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Article ; Online: Enhancing Biomolecule Analysis and 2DMS Experiments by Implementation of (Activated Ion) 193 nm UVPD on a FT-ICR Mass Spectrometer.

Theisen, Alina / Wootton, Christopher A / Haris, Anisha / Morgan, Tomos E / Lam, Yuko P Y / Barrow, Mark P / O'Connor, Peter B

Analytical chemistry

2022 Volume 94, Issue 45, Page(s) 15631–15638

Abstract: Ultraviolet photodissociation is a fast, photon-mediated fragmentation method that yields high sequence coverage and informative cleavages of biomolecules. In this work, 193 nm UVPD was coupled with a 12 Tesla FT-ICR mass spectrometer and 10.6 μm ... ...

Abstract	Ultraviolet photodissociation is a fast, photon-mediated fragmentation method that yields high sequence coverage and informative cleavages of biomolecules. In this work, 193 nm UVPD was coupled with a 12 Tesla FT-ICR mass spectrometer and 10.6 μm infrared multi-photon dissociation to provide gentle slow-heating of UV-irradiated ions. No internal instrument hardware modifications were required. Adjusting the timing of laser pulses to the ion motion within the ICR cell provided consistent fragmentation yield shot-to-shot and may also be used to monitor ion positions within the ICR cell. Single-pulse UVPD of the native-like 5+ charge state of ubiquitin resulted in 86.6% cleavage coverage. Additionally, IR activation post UVPD doubled the overall fragmentation yield and boosted the intensity of UVPD-specific x-type fragments up to 4-fold. This increased yield effect was also observed for the 6+ charge state of ubiquitin, albeit less pronounced. This indicates that gentle slow-heating serves to sever tethered fragments originating from non-covalently linked compact structures and makes activation post UVPD an attractive option to boost fragmentation efficiency for top-down studies. Lastly, UVPD was implemented and optimized as a fragmentation method for 2DMS, a data-independent acquisition method. UVPD-2DMS was demonstrated to be a viable method using BSA digest peptides as a model system.
MeSH term(s)	Tandem Mass Spectrometry/methods ; Ultraviolet Rays ; Ions ; Peptides ; Ubiquitin
Chemical Substances	Ions ; Peptides ; Ubiquitin
Language	English
Publishing date	2022-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c02354
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Article ; Online: Differentiation of Dihydroxylated Vitamin D

Haris, Anisha / Lam, Yuko P Y / Wootton, Christopher A / Theisen, Alina / Marzullo, Bryan P / Schorr, Pascal / Volmer, Dietrich A / O'Connor, Peter B

Journal of the American Society for Mass Spectrometry

2022 Volume 33, Issue 6, Page(s) 1022–1030

Abstract: Vitamin D compounds are a group of secosteroids derived from cholesterol that are vital for maintaining bone health in humans. Recent studies have shown extraskeletal effects of vitamin D, involving vitamin D metabolites such as the dihydroxylated ... ...

Abstract	Vitamin D compounds are a group of secosteroids derived from cholesterol that are vital for maintaining bone health in humans. Recent studies have shown extraskeletal effects of vitamin D, involving vitamin D metabolites such as the dihydroxylated vitamin D
MeSH term(s)	Cholecalciferol ; Chromatography, Liquid/methods ; Cyclotrons ; Humans ; Tandem Mass Spectrometry/methods ; Vitamin D ; Vitamins
Chemical Substances	Vitamins ; Vitamin D (1406-16-2) ; Cholecalciferol (1C6V77QF41)
Language	English
Publishing date	2022-05-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.2c00085
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Zs.MO 241: Show issues

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Article ; Online: Does deamidation affect inhibitory mechanisms towards amyloid protein aggregation?

Lam, Yuko P Y / Chiu, Cookson K C / Wootton, Christopher A / Hands-Portman, Ian / Li, Meng / Barrow, Mark P / O'Connor, Peter B

Chemical communications (Cambridge, England)

2020 Volume 56, Issue 68, Page(s) 9787–9790

Abstract: Deamidated amyloid proteins have been shown to accelerate fibril formation. Herein, the results show the inhibition performance and the interaction site between site-specific inhibitor and amyloid protein are significantly influenced by deamidation; ... ...

