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Rahman M, Marzullo B, Holman SW, Barrow M, Ray AD, O’Connor PB. Advancing PROTAC Characterization: Structural Insights through Adducts and Multimodal Tandem-MS Strategies. J Am Soc Mass Spectrom 2024; 35:285-299. [PMID: 38197777 PMCID: PMC10853971 DOI: 10.1021/jasms.3c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/11/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are specialized molecules that bind to a target protein and a ubiquitin ligase to facilitate protein degradation. Despite their significance, native PROTACs have not undergone tandem mass spectrometry (MS) analysis. To address this gap, we conducted a pioneering investigation on the fragmentation patterns of two PROTACs in development, dBET1 and VZ185. Employing diverse cations (sodium, lithium, and silver) and multiple tandem-MS techniques, we enhanced their structural characterization. Notably, lithium cations facilitated comprehensive positive-mode coverage for dBET1, while negative polarity mode offered richer insights. Employing de novo structure determination on 2DMS data from degradation studies yielded crucial insights. In the case of VZ185, various charge states were observed, with [M + 2H]2+ revealing fewer moieties than [M + H]+ due to charge-related factors. Augmenting structural details through silver adducts suggested both charge-directed and charge-remote fragmentation. This comprehensive investigation identifies frequently dissociated bonds across multiple fragmentation techniques, pinpointing optimal approaches for elucidating PROTAC structures. The findings contribute to advancing our understanding of PROTACs, pivotal for their continued development as promising therapeutic agents.
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Affiliation(s)
- Mohammed Rahman
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
- Department
of Physics, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Bryan Marzullo
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Stephen W. Holman
- Chemical
Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Mark Barrow
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Andrew D. Ray
- New
Modalities and Parenteral Development, Pharmaceutical Technology &
Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
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2
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Hannauer F, Black R, Ray AD, Stulz E, Langley GJ, Holman SW. Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022. Rapid Commun Mass Spectrom 2023; 37:e9596. [PMID: 37580500 PMCID: PMC10909466 DOI: 10.1002/rcm.9596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 08/16/2023]
Abstract
The fragmentation of oligonucleotides by mass spectrometry allows for the determination of their sequences. It is necessary to understand how oligonucleotides dissociate in the gas phase, which allows interpretation of data to obtain sequence information. Since 2014, a range of fragmentation mechanisms, including a novel internal rearrangement, have been proposed using different ion dissociation techniques. The recent publications have focused on the fragmentation of modified oligonucleotides such as locked nucleic acids, modified nucleobases (methylated, spacer, nebularine and aminopurine) and modification to the carbon 2'-position on the sugar ring; these modified oligonucleotides are of great interest as therapeutics. Comparisons of different dissociation techniques have been reported, including novel approaches such as plasma electron detachment dissociation and radical transfer dissociation. This review covers the period 2014-2022 and details the new knowledge gained with respect to oligonucleotide dissociation using tandem mass spectrometry (without priori sample digestion) during that time, with a specific focus on synthetic single-stranded oligonucleotides.
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Affiliation(s)
- Fabien Hannauer
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Rachelle Black
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Andrew D. Ray
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Eugen Stulz
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - G. John Langley
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Stephen W. Holman
- Chemical Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
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3
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Géhin C, O'Neill N, Moore A, Harrison M, Holman SW, Blom G. Dispersant-First Dispersive Liquid-Liquid Microextraction (DF-DLLME), a Novel Sample Preparation Procedure for NDMA Determination in Metformin Products. J Pharm Sci 2023; 112:2453-2462. [PMID: 37031864 DOI: 10.1016/j.xphs.2023.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/10/2023] [Accepted: 03/24/2023] [Indexed: 04/11/2023]
Abstract
Since December 2019, global batch recalls of metformin pharmaceutical products have highlighted an urgent need to control N-nitrosodimethylamine (NDMA) contamination to demonstrate patient safety and maintain supply of this essential medicine. Due to their formulation, the metformin extended-release products present difficult analytical challenges for conventional sample preparation procedures, such as artefactual (in-situ) NDMA formation, gelling, and precipitation. To overcome these challenges, a new version of dispersive liquid-liquid microextraction (DLLME) termed dispersant-first DLLME (DF-DLLME) was developed and optimized for the analysis of NDMA in metformin extended-release products using a detailed Design of Experiments (DoE) to optimize sample preparation. Gas chromatography-high resolution accurate mass-mass spectrometry (GC-HRAM-MS) combined with automated DF-DLLME were successfully applied to monitor the NDMA levels of two different metformin extended-release AstraZeneca products to ultra-trace levels (parts per billion). The additional benefits associated with DF-DLLME, which include automation, time/costs saving, and greener sample preparation, make this novel technique easier to transfer from a development to Quality Control (QC) environment. In addition, this also offers an attractive candidate for the wider platform analysis of N-nitrosamines in pharmaceutical drug products.
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Affiliation(s)
- Caroline Géhin
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Nicholas O'Neill
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Amy Moore
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Mark Harrison
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Giorgio Blom
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom.
