2022
DOI: 10.26434/CHEMRXIV-2022-65K4H
Abstract: Disulfide bonds in proteins have a substantial impact on protein structure, stability, and biological activity. Localizing disulfide bonds is critical for understanding protein folding and higher-order structure. Conventional top-down mass spectrometry (TD-MS) where only terminal fragments are assigned, for disulfide intact proteins can access disulfide information, but suffers from low fragmentation efficiency, limiting sequence coverage. Here, we show that assigning internal fragments generated from TD-MS enhances the sequence coverage of disulfide intact proteins by 20-60% by returning information from the interior of the protein sequence, which cannot be obtained by terminal fragments alone. The inclusion of internal fragments can extend the sequence information of disulfide intact proteins to near complete sequence coverage. Importantly, the enhanced sequence information that arise from the assignment of internal fragments can be used to determine the relative position of disulfide bonds and the exact disulfide connectivity between cysteines. The data presented here demonstrates the benefits of incorporating internal fragment analysis into TD-MS workflow for analyzing disulfide intact proteins, which would be valuable for characterizing biotherapeutic proteins such as monoclonal antibodies and antibody-drug conjugates.
Publisher: Wiley
Date: 17-12-2020
DOI: 10.1002/LIPD.12286
Publisher: American Chemical Society (ACS)
Date: 12-04-2017
DOI: 10.1021/ACS.ANALCHEM.7B00673
Abstract: Supercharging electrospray ionization can be a powerful tool for increasing charge states in mass spectra and generating unfolded ion structures, yet key details of its mechanism remain unclear. The structures of highly extended protein ions and the mechanism of supercharging were investigated using ion mobility-mass spectrometry. Head-to-tail-linked polyubiquitins (Ubq
Publisher: American Chemical Society (ACS)
Date: 02-03-2021
Publisher: Wiley
Date: 08-06-2017
Publisher: American Chemical Society (ACS)
Date: 08-12-2021
Publisher: American Chemical Society (ACS)
Date: 08-06-2021
Publisher: Netherlands Ornithologists' Union
Date: 03-2010
DOI: 10.5253/078.098.0106
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.ACA.2017.11.075
Abstract: Theta nanoelectrospray ionization of protein ions formed from aqueous buffer solutions that are mixed with denaturing solutions containing cyclic alkylcarbonates (e.g., vinyl ethylene carbonate VEC) results in a significant increase in the extent of ion charging compared to native mass spectrometry. For six proteins, the extent of ion charging can be significantly higher than that obtained using denaturing solutions and alternative native "supercharging" methods. In theta nanoelectrospray supercharging, the extent of charging scales with protein mass in agreement with an analytical scaling relationship for ions with elongated structures. Theta nanoelectrospray supercharging of non-covalent complexes from native solutions results in essentially the complete loss of protein-ligand and protein-protein interactions. Based on circular dichroism spectroscopy, VEC can effectively denature proteins in buffered solutions. These data provide evidence that enrichment of VEC in theta nanoelectrospray ionization generated droplets can denature proteins on the timescale of droplet desolvation and ion formation. This approach can be used to form highly charged protein ions from native solutions containing biological buffers, including some that are considered incompatible with native MS. Forming some protein ions in the highest reported charge states directly from native solutions is no longer a challenge in obtaining primary structural information using tandem mass spectrometry.
Publisher: Royal Society of Chemistry
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 29-07-2021
DOI: 10.1038/S42003-021-02415-4
Abstract: The factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with erse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin ( Fratercula arctica ) by assembling its reference genome and analyzing genome-wide resequencing data of 72 in iduals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.
