Mass spectrometry

Ion mobility review

Lanucara F, Holman SW, Gray CJ, Eyers CE. (2014) The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat Chem. 2014 Mar 21;6(4):281-94. doi: 10.1038/nchem.1889. [PDF] [PUBMED] [Abstract...]

Genentic programming for peptide 'flyability'

Wedge, David C., Gaskell, Simon J., Hubbard, Simon J., Kell, Douglas B., Lau, King Wai, Eyers, Claire. 2007. Peptide detectability following ESI mass spectrometry: prediction using genetic programming. Presented at Proceedings of the 9th annual conference on Genetic and evolutionary computation [Abstract...]

Unblocking the sink

Lanucara F, Chi Hoo Lee D, Eyers CE. (2013) J Am Soc Mass Spectrom. 2013 Dec 3. [Epub ahead of print] Unblocking the Sink: Improved CID-Based Analysis of Phosphorylated Peptides by Enzymatic Removal of the Basic C-Terminal Residue. [PDF][PUBMED] [Abstract...]

Quantification of proteins in the human osteoarthritic secretome

Peffers MJ, Beynon RJ, Clegg PD. (2013) Absolute quantification of selected proteins in the human osteoarthritic secretome. Int J Mol Sci. 14(10):20658-81. doi: 10.3390/ijms141020658. [PDF][PUBMED] [Abstract...]

Whole animal protein turnover studies

Claydon, A.J., Thom, M.D., Hurst, J.L. & Beynon, R.J. (2011) Protein turnover: measurement of proteome dynamics by whole animal metabolic labelling with stable isotope labelled amino acids. Proteomics 12:1194-1206 [PUBMED][PDF] [Abstract...]

Enzyme turnover and metabolic regulation

Arden, C, Petrie, J.L., Tudhope, S.J., Al-Oanzi, Z., Claydon, A.J., Beynon, R.J., Towle, H.C. & Agius, L. (2011) Diabetes Journal (in press) Elevated glucose represses liver glucokinase and induces its regulatory protein to safeguard hepatic phosphate homeostasis [PUBMED][PDF] [Abstract...]

Scent of sensecence

Garratt, .M, Stockely, P., Armstrong, S.D., Beynon, R/J. & Hurst, J.L. (2011) The scent of senescence: sexual signalling and female preference in house mice. J. Evol. Biol [PDF] doi: 10.111111/j.1420-9101.2011.02367.x [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. Nucl Acid Res. [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. J Proteomics [PUBMED][PDF] [Abstract...]

Strategies for dynamic SILAC

Claydon, A & Beynon R (2011) Methods Mol Biol. 759, 179-195. Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC [Abstract...]

The end of proteomics

Davidson GR, Armstrong SD, Beynon R (2011) Methods Mol Biol. 753:229-242. Positional proteomics at the N-terminus as a means of proteome simplification. [PUBMED][PDF]

Unkind cuts - proteolysis and proteomics

Brownridge, P. & Beynon, R.J. (2011) The importance of the digest: proteolysis and absolute quantification in proteomics. Methods, [PUBMED] [PDF] [Abstract...]

Global proteome quantification: dreams or reality?

Brownridge, P., Holman, S.W., Gaskell, S.J., Grant, C., Harman, V.M., Lanthaler, K., Lawless, C., O’cualain, R., Sims, P., Watkins, R & Beynon, R.J. (2011) Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy. Proteomics, 11, 2957-2970 [PUBMED][PDF] [Abstract...]

MUP molecular heterogeneity

Robertson, D.H.L., Gaskell, S.J., Cox, K., Evershed, R.P. & Beynon, R.J. Molecular heterogeneity in the Major Urinary Proteins of the house mouse, Mus musculus (1996) Biochem. J. 316, 265-272 [PUBMED] [PDF] [Abstract...]

PLP to monitor phosphorylase turnover

Beynon, R.J., Leyland, D.M., Evershed, R.P., Edwards, R.H.T. & Coburn, S.P. (1996) Measurement of the turnover of glycogen phosphorylase by gas chromatography/mass spectrometry using stable isotope derivatives of pyridoxine (Vitamin B6) Biochem J 317, 613-619 [PUBMED] [PDF] [Abstract...]