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4
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Akhtar N, Ashford MB, Beer L, Bowes A, Bristow T, Broo A, Buttar D, Coombes S, Cross R, Eriksson E, Guilbaud JB, Holman SW, Hughes LP, Jackman M, Lawrence MJ, Lee J, Li W, Linke R, Mahmoudi N, McCormick M, MacMillan B, Newling B, Ngeny M, Patterson C, Poulton A, Ray A, Sanderson N, Sonzini S, Tang Y, Treacher KE, Whittaker D, Wren S. The Global Characterisation of a Drug-Dendrimer Conjugate - PEGylated poly-lysine Dendrimer. J Pharm Sci 2023; 112:844-858. [PMID: 36372229 DOI: 10.1016/j.xphs.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
The recent emergence of drug-dendrimer conjugates within pharmaceutical industry research and development introduces a range of challenges for analytical and measurement science. These molecules are very high molecular weight (100-200kDa) with a significant degree of structural complexity. The characteristics and quality attributes that require understanding and definition, and impact efficacy and safety, are diverse. They relate to the intact conjugate, the various building blocks of these complex systems and the level of the free and bound active pharmaceutical ingredient (API). From an analytical and measurement science perspective, this necessitates the measurement of the molecular weight, impurity characterisation, the quantitation of the number of conjugated versus free API molecules, the determination of the impurity profiles of the building blocks, primary structure and both particle size and morphology. Here we report the first example of a global characterisation of a drug-dendrimer conjugate - PEGylated poly-lysine dendrimer currently under development (AZD0466). The impact of the wide variety of analytical and measurement techniques on the overall understanding of this complex molecular entity is discussed, with the relative capabilities of the various approaches compared. The results of this study are an essential platform for the research and development of the future generations of related dendrimer-based medicines.
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Affiliation(s)
- Nadim Akhtar
- New Modalities and Parenteral Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | | | - Louisa Beer
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Alex Bowes
- Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, UK
| | - Tony Bristow
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK.
| | - Anders Broo
- Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - David Buttar
- Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, UK
| | - Steve Coombes
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Rebecca Cross
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Emma Eriksson
- Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Leslie P Hughes
- Oral Product Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Mark Jackman
- Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, UK
| | - M Jayne Lawrence
- Division of Pharmacy & Optometry, Stopford Building, University of Manchester, 99 Oxford Road, Manchester, M13 9PG, UK
| | - Jessica Lee
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Weimin Li
- Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Rebecca Linke
- Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, UK
| | - Najet Mahmoudi
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - Marc McCormick
- Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, UK
| | - Bryce MacMillan
- UNB MRI Centre, Department of Physics, PO Box 4400, Fredericton, NB E3B 5A3, Canada
| | - Ben Newling
- UNB MRI Centre, Department of Physics, PO Box 4400, Fredericton, NB E3B 5A3, Canada
| | - Maryann Ngeny
- Oncology Regulatory Science & Strategy, AstraZeneca, Macclesfield, UK
| | - Claire Patterson
- Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, UK
| | - Andy Poulton
- Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, UK
| | - Andrew Ray
- New Modalities and Parenteral Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Natalie Sanderson
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Silvia Sonzini
- Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Yayan Tang
- Regulatory Affairs, R&D, AstraZeneca, Shanghai, China
| | - Kevin E Treacher
- New Modalities and Parenteral Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Dave Whittaker
- Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, UK
| | - Stephen Wren
- New Modalities and Parenteral Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
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5
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Holman SW, Langley GJ, Muddiman DC, Novak-Mitchell C. RCM protocols: improving reproducibility in the field of mass spectrometry. Rapid Commun Mass Spectrom 2023; 38 Suppl 1:e9677. [PMID: 38169149 DOI: 10.1002/rcm.9677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Affiliation(s)
- Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - G John Langley
- Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
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6
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Neves LX, Wilson RA, Brownridge P, Holman SW, Harman VM, Eyers CE, Beynon RJ, Castro-Borges W. Dissection of schistosome tissues under LC-MS compatible preservative conditions for quantitative proteomics. Rapid Commun Mass Spectrom 2023; 38 Suppl 1:e9523. [PMID: 37070167 DOI: 10.1002/rcm.9523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/31/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Schistosomes are blood flukes with specialised tissues and organs, each one playing a pivotal role in perpetuating the parasite life cycle. Herein, we describe a detailed methodology for preserving the proteome of adult Schistosoma mansoni worms during manual dissection for enrichment of tissues associated with the parasite's alimentary tract. We provide step-by-step directions for specimen storage and dissection while in preservative solution, tissue homogenisation, protein extraction and digestion using a methodology fully compatible with downstream quantitative liquid chromatography-mass spectrometry analysis. Our methodology uses label-free and QconCAT-based absolute quantification for detection of S. mansoni oesophageal gland products proposed as vaccine candidates. Through stabilisation of the proteome and minimising sample degradation during dissection our approach has allowed us to access the hidden proteome of target tissues not readily available from total lysates because of their small volume. This protocol can be replicated or adapted to other Schistosoma species lacking quantitative proteomics characterisation of specialised tissues for discovery of proteins with potential diagnostic and therapeutic utility.
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Affiliation(s)
- Leandro Xavier Neves
- Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
- Centre for Proteome Research, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - R Alan Wilson
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Philip Brownridge
- Centre for Proteome Research, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Victoria M Harman
- Centre for Proteome Research, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Claire E Eyers
- Centre for Proteome Research, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - William Castro-Borges
- Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
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7
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Elsemman IE, Rodriguez Prado A, Grigaitis P, Garcia Albornoz M, Harman V, Holman SW, van Heerden J, Bruggeman FJ, Bisschops MMM, Sonnenschein N, Hubbard S, Beynon R, Daran-Lapujade P, Nielsen J, Teusink B. Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Nat Commun 2022; 13:801. [PMID: 35145105 PMCID: PMC8831649 DOI: 10.1038/s41467-022-28467-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/27/2022] [Indexed: 01/20/2023] Open
Abstract
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation—known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells. Metabolically active organelles compete for cytosolic space and resources during metabolism rewiring. Here, the authors develop a computational model of yeast metabolism and resource allocation to predict condition- and compartment-specific proteome constraints that govern metabolic strategies.
