Quantification

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...]

CSF proteomics in bacterial meningitis

Emma C Wall, Philip Brownridge, Gavin Laing, Vanessa S Terra, Veronica Mlozowa, Brigitte Denis, Mulinda Nyirenda, Theresa Allain, Elisa Ramos-Sevillano, Enitan Carrol, Andrea Collins, Stephen B Gordon, David G Lalloo, Brendan Wren, Robert Beynon, Robert S Heyderman, Jeremy S Brown (2020) CSF Levels of Elongation Factor Tu Is Associated With Increased Mortality in Malawian Adults With Streptococcus pneumoniae Meningitis Front Cell Infect Microbiol doi: 10.3389/fcimb.2020.603623. eCollection 2020. [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 identify targets for schistosomiasis

Leandro X Neves, R Alan Wilson, Philip Brownridge, Victoria M Harman, Stephen W Holman, Robert J Beynon, Claire E Eyers, Ricardo DeMarco, William Castro-Borges (2020) Quantitative Proteomics of Enriched Esophageal and Gut Tissues from the Human Blood Fluke Schistosoma mansoni Pinpoints Secreted Proteins for Vaccine Development. [PDF] [PUBMED] [DOI] [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...]

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...]

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...]

Double standards in proteomics

Richard J. Bennett, Deborah M. Simpson, Stephen W. Holman, Sheila Ryan, Philip Brownridge, Claire E. Eyers, John Colyer, Robert J. Beynon (2017) DOSCATs: Double standards for protein quantification [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...]

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...]

The biggest absolute quantification study ever! A tale of 100 QconCATs for nearly 2,000 proteins

Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PF, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ. (2016) Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. [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...]

Proteomics and protein moonlighting

Beynon RJ, Hammond D, Harman V, Woolerton Y. (2014) The role of proteomics in studies of protein moonlighting. [PUBMED][PDF]
[Abstract...]

QconCAT compared to label-free for plasma proteins

Kramer G, Woolerton , van Straalen JP, Vissers JP, Dekker N, Langridge JI, Beynon RJ, Speijer D, Sturk A, Aerts JM. (2015) Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. [PUBMED][PDF] [Abstract...]

SRM data standards

Da Qi, Craig Lawless, Johan Teleman,Fredrik Levander, Stephen W. Holman, Simon Hubbard and Andrew Jones (2015) The representation of selected-reaction monitoring data in the mzQuantML data standard. [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...]

Quantitative proteomics in systems biology

Firczuk, H., Kannambath, S; Pahle, J; Claydon, Amy; Beynon, Robert, Duncan, John; Westerhoff, Hans; Mendes, Pedro & McCarthy, John (2013) An in vivo control map for the eukaryotic mRNA translation machinery. [PDF] [PUBMED] [Abstract...]

Extending Progenesis to embrace SILAC and Hi3

Qi, D., Brownridge, P., Xia, D., Mackay, K., Gonzalez-Galarza, F.F., Kenyani, J., Harman, V., Beynon, R.J. & Jones, A.R. (2012) A software toolkit and interface for performing stable isotope labelling and top3 quantification using Progenesis LC-MS OMICS [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...]

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...]

QconCAT protocols defined

Pratt, J.M., Simpson, D.M., Doherty, M.K., Rivers, J, Gaskell, S.J. Beynon , R.J. (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nature Protocols 1, 1029 - 1043 [PUBMED][PDF] [Abstract...]

FTICR based quantification

Johnson, H., Wong, S C C, D M Simpson, R J Beynon, and S J Gaskell (2008) . Protein quantification by selective isolation and fragmentation of isotopic pairs using FT-ICR MS. J Am Soc Mass Spectrom 19, 973-977 [PUBMED][PDF] [Abstract...]