Mass spectrometry

Proteomics of epileptogenesis

Karen Tse, Edward Beamer, Deborah Simpson, Robert J Beynon, Graeme J Sills, Thimmasettappa Thippeswamy (2021) The Impacts of Surgery and Intracerebral Electrodes in C57BL/6J Mouse Kainate Model of Epileptogenesis: Seizure Threshold, Proteomics, and Cytokine Profiles Front Neurol Jul 12;12:625017. doi: 10.3389/fneur.2021.625017 [PDF] [PUBMED] [DOI] [Abstract...]

March of the acronyms.. ALACATs (a la carte proteomics)

James Johnson, Victoria M Harman, Catarina Franco, Edward Emmott, Nichola Rockliffe, Yaqi Sun, Lu-Ning Liu, Ayako Takemori, Nobuaki Takemori, Robert J Beynon (2021) Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins (2021) BMC Biol 2021 Sep 8;19(1):195. doi: 10.1186/s12915-021-01135-9. [PDF] [PUBMED] [DOI] [Abstract...]

First 'zap the crap', now 'Fry the fly': REIMS for insect identification

Iris Wagner, Natalie I. Koch, Joscelyn Sarsby, Nicola White, Tom A. R. Price, Sam Jones, Jane L. Hurst, Robert J. Beynon, (2020) The application of rapid evaporative ionisation mass spectrometry (REIMS) in the analysis of Drosophila species – a potential new tool in entomology [PDF] [PUBMED] [DOI] [Abstract...]

Using QconCATs to establish protein complex stoichiometry

Mengru Yang, Deborah M Simpson, Nicolas Wenner, Philip Brownridge, Victoria M Harman, Jay C D Hinton, Robert J Beynon, Lu-Ning Liu (2020) Decoding the stoichiometric composition and organisation of bacterial metabolosomes [PDF] [PUBMED] [DOI] [Abstract...]

MS from gels, top down or bottom up

Ayako Takemori, David S Butcher, Victoria M Harman, Philip Brownridge, Keisuke Shima, Daisuke Higo, Jun Ishizaki, Hitoshi Hasegawa, Junpei Suzuki, Masakatsu Yamashita, Joseph A Loo, Rachel R Ogorzalek Loo, Robert J Beynon, Lissa C Anderson, Nobuaki Takemori (2020) PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry [PDF] [PUBMED] [DOI] [Abstract...]

Using proteomics to explore 'pseudogene' expression

Ian Goodhead, Frances Blow, Philip Brownridge, Margaret Hughes, John Kenny, Ritesh Krishna, Lynn McLean, Pisut Pongchaikul, Rob Beynon and Alistair C. Darby (202o) Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont [PDF] [PUBMED] [DOI] [Abstract...]

Global proteomics of carbon source metabolism in Saccharomyces

M Garcia-Albornoz 1, S W Holman, T Antonisse, P Daran-Lapujade, B Teusink, R J Beynon, S J Hubbard (2020) A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. [PDF] [PUBMED] [DOI] [Abstract...]

REIMS for the analysis of bacterial protein production

Joscelyn Sarsby, Lynn McLean, Victoria M Harman, Robert J Beynon (2019) Monitoring recombinant protein expression in bacteria by rapid evaporative ionisation mass spectrometry. [PDF] [PUBMED] [DOI] [Abstract...]

Zap the crap! Using REIMS to obtain valuable information from animal faeces

Davidson NB, Koch NI, Sarsby J, Jones E, Hurst JL, Beynon RJ. (2019) Rapid identification of species, sex and maturity by mass spectrometric analysis of animal faeces. [PDF][PUBMED] [Abstract...]

Role of RNA polymerase III through proteomics

Roza Szatkowska, Manuel Garcia-Albornoz,*, Katarzyna Roszkowska, Stephen W. Holman, Emil Furmanek, Simon J. Hubbard, Robert J. Beynon and Malgorzata Adamczyk (2019) Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1[PDF] [PUBMED] [Abstract...]