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Affiliation(s)
- Ibrahim E Elsemman
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark.,Department of Information Systems, Faculty of Computers and Information, Assiut University, Assiut, Egypt
| | - Angelica Rodriguez Prado
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Pranas Grigaitis
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Victoria Harman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Stephen W Holman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Johan van Heerden
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mark M M Bisschops
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Nikolaus Sonnenschein
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark
| | - Simon Hubbard
- Division of Evolution & Genomic Sciences, University of Manchester, Manchester, UK
| | - Rob Beynon
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Pascale Daran-Lapujade
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark. .,Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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8
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Ray AD, Clemens G, Holman SW. Application of open port sampling interface mass spectrometry (OPSI-MS) to deuterium exchange as an aid for structural elucidation. Rapid Commun Mass Spectrom 2021; 35 Suppl 2:e8536. [PMID: 31336014 DOI: 10.1002/rcm.8536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/19/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Deuterium exchange has been demonstrated to provide additional information to accurate mass measurement and collision-induced dissociation on unknown chemical structures. An enhanced method for rapid deuterium exchange could make this technique more routine for structural elucidation. Open port sampling interface mass spectrometry (OPSI-MS) with an aprotic solvent offers a rapid method for performing deuterium incorporation. METHODS Samples of standard drug molecules have been analysed by OPSI-MS directly from solids using a make-up flow of acetonitrile + 0.1% trifluoroacetic acid. The resultant spectra were compared with those obtained by OPSI-MS analysis of the samples dissolved in deuterium oxide (D2 O). Solutions of these molecules in acetonitrile/D2 O were analysed using an Atmospheric Solids Analysis Probe (ASAP) at different temperatures to compare the suitability of this technique. RESULTS The number of exchangeable hydrogens was obtained through deuterium exchange using the OPSI source, although there was some incomplete exchange or back-exchange observed. Molecules with one to five exchangeable hydrogens were successfully analysed. ASAP analysis produced more complicated spectra with higher levels of incomplete or back-exchanged ions; this was more pronounced at higher temperatures. CONCLUSIONS The use of OPSI provides a method for the rapid determination of the number of exchangeable hydrogens within a molecule. This yields useful information as an aid to the structural elucidation of unknowns. ASAP produces incomplete exchange and cannot be used for incorporation studies.
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Affiliation(s)
- Andrew D Ray
- Global Product Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
| | - Graeme Clemens
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
| | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
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9
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Garcia-Albornoz M, Holman SW, Antonisse T, Daran-Lapujade P, Teusink B, Beynon RJ, Hubbard SJ. A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. Mol Omics 2021; 16:59-72. [PMID: 31868867 DOI: 10.1039/c9mo00136k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrated regulatory networks can be powerful tools to examine and test properties of cellular systems, such as modelling environmental effects on the molecular bioeconomy, where protein levels are altered in response to changes in growth conditions. Although extensive regulatory pathways and protein interaction data sets exist which represent such networks, few have formally considered quantitative proteomics data to validate and extend them. We generate and consider such data here using a label-free proteomics strategy to quantify alterations in protein abundance for S. cerevisiae when grown on minimal media using glucose, galactose, maltose and trehalose as sole carbon sources. Using a high quality-controlled subset of proteins observed to be differentially abundant, we constructed a proteome-informed network, comprising 1850 transcription factor interactions and 37 chaperone interactions, which defines the major changes in the cellular proteome when growing under different carbon sources. Analysis of the differentially abundant proteins involved in the regulatory network pointed to their significant roles in specific metabolic pathways and function, including glucose homeostasis, amino acid biosynthesis, and carbohydrate metabolic process. We noted strong statistical enrichment in the differentially abundant proteome of targets of known transcription factors associated with stress responses and altered carbon metabolism. This shows how such integrated analysis can lend further experimental support to annotated regulatory interactions, since the proteomic changes capture both magnitude and direction of gene expression change at the level of the affected proteins. Overall this study highlights the power of quantitative proteomics to help define regulatory systems pertinent to environmental conditions.
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Affiliation(s)
- M Garcia-Albornoz
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester M13 9PT, UK.
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10
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Holman SW. Response to "In defense of the quasimolecular ion". J Mass Spectrom 2021; 56:e4724. [PMID: 33843106 DOI: 10.1002/jms.4724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
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11
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Holman SW, Bristow T. Response to "Molecular ion: A more contemporary definition". J Mass Spectrom 2020; 55:e4649. [PMID: 32996192 DOI: 10.1002/jms.4649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - Tony Bristow
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
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12
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Lewis Z, Jackson BA, Crampton A, Ray AD, Holman SW. Towards a generic method for ion chromatography/mass spectrometry of low-molecular-weight amines in pharmaceutical drug discovery and development. Rapid Commun Mass Spectrom 2020; 34 Suppl 4:e8680. [PMID: 31778589 DOI: 10.1002/rcm.8680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Low-molecular-weight amines are encountered in pharmaceutical analysis, e.g. as reactants in chemical syntheses, but are challenging to analyse using ultrahigh-performance liquid chromatography/mass spectrometry (UHPLC/MS) due to their high polarity causing poor retention. Ion chromatography/mass spectrometry (IC/MS) is an emerging technique for polar molecule analysis that offers better separation. A generic IC/MS method would overcome problems associated with using UHPLC/MS in drug discovery and development environments. METHODS Amine standards were analysed using IC/MS with gradient elution (variety of column temperatures evaluated). An electrospray ionisation (ESI) quadrupole mass spectrometer was operated in positive ion polarity in scanning mode. The make-up flow composition was evaluated by assessing the performance of a range of organic modifiers (acetonitrile, ethanol, methanol) and additives (acetic acid, formic acid, methanesulfonic acid). The ESI conditions were optimised to minimise adduct formation and promote generation of protonated molecules. RESULTS The performance attributes were investigated and optimised for low-molecular-weight amine analysis. Organic solvents and acidic additives were evaluated as make-up flow components to promote ESI, with 0.05% acetic acid in ethanol optimal for producing protonated molecules. The hydrogen bonding capability of amines led to abundant protonated molecule-solvent complexes; optimisation of source conditions reduced these, with collision-induced dissociation voltage having a strong effect. The detection limit was ≤1.78 ng for the amines analysed, which is fit-for-purpose for an open-access chemistry environment. CONCLUSIONS This study demonstrates the value of IC/MS for analysing low-molecular-weight amines. Good chromatographic separation of mixtures was possible without derivatisation. Ionisation efficiency was greatest using a make-up flow of 0.05% acetic acid in ethanol, and optimisation of ESI source conditions promoted protonated molecule generation for easy determination of molecular weight.