Protein binding in chemical communication

Beynon, R.J., Robertson, D.H.L., Hubbard, S. J., Gaskell, S.J. & Hurst, J.L. (1999) The role of protein binding in chemical communication: major urinary proteins in the house mouse. in "Chemical Signals in Vertebrates" (R.E. Johnston, D. Müller-Schwarze and P.W.Sorensen eds) Plenum Press pp 137-147 [Abstract...]

Intact mass proteomics

Hayter J.R., Robertson, D.H.L., Gaskell, S.J. & Beynon, R.J. (2003) Proteome analysis of intact proteins in complex mixtures. Mol. Cell. Proteomics 2, 85-95 [PUBMED] [PDF] [Abstract...]

Metabolic labelling in proteomics

Beynon RJ, Pratt J.M. (2005) Metabolic labelling of proteins for proteomics. Mol Cell Proteomics. 4, 857-872 [PUBMED] [PDF] [Abstract...]

Proteome dynamics review

Beynon RJ.(2005) The dynamics of the proteome: strategies for measuring protein turnover on a proteome-wide scale. Brief Funct Genomic Proteomic. 3, 382-390 [PUBMED] [PDF] [Abstract...]

First paper on dynamic SILAC in intact animals

Doherty, M.K., Whitehead, C., McCormack, H., Gaskell, S.J. & Beynon, R.J. (2005) Proteome dynamics in complex organisms: using stable isotopes to monitor individual protein turnover rates. Proteomics 5, 522-533 [PUBMED] [PDF] [Abstract...]

Identification of an atypical male-specific MUP in mouse urine

Armstrong, S.D., Robertson, D.H.L., Cheetham, S.A., Hurst, J.L. & Beynon, R.J. (2005) Structural and functional differences in isoforms of Major Urinary Proteins: a male specific protein that preferentially binds a male pheromone. Biochem. J. 391, 343-350 [PUBMED] [PDF] [Abstract...]

Copper toxicity in sheep

Haywood, S. Simpson, D.M, Ross, G. & Beynon, R.J. (2005) The unique response of North Ronaldsay sheep to copper challenge compared with Cambridge sheep: oxidative stress, mitochondrial damage and hepatic stellate cell activation. J. Comp. Path.133, 114-127 [PUBMED] [PDF] [Abstract...]

Proteasome proteolysis

Hayter JR, Doherty MK, Whitehead C, McCormack H, Gaskell SJ & Beynon RJ. (2005) The subunit structure and dynamics of the 20S proteasome in chicken skeletal muscle. Mol. Cell. Proteomics. 4, 1370-1381 [PUBMED] [PDF] [Abstract...]

First paper describing QconCAT

Beynon, R.J., Doherty, M.K., Pratt, J.M. & Gaskell, S.J. (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides rates. Nature Methods 2, 587-589 [PUBMED] [PDF [Abstract...]

Muscle proteomics: anabolic agent effects

Burniston JG, McLean L, Beynon RJ, Goldspink DF.   (2007) Anabolic effects of a non-myotoxic dose of the beta(2)-adrenergic receptor agonist clenbuterol on rat plantaris muscle. Muscle & Nerve. 35, 217-223 [PUBMED] [PDF] [Abstract...]

Proteomics of oxidative stress in mice

Aphrodite Vasilaki, Deborah Simpson, Francis McArdle, Lynne McLean, Robert J. Beynon, Holly Van Remmen, Arlan G. Richardson, Anne McArdle, John A Faulkner and Malcolm J. Jackson (2007) Formation of 3-nitrotyrosines in carbonic anhydrase III is a sensitive marker of oxidative stress in skeletal muscle PROTEOMICS – Clinical Applications 1: 362–372 [PDF] [Abstract...]

Proteomics and animal disease

Mary K. Doherty, Robert J. Beynon and Phillip D. Whitfield (2007) Proteomics and naturally occurring animal diseases: Opportunities for animal and human medicine PROTEOMICS – Clinical Applications 2: 135–141 [PDF] [Abstract...]