Heparin binding proteome

Quentin M. Nunes, Dunhao Su, Philip J. Brownridge, Deborah M. Simpson, Changye Sun, Yong Li, Thao P. Bui, Xiaoying Zhang, Wei Huang, Daniel J. Rigden, Robert J. Beynon, Robert Sutton, David G. Fernig (2019) The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis [PDF] [PUBMED] [Abstract...]

Caught in a trap - proteomics of NETS

Elinor A. Chapman, Max Lyon, Deborah Simpson, David Mason, RobertJ.Beynon, RobertJ.Moots and HelenL.Wright (2019) Caught in a Trap? Proteomic Analysis of Neutrophil Extracellular Traps in Rheumatoid Arthritis and Systemic Lupus Erythematosus [PDF] [PUBMED] [Abstract...]

Synovial fluid proteomes

James R. Anderson, Aibek Smagul, Deborah Simpson, Peter D. Clegg, Luis M. Rubio-Martinez, Mandy J. Peffers (2019) The synovial fluid proteome differentiates between septic and nonseptic articular pathologies. [PUBMED] [PDF] [Abstract...]

Using protemics to define MMP7 processing

Garalla HM, Lertkowit N, Tiszlavicz L, Reisz Z, Holmberg C, Beynon R, Simpson D, Varga A, Kumar JD, Dodd S, Pritchard DM, Moore AR, Rosztóczy AI, Wittman T, Simpson A, Dockray GJ, Varro A. (2018) Matrix metalloproteinase (MMP)-7 in Barrett's esophagus and esophageal adenocarcinoma: expression, metabolism, and functional significance. [PUBMED] [PDF] [Abstract...]

MUPs shape the volatile odours of mice

Roberts SA, Prescott MC, Davidson AJ, McLean L, Beynon RJ, Hurst JL. (2018) Individual odour signatures that mice learn are shaped by involatile major urinary proteins (MUPs). [PUBMED] [PDF] [Abstract...]

SIDLS: stable isotope labelling for secretome dynamics

Hammond DE, Kumar JD, Raymond L, Simpson DM, Beynon RJ, Dockray GJ, Varro A. (2018) Stable Isotope Dynamic Labeling of Secretomes (SIDLS) Identifies Authentic Secretory Proteins Released by Cancer and Stromal Cells. [PDF] [PUBMED] [Abstract...]

Proteomics in craniopharyngioma

John R. Apps · Gabriela Carreno · Jose Mario Gonzalez‐Meljem · Scott Haston · Romain Guiho ·Julie E. Cooper · Saba Manshaei · Nital Jani · Annett Hlsken · Benedetta Pettorini · Robert J. Beynon · Deborah M. Simpson · Helen C. Fraser · Ying Hong · Shirleen Hallang · Thomas J. Stone1 · Alex Virasami · Andrew M. Donson · David Jones · Kristian Aquilina · Helen Spoudeas1· Abhijit R. Joshi · Richard Grundy · Lisa C. D. Storer · Márta Korbonits · David A. Hilton · Kyoko Tossell · Selvam Thavaraj · Mark A. Ungless · Jesus Gil1 · Rolf Buslei · Todd Hankinson · Darren Hargrave · Colin Goding · Cynthia L. Andoniadou · Paul Brogan · Thomas S. Jacques · Hywel J. Williams · Juan Pedro Martinez‐Barbera (2018) Tumour compartment transcriptomics demonstrates the activation of in ammatory and odontogenic programmes in human adamantinomatous craniopharyngioma and identi es the MAPK/ERK pathway as a novel therapeutic target. [PUBMED] [PDF] [Abstract...]

Nextgen QconCATs - MEERCAT!

Takemori N, Takemori A, Tanaka Y, Endo Y, Hurst JL, Gómez-Baena G, Harman VM, Beynon RJ. (2017) MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification. [PDF] [PUBMED] [Abstract...]

A new lipocalin, fully sequenced, from bank voles

Loxley GM, Unsworth J, Turton MJ, Jebb A, Lilley KS, Simpson DM, Rigden DJ, Hurst JL, Beynon RJ. (2017) Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus. [PDF] [PUBMED]
[Abstract...]