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Affiliation(s)
- Zoe Lewis
- Global Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Bethany A Jackson
- Global Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
| | - Alex Crampton
- Global Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
| | - Andrew D Ray
- Global Product Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
| | - Stephen W Holman
- Global Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
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13
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Neves LX, Wilson RA, Brownridge P, Harman VM, Holman SW, Beynon RJ, Eyers CE, DeMarco R, Castro-Borges W. Quantitative Proteomics of Enriched Esophageal and Gut Tissues from the Human Blood Fluke Schistosoma mansoni Pinpoints Secreted Proteins for Vaccine Development. J Proteome Res 2019; 19:314-326. [PMID: 31729880 DOI: 10.1021/acs.jproteome.9b00531] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Schistosomes are blood-dwelling helminth parasites that cause schistosomiasis, a debilitating disease resulting in inflammation and, in extreme cases, multiple organ damage. Major challenges to control the transmission persist, and the discovery of protective antigens remains of critical importance for vaccine development. Rhesus macaques can self-cure following schistosome infection, generating antibodies that target proteins from the tegument, gut, and esophagus, the last of which is the least investigated. We developed a dissection technique that permitted increased sensitivity in a comparative proteomics profiling of schistosome esophagus and gut. Proteome analysis of the male schistosome esophagus identified 13 proteins encoded by microexon genes (MEGs), 11 of which were uniquely located in the esophageal glands. Based on this and transcriptome information, a QconCAT was designed for the absolute quantification of selected targets. MEGs 12, 4.2, and 4.1 and venom allergen-like protein 7 were the most abundant, spanning over 245 million to 6 million copies per cell, while aspartyl protease, palmitoyl thioesterase, and galactosyl transferase were present at <1 million copies. Antigenic variation by alternative splicing of MEG proteins was confirmed together with a specialized machinery for protein glycosylation/secretion in the esophagus. Moreover, some gastrodermal secretions were highly enriched in the gut, while others were more uniformly distributed throughout the parasite, potentially indicating lysosomal activity. Collectively, our findings provide a more rational, better-oriented selection of schistosome vaccine candidates in the context of a proven model of protective immunity.
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Affiliation(s)
- Leandro X Neves
- Departamento de Ciências Biológicas , Universidade Federal de Ouro Preto , Campus Morro do Cruzeiro , Ouro Preto 35400-000 , Minas Gerais , Brazil
| | - R Alan Wilson
- Centre for Immunology and Infection, Department of Biology , University of York , Heslington, York YO10 5DD , United Kingdom
| | - Philip Brownridge
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Liverpool L69 7ZB , United Kingdom
| | - Victoria M Harman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Liverpool L69 7ZB , United Kingdom
| | - Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Liverpool L69 7ZB , United Kingdom
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Liverpool L69 7ZB , United Kingdom
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Liverpool L69 7ZB , United Kingdom
| | - Ricardo DeMarco
- Instituto de Física de São Carlos , Universidade de São Paulo , São Carlos 13566-590 , Brazil
| | - William Castro-Borges
- Departamento de Ciências Biológicas , Universidade Federal de Ouro Preto , Campus Morro do Cruzeiro , Ouro Preto 35400-000 , Minas Gerais , Brazil
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14
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Szatkowska R, Garcia-Albornoz M, Roszkowska K, Holman SW, Furmanek E, Hubbard SJ, Beynon RJ, Adamczyk M. Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1. Biochem J 2019; 476:1053-1082. [PMID: 30885983 PMCID: PMC6448137 DOI: 10.1042/bcj20180701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 02/07/2023]
Abstract
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III)-driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on the Saccharomyces cerevisiae proteome and metabolism under glucose-rich conditions. We show for the first time that RNAP III is tightly coupled to the glycolytic system at the molecular systems level. Decreased RNAP III activity or the absence of the RNAP III negative regulator, Maf1 elicit broad changes in the abundance profiles of enzymes engaged in fundamental metabolism in S. cerevisiae In a mutant compromised in RNAP III activity, there is a repartitioning towards amino acids synthesis de novo at the expense of glycolytic throughput. Conversely, cells lacking Maf1 protein have greater potential for glycolytic flux.
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Affiliation(s)
- Roza Szatkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Manuel Garcia-Albornoz
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Katarzyna Roszkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Emil Furmanek
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Simon J Hubbard
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Malgorzata Adamczyk
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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15
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Lanucara F, Lam C, Mann J, Monie TP, Colombo SAP, Holman SW, Boyd J, Dange MC, Mann DA, White MRH, Eyers CE. Dynamic phosphorylation of RelA on Ser42 and Ser45 in response to TNFα stimulation regulates DNA binding and transcription. Open Biol 2017; 6:rsob.160055. [PMID: 27466442 PMCID: PMC4967822 DOI: 10.1098/rsob.160055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/01/2016] [Indexed: 12/14/2022] Open
Abstract
The NF-κB signalling module controls transcription through a network of protein kinases such as the IKKs, as well as inhibitory proteins (IκBs) and transcription factors including RelA/p65. Phosphorylation of the NF-κB subunits is critical for dictating system dynamics. Using both non-targeted discovery and quantitative selected reaction monitoring-targeted proteomics, we show that the cytokine TNFα induces dynamic multisite phosphorylation of RelA at a number of previously unidentified residues. Putative roles for many of these phosphorylation sites on RelA were predicted by modelling of various crystal structures. Stoichiometry of phosphorylation determination of Ser45 and Ser42 revealed preferential early phosphorylation of Ser45 in response to TNFα. Quantitative analyses subsequently confirmed differential roles for pSer42 and pSer45 in promoter-specific DNA binding and a role for both of these phosphosites in regulating transcription from the IL-6 promoter. These temporal dynamics suggest that RelA-mediated transcription is likely to be controlled by functionally distinct NF-κB proteoforms carrying different combinations of modifications, rather than a simple ‘one modification, one effect’ system.