Abstract	Deamidated amyloid proteins have been shown to accelerate fibril formation. Herein, the results show the inhibition performance and the interaction site between site-specific inhibitor and amyloid protein are significantly influenced by deamidation; while the inhibition mechanism of non-site specific inhibitor shows no significant disruption caused by amyloid protein deamidation.
MeSH term(s)	Amino Acid Sequence ; Amyloid/chemistry ; Amyloid/metabolism ; Catechin/analogs & derivatives ; Catechin/chemistry ; Catechin/metabolism ; Catechin/pharmacology ; Humans ; Islet Amyloid Polypeptide/chemistry ; Islet Amyloid Polypeptide/metabolism ; Microscopy, Electron, Transmission ; Protein Aggregates/drug effects ; Spectrometry, Fluorescence
Chemical Substances	Amyloid ; Islet Amyloid Polypeptide ; Protein Aggregates ; Catechin (8R1V1STN48) ; epigallocatechin gallate (BQM438CTEL)
Language	English
Publishing date	2020-08-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d0cc03548c
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Article ; Online: Metallocomplex-Peptide Interactions Studied by Ultrahigh Resolution Mass Spectrometry.

Chiu, Cookson K C / Lam, Yuko P Y / Wootton, Christopher A / Barrow, Mark P / Sadler, Peter J / O'Connor, Peter B

Journal of the American Society for Mass Spectrometry

2020 Volume 31, Issue 3, Page(s) 594–601

Abstract: ... The ... ...

Abstract	The Os
MeSH term(s)	Amino Acid Sequence ; Animals ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/metabolism ; Binding Sites ; Cattle ; Coordination Complexes/chemistry ; Coordination Complexes/metabolism ; Models, Molecular ; Osmium/chemistry ; Osmium/metabolism ; Peptides/chemistry ; Peptides/metabolism ; Protein Binding ; Serum Albumin, Bovine/chemistry ; Serum Albumin, Bovine/metabolism ; Tandem Mass Spectrometry/methods
Chemical Substances	Antineoplastic Agents ; Coordination Complexes ; Peptides ; Serum Albumin, Bovine (27432CM55Q) ; Osmium (2E7M255OPY)
Language	English
Publishing date	2020-02-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.9b00054
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Zs.MO 241: Show issues

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Article: Does deamidation affect inhibitory mechanisms towards amyloid protein aggregation?

Lam, Yuko P. Y. / Chiu, Cookson K. C. / Wootton, Christopher A. / Hands-Portman, Ian / Li, Meng / Barrow, Mark P. / O'Connor, Peter B.

Chemical communications. 2020 Aug. 25, v. 56, no. 68

2020

Abstract	Deamidated amyloid proteins have been shown to accelerate fibril formation. Herein, the results show the inhibition performance and the interaction site between site-specific inhibitor and amyloid protein are significantly influenced by deamidation; while the inhibition mechanism of non-site specific inhibitor shows no significant disruption caused by amyloid protein deamidation.
Keywords	amyloid ; chemical communication ; deamidation
Language	English
Dates of publication	2020-0825
Size	p. 9787-9790.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d0cc03548c
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Article ; Online: Two-dimensional mass spectrometry: new perspectives for tandem mass spectrometry.

van Agthoven, Maria A / Lam, Yuko P Y / O'Connor, Peter B / Rolando, Christian / Delsuc, Marc-André

European biophysics journal : EBJ

2019 Volume 48, Issue 3, Page(s) 213–229

Abstract: Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex ...

Abstract	Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion-neutral, ion-electron, or ion-photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation. Two-dimensional mass spectrometry (2D MS) offers a method to correlate precursor and fragment ions without requiring precursor isolation. 2D MS therefore enables easy access to the fragmentation patterns of all compounds from complex samples. In this article, the principles of FT-ICR MS are reviewed and the 2D MS experiment is explained. Data processing for 2D MS is detailed, and the interpretation of 2D mass spectra is described.
MeSH term(s)	Cyclotrons ; Fourier Analysis ; Tandem Mass Spectrometry/instrumentation ; Tandem Mass Spectrometry/methods
Language	English
Publishing date	2019-03-13
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	283671-3
ISSN	1432-1017 ; 0175-7571
ISSN (online)	1432-1017
ISSN	0175-7571
DOI	10.1007/s00249-019-01348-5
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Zs.A 1121: Show issues

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Article ; Online: Determination of the Aggregate Binding Site of Amyloid Protofibrils Using Electron Capture Dissociation Tandem Mass Spectrometry.