New paper on CSF proteomics in paediatric meningitis

Guadalupe Gómez-Baena, Richard J. Bennett, Carmen Martínez-Rodríguez, Małgorzata Wnk, Gavin Laing, Graeme Hickey, Lynn McLean, Robert J. Beynon & Enitan D. Carrol (2017) Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis. [PDF] [PUBMED]

[Abstract...]

Proteomics suppporting supramolecular studies

M. Faulkner, J. Rodriguez-Ramos, G. F. Dykes, S. V. Owen, S. Casella, D. Simpson, R. Beynon and L. Liu (2017) Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes [PUBMED] [PDF] [Abstract...]

Proteomics to identify galectin binding partners

Colomb F, Wang W, Simpson D, Zafar M, Beynon R, Rhodes JM, Yu LG. (2017) Galectin-3 interacts with the cell surface glycoprotein CD146 (MCAM, MUC18) and induces secretion of metastasis-promoting cytokines from vascular endothelial cells. [PDF] [PUBMED] [Abstract...]

MUP variation in mouse subspecies

Hurst JL, Beynon RJ, Armstrong SD, Davidson AJ, Roberts SA, Gómez-Baena G, Smadja CM, Ganem G. (2017) Molecular heterogeneity in major urinary proteins of Mus musculus subspecies: potential candidates involved in speciation. [PDF] [PUBMED] [Abstract...]

Proteomics of a marine organism

María del Carmen Muñoz-Marín, Guadalupe Gómez-Baena, Jesús Díez, Robert J. Beynon, David González-Ballester. Mikhail V. Zubkov and José M. García-Fernández (2017) Glucose Uptake in Prochlorococcus: Diversity of Kinetics and Effects on the Metabolism [PDF] [OA] [Abstract...]

Complete de novo sequencing of a mouse lemur protein

Jennifer Unsworth, Grace M. Loxley, Amanda Davidson, Jane L. Hurst, Guadalupe Gómez-Baena, Nicholas I. Mundy, Robert J. Beynon, Elke Zimmermann & Ute Radespiel. (2017) Characterisation of urinary WFDC12 in small nocturnal basal primates, mouse lemurs (Microcebus spp.) [PDF] [PUBMED] [Abstract...]

Connective tissue proteomics

Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD (2016). Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition. [PUBMED] [PDF] [Abstract...]

The joys of running a training course!

A short article, written for the Biochemist, explaining the role of the Society in training provision and our experiences of running the Quantitative Proteomics Course [PDF] [Abstract...]

Improving the quality of turnover measurement

Stephen W. Holman, Dean E. Hammond, Deborah M. Simpson, John Waters, Jane L. Hurst and Robert J. Beynon (2016) Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM MS). [PUBMED] [PDF] [Abstract...]

Proteomics of dystrophic muscle

Arecco N, Clarke CJ, Jones FK, Simpson DM, Mason D, Beynon RJ, Pisconti A. (2016) Elastase levels and activity are increased in dystrophic muscle and impair myoblast cell survival, proliferation and differentiation. [PDF] [PUBMED] [Abstract...]

Quantitative analysis of the yeast 'chaperome'

Rebecca J. Mackenzie, Craig Lawless [2], Stephen W. Holman, Karin Lanthaler, Robert J. Beynon, Chris M. Grant, Simon J. Hubbard and Claire E. Eyers (2106) Absolute protein quantification of the yeast chaperome under conditions of heat shock [PDF] [PUBMED] [Abstract...]

Proteomics of ocular cancer secretomes reveal malignancy potential

Angi, M., Kalirai, H, Prendegast, S., Simpson, D.M., Hammond, D.E., Madigan, M. C., Beynon, R.J. & Coupland, S.E. (2016) Proteomic analysis of uveal melanoma secretome reveals novel biological insights and potential biomarkers. [PDF] [PUBMED] [Abstract...]

Proteome dynamics in a non-model species - the challenges!