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Affiliation(s)
- Francesco Lanucara
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Connie Lam
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jelena Mann
- Fibrosis Laboratory, Liver Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tom P Monie
- MRC Human Nutrition Research, University of Cambridge, Cambridge CB2 1GA, UK
| | - Stefano A P Colombo
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - James Boyd
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Manohar C Dange
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Derek A Mann
- Fibrosis Laboratory, Liver Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Michael R H White
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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16
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Bennett RJ, Simpson DM, Holman SW, Ryan S, Brownridge P, Eyers CE, Colyer J, Beynon RJ. DOSCATs: Double standards for protein quantification. Sci Rep 2017; 7:45570. [PMID: 28368040 PMCID: PMC5377311 DOI: 10.1038/srep45570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/27/2017] [Indexed: 12/12/2022] Open
Abstract
The two most common techniques for absolute protein quantification are based on either mass spectrometry (MS) or on immunochemical techniques, such as western blotting (WB). Western blotting is most often used for protein identification or relative quantification, but can also be deployed for absolute quantification if appropriate calibration standards are used. MS based techniques offer superior data quality and reproducibility, but WB offers greater sensitivity and accessibility to most researchers. It would be advantageous to apply both techniques for orthogonal quantification, but workflows rarely overlap. We describe DOSCATs (DOuble Standard conCATamers), novel calibration standards based on QconCAT technology, to unite these platforms. DOSCATs combine a series of epitope sequences concatenated with tryptic peptides in a single artificial protein to create internal tryptic peptide standards for MS as well as an intact protein bearing multiple linear epitopes. A DOSCAT protein was designed and constructed to quantify five proteins of the NF-κB pathway. For three target proteins, protein fold change and absolute copy per cell values measured by MS and WB were in excellent agreement. This demonstrates that DOSCATs can be used as multiplexed, dual purpose standards, readily deployed in a single workflow, supporting seamless quantitative transition from MS to WB.
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Affiliation(s)
- Richard J Bennett
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Sheila Ryan
- Institute of Ageing and Chronic Disease, The Apex Building, 6 West Derby St., Liverpool L7 8TX, UK
| | - Philip Brownridge
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - John Colyer
- Badrilla Ltd. Leeds Innovation Centre, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
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17
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Holman SW, Hammond DE, Simpson DM, Waters J, Hurst JL, Beynon RJ. Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS). Philos Trans A Math Phys Eng Sci 2016; 374:rsta.2015.0362. [PMID: 27644981 PMCID: PMC5031629 DOI: 10.1098/rsta.2015.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 05/28/2023]
Abstract
Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure turnover rates with high confidence are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared with selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data are acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focused studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - John Waters
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Jane L Hurst
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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18
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Jarnuczak AF, Lee DCH, Lawless C, Holman SW, Eyers CE, Hubbard SJ. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics. J Proteome Res 2016; 15:2945-59. [PMID: 27454336 DOI: 10.1021/acs.jproteome.6b00048] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of a standard. A deeper understanding of the governing principles of peptide ionization and exploitation of the inherent ionization and detection parameters of individual peptides is thus of great value. Here, using the yeast proteome as a model system, we establish the concept of peptide F-factor as a measure of detectability, closely related to ionization efficiency. F-factor is calculated by normalizing peptide precursor ion intensity by absolute abundance of the parent protein. We investigated F-factor characteristics in different shotgun proteomics experiments, including across multiple ESI-based LC-MS platforms. We show that F-factors mirror previously observed physicochemical predictors as peptide detectability but demonstrate a nonlinear relationship between hydrophobicity and peptide detectability. Similarly, we use F-factors to show how peptide ion coelution adversely affects detectability and ionization. We suggest that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex peptide mixtures, selection of surrogate peptides in targeted MS studies, and for calibration of peptide ion signal in label-free workflows. Data are available via ProteomeXchange with identifier PXD003472.
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Affiliation(s)
- Andrew F Jarnuczak
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Dave C H Lee
- Faculty of Biology, Medicine and Health, University of Manchester , Second Floor, Wolfson Molecular Imaging Centre, 27 Palatine Road, Withington, Manchester, M20 3JL, United Kingdom
| | - Craig Lawless
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Stephen W Holman
- Centre for Proteome Research, University of Liverpool , Department of Biochemistry, Institute of Integrative Biology, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Claire E Eyers
- Centre for Proteome Research, University of Liverpool , Department of Biochemistry, Institute of Integrative Biology, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
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19
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Mackenzie RJ, Lawless C, Holman SW, Lanthaler K, Beynon RJ, Grant CM, Hubbard SJ, Eyers CE. Absolute protein quantification of the yeast chaperome under conditions of heat shock. Proteomics 2016; 16:2128-40. [PMID: 27252046 PMCID: PMC4996341 DOI: 10.1002/pmic.201500503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/05/2016] [Accepted: 05/31/2016] [Indexed: 11/10/2022]
Abstract
Chaperones are fundamental to regulating the heat shock response, mediating protein recovery from thermal-induced misfolding and aggregation. Using the QconCAT strategy and selected reaction monitoring (SRM) for absolute protein quantification, we have determined copy per cell values for 49 key chaperones in Saccharomyces cerevisiae under conditions of normal growth and heat shock. This work extends a previous chemostat quantification study by including up to five Q-peptides per protein to improve confidence in protein quantification. In contrast to the global proteome profile of S. cerevisiae in response to heat shock, which remains largely unchanged as determined by label-free quantification, many of the chaperones are upregulated with an average two-fold increase in protein abundance. Interestingly, eight of the significantly upregulated chaperones are direct gene targets of heat shock transcription factor-1. By performing absolute quantification of chaperones under heat stress for the first time, we were able to evaluate the individual protein-level response. Furthermore, this SRM data was used to calibrate label-free quantification values for the proteome in absolute terms, thus improving relative quantification between the two conditions. This study significantly enhances the largely transcriptomic data available in the field and illustrates a more nuanced response at the protein level.