Lam, Yuko P Y / Wootton, Christopher A / Hands-Portman, Ian / Wei, Juan / Chiu, Cookson K C / Romero-Canelon, I / Lermyte, Frederik / Barrow, Mark P / O'Connor, Peter B

Journal of the American Society for Mass Spectrometry

2020 Volume 31, Issue 2, Page(s) 267–276

Abstract: Amyloid fibril formation is a hallmark in a range of human diseases. Analysis of the molecular details of amyloid aggregation, however, is limited by the difficulties in solubilizing, separating, and identifying the aggregated biomolecules. Additional ... ...

Abstract	Amyloid fibril formation is a hallmark in a range of human diseases. Analysis of the molecular details of amyloid aggregation, however, is limited by the difficulties in solubilizing, separating, and identifying the aggregated biomolecules. Additional labeling or protein modification is required in many current analytical techniques in order to provide molecular details of amyloid protein aggregation, but these modifications may result in protein structure disruption. Herein, ultrahigh resolution mass spectrometry (MS) with electron capture dissociation tandem MS (ECD MS/MS) has been applied to monitor the formation of early oligomers of human islet amyloid polypeptide (hIAPP), which aggregate rapidly in the pancreas of type II diabetes (T2D) patients. ECD MS/MS results show the aggregation region of the early oligomers is at the Ser-28/Ser-29 residue of a hIAPP unit and at the Asn-35 residue of another hIAPP unit near the C-terminus in the gas phase. These data contribute to the understanding of the binding site between hIAPP units which may help for specific target region therapeutic development in the future. Furthermore, MS has also been applied to quantify the amount of soluble amyloid protein remaining in the incubated solutions, which can be used to estimate the aggregation rate of amyloid protein during incubation (28 days). These data are further correlated with the results obtained using fluorescence spectroscopy and transmission electron microscopy (TEM) to generate a general overview of amyloid protein aggregation. The methods demonstrated in this article not only explore the aggregation site of hIAPP down to an amino acid residue level, but are also applicable to many amyloid protein aggregation studies.
MeSH term(s)	Amyloid/chemistry ; Amyloid/ultrastructure ; Binding Sites/physiology ; Humans ; Islet Amyloid Polypeptide/chemistry ; Islet Amyloid Polypeptide/ultrastructure ; Models, Molecular ; Protein Multimerization ; Solubility ; Tandem Mass Spectrometry/methods
Chemical Substances	Amyloid ; Islet Amyloid Polypeptide
Language	English
Publishing date	2020-01-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.9b00053
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Zs.MO 241: Show issues

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Article ; Online: Automatic assignment of metal-containing peptides in proteomic LC-MS and MS/MS data sets.

Wootton, Christopher A / Lam, Yuko P Y / Willetts, Matthew / van Agthoven, Maria A / Barrow, Mark P / Sadler, Peter J / O Connor, Peter B

The Analyst

2017 Volume 142, Issue 11, Page(s) 2029–2037

Abstract: Transition metal-containing proteins and enzymes are critical for the maintenance of cellular function and metal-based (metallo)drugs are commonly used for the treatment of many diseases, such as cancer. Detection and characterisation of metallodrug ... ...

Abstract	Transition metal-containing proteins and enzymes are critical for the maintenance of cellular function and metal-based (metallo)drugs are commonly used for the treatment of many diseases, such as cancer. Detection and characterisation of metallodrug targets is crucial for improving drug-design and therapeutic efficacy. Due to the unique isotopic ratios of many metal species, and the complexity of proteomic samples, standard MS data analysis of these species is unsuitable for accurate assignment. Herein a new method for differentiating metal-containing species within complex LCMS data is presented based upon the Smart Numerical Annotation Procedure (SNAP). SNAP-LC accounts for the change in isotopic envelopes for analytes containing non-standard species, such as metals, and will accurately identify, record, and display the particular spectra within extended LCMS runs that contain target species, and produce accurate lists of matched peaks, greatly assisting the identification and assignment of modified species and tailored to the metals of interest. Analysis of metallated species obtained from tryptic digests of common blood proteins after reactions with three candidate metallodrugs is presented as proof-of-concept examples and demonstrates the effectiveness of SNAP-LC for the fast and accurate elucidation of metallodrug targets.
MeSH term(s)	Chromatography, Liquid ; Metals/chemistry ; Peptides/chemistry ; Proteomics ; Tandem Mass Spectrometry
Chemical Substances	Metals ; Peptides
Language	English
Publishing date	2017-05-17
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/c7an00075h
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Zs.A 2423: Show issues

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Article ; Online: Metal Ion Binding to the Amyloid β Monomer Studied by Native Top-Down FTICR Mass Spectrometry.