Publisher: American Chemical Society (ACS)
Date: 16-09-2022
DOI: 10.1021/ACS.ANALCHEM.2C01654
Abstract: Theta capillary nanoelectrospray ionization (θ-nanoESI) can be used to "supercharge" protein ions directly from solution for detection by mass spectrometry (MS). In native top-down MS, the extent of protein charging is low. Given that ions with more charge fragment more readily, increasing charge can enhance the extent of sequence information obtained by top-down MS. For θ-nanoESI, dual-channeled nanoESI emitters are used to mix two solutions in low to sub-μs prior to MS. The mechanism for θ-nanoESI mixing has been reported to primarily occur: (i) in a single shared Taylor cone and in the droplets formed from the Taylor cone or (ii) by the fusion of droplets formed from two separate Taylor cones. Using θ-nanoESI-ion mobility MS, native protein solutions were rapidly mixed with denaturing supercharging solutions to form protein ions in significantly higher charge states and with more elongated structures than those formed by premixing the solutions prior to nanoESI-MS. If θ-nanoESI mixing occurred in the Taylor cone and in the droplets resulting from the single Taylor cone, then the extent of protein charging and unfolding should be comparable to or less than that obtained by premixing solutions. Thus, these data are consistent with mixing occurring via droplet fusion rather than in the Taylor cone prior to ESI droplet formation. These data also suggest that highly charged protein ions can be formed by the near-complete mixing of each solution. The presence of supercharging additives in premixed solutions can suppress volatile electrolyte evaporation, limiting the extent of protein charging compared to when the additive is delivered via one channel of a θ-nanoESI emitter. In θ-nanoESI, the formation of two Taylor cones can presumably result in substantial electrolyte evaporation from the ESI droplets containing native-like proteins prior to droplet fusion, thereby enhancing ion charging.
Publisher: Cold Spring Harbor Laboratory
Date: 31-12-2016
DOI: 10.1101/2019.12.30.891283
Abstract: The enzyme enoyl-ACP reductase (also called FabI in bacteria) is an essential member of the fatty acid synthase II pathway in plants and bacteria. This enzyme is the target of the antibacterial drug triclosan and has been the subject of extensive studies for the past 20 years. Despite the large number of reports describing the biochemistry of this enzyme, there have been no studies that provided direct observation of the protein and its various ligands. Here we describe the use of native MS to characterize the protein-ligand interactions of FabI with its coenzymes NAD + and NADH and with the inhibitor triclosan. Measurements of the gas-phase affinities of the enzyme for these ligands yielded values that are in close agreement with solution-phase affinity measurements. Additionally, FabI is a homotetramer and we were able to measure the affinity of each subunit for each coenzyme, which revealed that both coenzymes exhibit a positive homotropic allosteric effect. An allosteric effect was also observed in association with the inhibitor triclosan. These observations provide new insights into this well-studied enzyme and suggest that there may still be gaps in the existing mechanistic models that explain FabI inhibition.
Publisher: Wiley
Date: 04-05-2017
Abstract: The basicity of highly protonated cytochrome c (cyt c) and myoglobin (myo) ions were investigated using tandem mass spectrometry, ion-molecule reactions (IMRs), and theoretical calculations as a function of charge state. Surprisingly, highly charged protein ions (HCPI) can readily protonate non-polar molecules and inert gases, including Ar, O
Publisher: American Chemical Society (ACS)
Date: 03-08-2020
Publisher: American Chemical Society (ACS)
Date: 05-01-2021
DOI: 10.26434/CHEMRXIV.13518050
Abstract: Here we describe ClipsMS, an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation. Further, ClipsMS can be used to locate various modifications on the protein sequence. Using ClipsMS to assign TD-MS generated product ions, we demonstrate that for apo-myoglobin, the inclusion of internal fragments increases the sequence coverage up to 78%. Interestingly, many internal fragments cover complimentary regions to the terminal fragments that enhance the information that is extracted from a single top-down mass spectrum. Analysis of oxidized apo-myoglobin using terminal and internal fragment matching by ClipsMS confirmed the locations of oxidation sites on the two methionine residues. Internal fragments can be beneficial for top-down protein fragmentation analysis, and ClipsMS can be a valuable tool for assigning both terminal and internal fragments present in a top-down mass spectrum.
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D2AN01517J
Location: Australia
Location: United States of America
No related grants have been discovered for Muhammad Zenaidee.