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Affiliation(s)
- Rebecca J Mackenzie
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK.,Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Craig Lawless
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
| | - Karin Lanthaler
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
| | - Chris M Grant
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Simon J Hubbard
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Claire E Eyers
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
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20
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Abstract
This study introduces a new reversed-phase liquid chromatography retention time (RT) standard, RePLiCal (Reversed-phase liquid chromatography calibrant), produced using QconCAT technology. The synthetic protein contains 27 lysine-terminating calibrant peptides, meaning that the same complement of standards can be generated using either Lys-C or trypsin-based digestion protocols. RePLiCal was designed such that each constituent peptide is unique with respect to all eukaryotic proteomes, thereby enabling integration into a wide range of proteomic analyses. RePLiCal has been benchmarked against three commercially available peptide RT standard kits and outperforms all in terms of LC gradient coverage. RePLiCal also provides a higher number of calibrant points for chromatographic retention time standardization and normalization. The standard provides stable RTs over long analysis times and can be readily transferred between different LC gradients and nUHPLC instruments. Moreover, RePLiCal can be used to predict RTs for other peptides in a timely manner. Furthermore, it is shown that RePLiCal can be used effectively to evaluate trapping column performance for nUHPLC instruments using trap-elute configurations, to optimize gradients to maximize peptide and protein identification rates, and to recalibrate the m/z scale of mass spectrometry data post-acquisition.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Lynn McLean
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
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21
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Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PFG, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ. Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. Mol Cell Proteomics 2016; 15:1309-22. [PMID: 26750110 PMCID: PMC4824857 DOI: 10.1074/mcp.m115.054288] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Indexed: 11/06/2022] Open
Abstract
Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference data set quantifying over 1800 Saccharomyces cerevisiae proteins by direct means using protein-specific stable-isotope labeled internal standards and selected reaction monitoring (SRM) mass spectrometry, far exceeding any previous study. This was achieved by careful design of over 100 QconCAT recombinant proteins as standards, defining 1167 proteins in terms of copies per cell and upper limits on a further 668, with robust CVs routinely less than 20%. The selected reaction monitoring-derived proteome is compared with existing quantitative data sets, highlighting the disparities between methodologies. Coupled with a quantification of the transcriptome by RNA-seq taken from the same cells, these data support revised estimates of several fundamental molecular parameters: a total protein count of ∼100 million molecules-per-cell, a median of ∼1000 proteins-per-transcript, and a linear model of protein translation explaining 70% of the variance in translation rate. This work contributes a “gold-standard” reference yeast proteome (including 532 values based on high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies.
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Affiliation(s)
- Craig Lawless
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Stephen W Holman
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Philip Brownridge
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Karin Lanthaler
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Victoria M Harman
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rachel Watkins
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Dean E Hammond
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rebecca L Miller
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Paul F G Sims
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Christopher M Grant
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Claire E Eyers
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Robert J Beynon
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Simon J Hubbard
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK;
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22
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Strzelecka D, Holman SW, Eyers CE. Evaluation of dimethyl sulfoxide (DMSO) as a mobile phase additive during top 3 label-free quantitative proteomics. Int J Mass Spectrom 2015; 391:157-160. [PMID: 26869853 PMCID: PMC4708063 DOI: 10.1016/j.ijms.2015.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Dimethyl sulfoxide (DMSO) has been advocated as a beneficial additive to electrospray solvents for peptide analysis due to the improved ionisation efficiency conferred. Previous reports have shown that the resultant improvements in peptide ion signal intensities are non-uniform. As a result, it was hypothesised that inclusion of DMSO in electrospray solvents could be detrimental to the outcome of intensity-based label-free absolute quantification approaches, specifically the top 3 method. The effect of DMSO as a mobile phase additive in top 3 label-free quantification was therefore evaluated. We show that inclusion of DMSO enhances data quality, improving the precision and number of proteins quantified, with no significant change to the quantification values observed in its absence.
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Key Words
- DIA, data-independent acquisition
- DMSO
- DMSO, dimethyl sulfoxide
- ESI, electrospray ionisation
- HDMSE, ion mobility-assisted MSE
- LC, liquid chromatography
- LC–MS
- Label-free
- MS, mass spectrometry
- MS/MS, tandem mass spectrometry
- MSE, mass spectrometry with elevated energy (a form of data-independent tandem mass spectrometry)
- Peptide
- Proteomics
- Q-ToF, quadrupole-time-of-flight
- Quantification
- SWATH, sequential window acquisition of all theoretical fragment ion spectra
- cpc, copies per cell
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Affiliation(s)
- Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Stephen W. Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
- Corresponding author. Tel.: +44 151 795 4424.
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23
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Qi D, Lawless C, Teleman J, Levander F, Holman SW, Hubbard S, Jones AR. Representation of selected-reaction monitoring data in the mzQuantML data standard. Proteomics 2015; 15:2592-6. [PMID: 25884107 PMCID: PMC4692094 DOI: 10.1002/pmic.201400281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 03/02/2015] [Accepted: 04/14/2015] [Indexed: 11/06/2022]
Abstract
The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, to support submissions to public repositories, development of visualization software and pipeline/modular approaches. The standard is designed around a common core that can be extended to support particular types of technique through the release of semantic rules that are checked by validation software. The first release of mzQuantML supported four quantitative proteomics techniques via four sets of semantic rules: (i) intensity-based (MS(1) ) label free, (ii) MS(1) label-based (such as SILAC or N(15) ), (iii) MS(2) tag-based (iTRAQ or tandem mass tags), and (iv) spectral counting. We present an update to mzQuantML for supporting SRM techniques. The update includes representing the quantitative measurements, and associated meta-data, for SRM transitions, the mechanism for inferring peptide-level or protein-level quantitative values, and support for both label-based or label-free SRM protocols, through the creation of semantic rules and controlled vocabulary terms. We have updated the specification document for mzQuantML (version 1.0.1) and the mzQuantML validator to ensure that consistent files are produced by different exporters. We also report the capabilities for production of mzQuantML files from popular SRM software packages, such as Skyline and Anubis.