Hammond DE, Claydon AJ, Simpson DM, Edward D, Stockley P, Hurst JL, Beynon RJ. (2016) Proteome Dynamics: Tissue Variation in the Kinetics of Proteostasis in Intact Animals. [PUBMED] [PDF] [Abstract...]

Genetics of individual MUP variation

Sheehan MJ, Lee V, Corbett-Detig R, Bi K, Beynon RJ, Hurst JL, Nachman MW. (2016) Selection on Coding and Regulatory Variation Maintains Individuality in Major Urinary Protein Scent Marks in Wild Mice. [PUBMED] [PDF] [Abstract...]

QconCATs in equine wound healing

Bundgaard L, Bendixen E, Sørensen MA, Harman VM, Beynon RJ, Petersen LJ, Jacobsen S. (2016) A selected reaction monitoring based analysis of acute phase proteins in interstitial fluids from experimental equine wounds healing by secondary intention. [PUBMED] [PDF] [Abstract...]

Sperm proteomes, gone large

Bayram HL, Claydon AJ, Brownridge PJ, Hurst JL, Mileham A, Stockley P, Beynon RJ, Hammond DE.(2016) Cross-species proteomics in analysis of mammalian sperm proteins. [PUBMED] [PDF] [Abstract...]

Of mice, mups and mass spectrometry

Robert J. Beynon, Stuart D. Armstrong, Amy J. Claydon, Amanda J. Davidson, Claire E. Eyers, James I. Langridge, Guadalupe Gómez-Baena, Victoria M. Harman, Jane L. Hurst, Victoria Lee, Lynn McLean, Rebecca Pattison, Sarah A. Roberts, Deborah M. Simpson, Jenny Unsworth, Matthias Vonderach, Jonathan Williams and Yvonne E. Woolerton (2015) Mass spectrometry for structural analysis and quantification of the Major Urinary Proteins of the house mouse. [PDF] [NotEvenIndexedInPubmed?] [Abstract...]

Proteome plasticity in sperm competition

Ramm SA, Edward DA, Claydon AJ, Hammond DE, Brownridge, Hurst JL, Beynon RJ, Stockley P. (2015) Sperm competition risk drives plasticity in seminal fluid composition. [PUBMED] [PDF] [Abstract...]

QconCAT for equine acute phase proteins

Bundgaard L, Jacobsen S, Dyrlund TF, Sørensen MA, Harman VM, Beynon RJ, Brownridge PJ, Petersen LJ, Bendixen E. (2014) Development of a method for absolute quantification of equine acute phase proteins using concatenated peptide standards and selected reaction monitoring. [PUBMED][PDF]
[Abstract...]

MUP complexity and analytical challenges

Beynon RJ, Armstrong SD, Gómez-Baena G, Lee V, Simpson D, Unsworth J, Hurst JL. (2014) The complexity of protein semiochemistry in mammals. [PUBMED][PDF] [Abstract...]

Rats have MUPs too - but different!

Gómez-Baena G, Armstrong SD, Phelan MM, Hurst JL, Beynon RJ. (2014). The major urinary protein system in the rat. [PUBMED][PDF] [Abstract...]

Proteomics of myofibroblasts

Balabanova S, Holmberg C, Steele I, Ebrahimi B, Rainbow L, Burdyga T, McCaig C, Tiszlavicz L, Lertkowit N, Giger OT, Oliver S, Prior I, Dimaline R, Simpson D, Beynon R, Hegyi P, Wang TC, Dockray GJ, Varro A. (2014) The neuroendocrine phenotype of gastric myofibroblasts and its loss with cancer progression. [PDF] [PUBMED] [Abstract...]

Who's got the biggest workload? Analysis of chaperone abundance and workload

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 (2012). [PUBMED][PDF] [Abstract...]

A degrading synthesis of proteome turnover research!

Claydon, A.C. & Beynon, R.J. (2012) Proteome dynamics: revisiting turnover with a global perspective. [PUBMED][PDF] [Abstract...]