Lermyte, Frederik / Everett, James / Lam, Yuko P Y / Wootton, Christopher A / Brooks, Jake / Barrow, Mark P / Telling, Neil D / Sadler, Peter J / O'Connor, Peter B / Collingwood, Joanna F

Journal of the American Society for Mass Spectrometry

2019 Volume 30, Issue 10, Page(s) 2123–2134

Abstract: Native top-down mass spectrometry is a fast, robust biophysical technique that can provide molecular-scale information on the interaction between proteins or peptides and ligands, including metal cations. Here we have analyzed complexes of the full- ... ...

Abstract	Native top-down mass spectrometry is a fast, robust biophysical technique that can provide molecular-scale information on the interaction between proteins or peptides and ligands, including metal cations. Here we have analyzed complexes of the full-length amyloid β (1-42) monomer with a range of (patho)physiologically relevant metal cations using native Fourier transform ion cyclotron resonance mass spectrometry and three different fragmentation methods-collision-induced dissociation, electron capture dissociation, and infrared multiphoton dissociation-all yielding consistent results. Amyloid β is of particular interest as its oligomerization and aggregation are major events in the etiology of Alzheimer's disease, and it is known that interactions between the peptide and bioavailable metal cations have the potential to significantly damage neurons. Those metals which exhibited the strongest binding to the peptide (Cu
MeSH term(s)	Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/metabolism ; Humans ; Mass Spectrometry/methods ; Metals/chemistry ; Metals/metabolism ; Protein Binding ; Spectroscopy, Fourier Transform Infrared
Chemical Substances	Amyloid beta-Peptides ; Metals
Language	English
Publishing date	2019-07-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1007/s13361-019-02283-7
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Zs.MO 241: Show issues

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Article ; Online: Discovery of novel, potent, isosteviol-based antithrombotic agents.

Chen, Peng / Zhang, Dianwen / Li, Meng / Wu, Qiong / Lam, Yuko P Y / Guo, Yan / Chen, Chen / Bai, Nan / Malhotra, Shipra / Li, Wei / O'Connor, Peter B / Fu, Hongzheng

European journal of medicinal chemistry

2019 Volume 183, Page(s) 111722

Abstract: Thrombosis is a pathological coagulation process and can lead to many serious thrombotic diseases. Here, we report a novel potent antithrombotic compound (6k) based on isosteviol with anticoagulant and antiplatelet activities. 6k selectively inhibited ... ...

Abstract	Thrombosis is a pathological coagulation process and can lead to many serious thrombotic diseases. Here, we report a novel potent antithrombotic compound (6k) based on isosteviol with anticoagulant and antiplatelet activities. 6k selectively inhibited FXa (K
MeSH term(s)	Animals ; Diterpenes, Kaurane/chemistry ; Diterpenes, Kaurane/pharmacology ; Drug Discovery ; Factor Xa Inhibitors/chemistry ; Factor Xa Inhibitors/pharmacology ; Female ; Fibrinolytic Agents/chemistry ; Fibrinolytic Agents/pharmacology ; Humans ; Male ; Partial Thromboplastin Time ; Platelet Aggregation/drug effects ; Platelet Aggregation Inhibitors/chemistry ; Platelet Aggregation Inhibitors/pharmacology ; Rats ; Rats, Wistar ; Thrombin/metabolism ; Thrombosis/drug therapy
Chemical Substances	Diterpenes, Kaurane ; Factor Xa Inhibitors ; Fibrinolytic Agents ; Platelet Aggregation Inhibitors ; isosteviol (091QB7QO95) ; Thrombin (EC 3.4.21.5)
Language	English
Publishing date	2019-09-19
Publishing country	France
Document type	Journal Article
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2019.111722
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