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Affiliation(s)
- Da Qi
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Craig Lawless
- The Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Johan Teleman
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden.,Bioinformatics Infrastructure for Life Sciences (BILS), Lund University, Lund, Sweden
| | - Stephen W Holman
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Simon Hubbard
- The Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Chawner R, Holman SW, Gaskell SJ, Eyers CE. Peptide scrambling during collision-induced dissociation is influenced by N-terminal residue basicity. J Am Soc Mass Spectrom 2014; 25:1927-1938. [PMID: 25135610 PMCID: PMC4197365 DOI: 10.1007/s13361-014-0968-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 06/03/2023]
Abstract
'Bottom up' proteomic studies typically use tandem mass spectrometry data to infer peptide ion sequence, enabling identification of the protein whence they derive. The majority of such studies employ collision-induced dissociation (CID) to induce fragmentation of the peptide structure giving diagnostic b-, y-, and a- ions. Recently, rearrangement processes that result in scrambling of the original peptide sequence during CID have been reported for these ions. Such processes have the potential to adversely affect ion accounting (and thus scores from automated search algorithms) in tandem mass spectra, and in extreme cases could lead to false peptide identification. Here, analysis of peptide species produced by Lys-N proteolysis of standard proteins is performed and sequences that exhibit such rearrangement processes identified. The effect of increasing the gas-phase basicity of the N-terminal lysine residue through derivatization to homoarginine toward such sequence scrambling is then assessed. The presence of a highly basic homoarginine (or arginine) residue at the N-terminus is found to disfavor/inhibit sequence scrambling with a coincident increase in the formation of b(n-1)+H(2)O product ions. Finally, further analysis of a sequence produced by Lys-C proteolysis provides evidence toward a potential mechanism for the apparent inhibition of sequence scrambling during resonance excitation CID.
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Affiliation(s)
- Ross Chawner
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN UK
- Waters Corporation, Stamford Avenue, Wilmslow, SK9 4AX UK
| | - Stephen W. Holman
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN UK
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | | | - Claire E. Eyers
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN UK
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
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Lanucara F, Holman SW, Gray CJ, Eyers CE. The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat Chem 2014; 6:281-94. [DOI: 10.1038/nchem.1889] [Citation(s) in RCA: 655] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 02/11/2014] [Indexed: 02/07/2023]
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Brownridge P, Lawless C, Payapilly AB, Lanthaler K, Holman SW, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. Quantitative analysis of chaperone network throughput in budding yeast. Proteomics 2013; 13:1276-91. [PMID: 23420633 PMCID: PMC3791555 DOI: 10.1002/pmic.201200412] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/29/2012] [Accepted: 11/08/2012] [Indexed: 11/08/2022]
Abstract
The network of molecular chaperones mediates the folding and translocation of the many proteins encoded in the genome of eukaryotic organisms, as well as a response to stress. It has been particularly well characterised in the budding yeast, Saccharomyces cerevisiae, where 63 known chaperones have been annotated and recent affinity purification and MS/MS experiments have helped characterise the attendant network of chaperone targets to a high degree. In this study, we apply our QconCAT methodology to directly quantify the set of yeast chaperones in absolute terms (copies per cell) via SRM MS. Firstly, we compare these to existing quantitative estimates of these yeast proteins, highlighting differences between approaches. Secondly, we cast the results into the context of the chaperone target network and show a distinct relationship between abundance of individual chaperones and their targets. This allows us to characterise the 'throughput' of protein molecules passing through individual chaperones and their groups on a proteome-wide scale in an unstressed model eukaryote for the first time. The results demonstrate specialisations of the chaperone classes, which display different overall workloads, efficiencies and preference for the sub-cellular localisation of their targets. The novel integration of the interactome data with quantification supports re-estimates of the level of protein throughout going through molecular chaperones. Additionally, although chaperones target fewer than 40% of annotated proteins we show that they mediate the folding of the majority of protein molecules (∼62% of the total protein flux in the cell), highlighting their importance.
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Affiliation(s)
- Philip Brownridge
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Holman SW, Wright P, Langley GJ. The low-energy collision-induced dissociation product ion spectra of protonated beta-blockers reveal an analogy to fragmentation behaviour under electron ionisation conditions. J Mass Spectrom 2011; 46:1182-1185. [PMID: 22124991 DOI: 10.1002/jms.2006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Brownridge P, Holman SW, Gaskell SJ, Grant CM, Harman VM, Hubbard SJ, Lanthaler K, Lawless C, O'cualain R, Sims P, Watkins R, Beynon RJ. Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy. Proteomics 2011; 11:2957-70. [DOI: 10.1002/pmic.201100039] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 04/08/2011] [Accepted: 04/19/2011] [Indexed: 12/30/2022]
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Holman SW, Wright P, Wells NJ, Langley GJ. Evidence for site-specific intra-ionic hydrogen/deuterium exchange in the low-energy collision-induced dissociation product ion spectra of protonated small molecules generated by electrospray ionisation. J Mass Spectrom 2010; 45:347-357. [PMID: 20069530 DOI: 10.1002/jms.1714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The experimental investigation of site-specific intra-ionic hydrogen/deuterium (H/D) exchange in the low-energy collision-induced dissociation (CID) product ion spectra of protonated small molecules generated by electrospray ionisation (ESI) is presented. The observation of intra-ionic H/D exchange in such ions under low-energy CID conditions has hitherto been rarely reported. The data suggest that the intra-ionic H/D exchange takes place in a site-specific manner between the ionising deuteron, localised at either a tertiary amine or a tertiary amine-N-oxide, and a gamma-hydrogen relative to the nitrogen atom. Nuclear magnetic resonance (NMR) spectroscopy measurements showed that no H/D exchange takes place in solution, indicating that the reaction occurs in the gas phase. The compounds analysed in this study suggested that electron-withdrawing groups bonded to the carbon atom bearing the gamma-hydrogen can preclude exchange. The effect of the electron-withdrawing group appears dependent upon its electronegativity, with lower chi value groups still allowing exchange to take place. However, the limited dataset available in this study prevented robust conclusions being drawn regarding the effect of the electron-withdrawing group. The observation of site-specific intra-ionic H/D exchange has application in the area of structural elucidation, where it could be used to introduce an isotopic label into the carbon skeleton of a molecule containing specific structural features. This could increase the throughput, and minimise the cost, of such studies due to the obviation of the need to produce a deuterium-labelled analogue by synthetic means.