Designing QconCATs for a mammalian pathway

Simpson, D.M. & Beynon, R.J. (2012) QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification. [PUBMED][PDF] [Abstract...]

Asymetric equalisation with combinatorial beads

Jenny Rivers, Chris Hughes, Thérèse McKenna, Yvonne Woolerton, Johannes P. C. Vissers, James I. Langridge and Robert J. Beynon (2011) Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library [PUBMED] [PDF]
[Abstract...]

Quantification of a metabolic pathway

Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, Dunn W, Winder CL, Lanthaler K, Pir P, Malys N, Kell DB, Oliver SG, Gaskell SJ, Beynon RJ. (2011) Absolute quantification of a metabolic pathway in yeast: deployment of a complete QconCAT approach. [PUBMED][PDF] [Abstract...]

Yeast complex proteomics

Drummond, S., Hildyard, J., Firczuk, H., Reamtong, O., Li, N.,Kannambath, S., Claydon, A., Beynon, R., Eyers, C.E. McCarthy, J.E.G (2011) Diauxic shift-dependent relocalization of decapping activators Dhh1 and Pat1 to polysomal complexes. [PUBMED][PDF] [Abstract...]

Schistosome parasite QconCAT

Castro-Borgesa, W., Simpson, D.M., Dowlea, A., Curwen, R.S., Thomas-Oates, J., Beynon, R.J. & Wilson, A. R. (2011) Abundance of tegument surface proteins in the human blood fluke Schistosoma mansoni determined by QconCAT proteomics. [PUBMED][PDF] [Abstract...]

Strategies for dynamic SILAC

Claydon, A & Beynon R (2011) Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC [PUBMED] [PDF] [Abstract...]

The end of proteomics

Davidson GR, Armstrong SD, Beynon R (2011) Positional proteomics at the N-terminus as a means of proteome simplification. [PUBMED][PDF]
[Abstract...]

Proteomics of HGF/EGF signalling

Hammond DE, Hyde R, Kratchmarova I, Beynon RJ, Blagoev B, Clague MJ. (2010) J Proteome Res. 9(5):2734-2742. Quantitative analysis of HGF and EGF-dependent phosphotyrosine signaling networks.[PUBMED][PDF] [Abstract...]

Acetone modifies peptides! Be careful if you're using acetone precipitation.

Simpson DM, Beynon RJ. (2010) Acetone precipitation of proteins and the modification of peptides. J Proteome Res. 9, 444-450 [PUBMED][PDF] [Abstract...]

Cross-species proteomics

Wright JC, Beynon RJ, Hubbard SJ. Cross species proteomics. (2010) Methods Mol Biol. 604:123-135 [PUBMED][PDF] [Abstract...]

Hardware accelerated proteomics

Coca D, Bogdan I, Beynon RJ. A high-performance reconfigurable computing solution for peptide mass fingerprinting. (2010) Methods Mol Biol. 604:163-185 [PUBMED][PDF] [Abstract...]

Parasite proteomics

Smith, S.K., Nisbet, A.J., Meikle, L.I., Inglis, N.F., Sales, J., Beynon, R.J. & Matthews, J.B. (2010) Proteomic analysis of excretory/secretory products released by Teladorsagia circumcincta larvae early post-infection. Parasite Immunology 31, 10-19 [PUBMED][PDF] [Abstract...]

Proteomics and genome annotation

Wright, J.C., Sugden, D., Francis-McIntyre, S., Riba-Gacia, I., Gaskell, S.J., Grigoriev, I V., Baker, S.E., Beynon, R.J. & Hubbard, S.J. (2009)Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics. 10, 61 [PUBMED][PDF] [Abstract...]

Seminal vesicle protein evolution

Ramm, S.A., McDonald, L.M., Hurst, JL., Beynon, R.J. & Stockley, P.S. (2009) Comparative Proteomics Reveals Evidence for Evolutionary Diversification of Rodent Seminal Fluid and Its Functional Significance in Sperm Competition. Mol. Biol. Evol. 26, 189-198 [PUBMED] [PDF] [Abstract...]