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Affiliation(s)
- Stephen W Holman
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
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Holman SW, Wright P, Langley GJ. A Rapid Methodology for the Characterization of Dialkyl Tertiary Amine-N-Oxide Metabolites Using Structurally Dependent Dissociation Pathways and Reconstructed Ion Current Chromatograms. Anal Chem 2010; 82:2347-54. [DOI: 10.1021/ac902540b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephen W. Holman
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K., and Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Patricia Wright
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K., and Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - G. John Langley
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K., and Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Ramsgate Road, Sandwich, CT13 9NJ, U.K
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Holman SW, Wright P, Langley GJ. High-throughput approaches towards the definitive identification of pharmaceutical drug metabolites. 2. An example of how unexpected dissociation behaviour could preclude correct assignment of sites of metabolism. Rapid Commun Mass Spectrom 2009; 23:2017-2025. [PMID: 19489039 DOI: 10.1002/rcm.4103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
S-oxidation is a common metabolic route for sulfur-containing compounds. Whilst investigating the dissociation of a series of chemically synthesised model S-oxide metabolites, two unexpected losses of 62 m/z units were observed in the collision-induced dissociation (CID) product ion spectrum of protonated 3-dimethylaminomethyl-4-(4-methanesulfinyl-3-methylphenoxy)benzenesulfonamide. A single loss was initially assigned using the low-resolution product ion spectrum, acquired by electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS), as methanethial, S-oxide via a charge-remote, four-centred rearrangement. This assignment was consistent with well-documented hydrogen rearrangements in the literature. Further, the loss was not observed for the parent compound. Thus, it was inferred that the site of metabolism was involved in the dissociation and the attractive nature of the four-centred rearrangement meant that the loss of methanethial, S-oxide was a logical assignment. However, deuterium-labelling experiments and accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS), showed that the nominal loss of 62 m/z units occurs via two distinct dissociation pathways. Neither of these losses was of methanethial, S-oxide as initially hypothesised from the low-resolution product ion spectrum of the protonated molecule. Mechanisms consistent with the experimental findings are postulated. An MS(3) spectrum of the fully exchanged, deuterated species supported the proposed mechanisms by suggesting that 3-dimethylaminomethyl-4-(4-methanesulfinyl-3-methylphenoxy)benzenesulfonamide has multiple sites of protonation in the gas phase. The planar structures of the posited product ions are likely to provide the driving force for the rearrangements. The relevance of the observations with regards to pharmaceutical drug metabolite identification is discussed.
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Affiliation(s)
- Stephen W Holman
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
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Holman SW, Wright P, Langley GJ. High-throughput approaches towards the definitive identification of pharmaceutical drug metabolites. 1. Evidence for an ortho effect on the fragmentation of 4-benzenesulfinyl-3-methylphenylamine using electrospray ionisation mass spectrometry. Rapid Commun Mass Spectrom 2008; 22:2355-2365. [PMID: 18613294 DOI: 10.1002/rcm.3623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A 50 m/z unit loss from protonated 4-benzenesulfinyl-3-methylphenylamine has been observed and investigated using electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS). It was hypothesised that the specific fragmentation was affected by the presence of an ortho methyl group in relation to the sulfoxide functionality, i.e. an ortho effect influences the preferred dissociation pathway. This was because the des-methyl homologue did not display a 50 m/z unit loss. This fragmentation was shown to be a two-step process with sequential losses of a hydroxyl radical and a thiol radical. Molecular modelling calculations showed that the most favourable site of protonation for 4-benzenesulfinyl-3-methylphenylamine was the sulfoxide oxygen, which would facilitate the loss of a hydroxyl radical. Subsequent deuterium-exchange experiments confirmed that the loss was a hydroxyl radical and afforded definitive assignment of the site of protonation. Furthermore, the involvement of a single exchangeable hydrogen atom in the overall 50 m/z unit loss was demonstrated. Thus, supportive evidence was provided for the involvement of the ortho methyl group in the second stage of the fragmentation, leading to the loss of the thiol radical. Accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS), verified the elemental formulae of the individual losses. The ion structure following the 50 m/z unit loss was proposed to be a protonated aminofluorene and was supported by comparing the product ion spectrum of commercially available protonated 2-aminofluorene with the MS4 data of protonated 4-benzenesulfinyl-3-methylphenylamine. Fragmentation mechanisms are proposed. The relevance of the loss with regards to pharmaceutical drug metabolite identification is discussed.
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Affiliation(s)
- Stephen W Holman
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
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Holman SW. MARGINAL TABS FOR LOGARITHM TABLES. Science 1900; 11:396. [PMID: 17768840 DOI: 10.1126/science.11.271.396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Holman SW. MATTER, ENERGY, FORCE AND WORK. Science 1899; 9:154. [PMID: 17747987 DOI: 10.1126/science.9.213.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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