Proteomics of copper toxicity

Simpson, D. M., Mobasheri, A., Haywood, S. & Beynon, R. J. (2007) A proteomics study of the response of North Ronaldsay sheep to copper challenge. BMC Veterinary Research BMC Vet Res. 27, 36 [PUBMED][PDF] [Abstract...]

Mass spectrometry identification of proteins

Nominated in Faculty of 1000 by Harald Stenmark. McCullough, J., Row, P.E. Lorenzo, O, Doherty, M., Beynon, R.J., Clague, M.J. and Urbé, S (2006) Activation of the Endosome-Associated Ubiquitin Isopeptidase AMSH by STAM, a Component of the Multivesicular Body-Sorting Machinery Current Biology 16, 160-165.[PUBMED][PDF] [Abstract...]

Proteome dynamics

Doherty MK, Beynon RJ. (2006) Protein turnover on the scale of the proteome. Expert Rev Proteomics. 1, 97-110[PUBMED] [PDF] [Abstract...]

Proteome turnover: why is it not being studied?

Beynon, R.J. & Pratt, J.M. (2006) Strategies for measuring dynamics: the temporal component of proteomics. Methods Biochem Anal. 2006;49:15-25 [PUBMED] [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...]

Isolation of N-terminal peptides

Nominated in Faculty of 1000 by Ruedi Aebersold. McDonald, L. & Beynon, R.J. (2006) Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization. Nature Protocols 1, 1790 - 1798 [PUBMED] [PDF] [Abstract...]

Cauxin in big cat urine

McLean, L., Hurst, J.L., Gaskell, C.J., Lewis, J. C. M & Beynon, R.J. (2007) Characterization of Cauxin in the Urine of Domestic and Big Cats (2007) J. Chem. Ecol 3, 1997-2009 [PUBMED][PDF] [Abstract...]

Muscle proteomics

Burniston J G, McLean L, Beynon R J and Goldspink D F (2007) Anabolic effects of a non-myotoxic dose of the beta2-adrenergic receptor agonist clenbuterol on rat plantaris muscle. Muscle Nerve 35, 217-23 [PUBMED][PDF] [Abstract...]

Global cooling

Mclean, L., Young, I.S. Doherty, M.K., Robertson, D.H.L., Cossins, A.R., Gracey, A. Y., Beynon, R.J. & Whitfield, P.D. (2007) Global cooling: Cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics Proteomics 7, 2667-2681 [PUBMED][PDF] [Abstract...]

Pre-eclampsia biomarkers

Myers JE, Hart S, Armstrong S, Mires GJ, Beynon R, Gaskell SJ, Baker PN. (2007) Evidence for multiple circulating factors in preeclampsia. Am J Obstet Gynecol. 196, 266.e1-6. [PUBMED][PDF] [Abstract...]

Absolute quantification by QconCAT

Rivers J, Simpson DM, Robertson DH, Gaskell SJ, Beynon RJ.(2007) Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol Cell Proteomics. 6, 1416-1427. [PUBMED][PDF] [Abstract...]

Avian Proteomics

Doherty, M.K., Mclean, L. & Beynon, R.J. (2007) Avian Proteomics: Advances, Challenges and New Technologies. Cytogenetic and Genome Research 117, 358-369.[PUBMED][PDF] [Abstract...]

FPGA acceleration of proteomics data processing

Bogdan I, Coca D, Rivers J, Beynon RJ. (2007) Hardware acceleration of processing of mass spectrometric data for proteomics.Bioinformatics. 23, 724-31.[PUBMED][PDF] [Abstract...]

MUPs in an aboriginal mouse

 Robertson, D.H.L., Hurst, J.L., Searle, J.B., Gunduz, I. & Beynon, R.J. (2007) Characterization and Comparison of Major Urinary Proteins from the House Mouse, Mus musculus domesticus, and the Aboriginal Mouse, Mus macedonicus. J. Chem. Ecol. 33, 613-630.[PUBMED][PDF] [Abstract...]

FTICR resolution of similar mass proteins

Robertson DH, Wong SC, Beynon RJ, Hurst JL, Gaskell SJ. (2008) Observation of heterogeneous gene products by FT-ICR MS. J. Am. Soc. Mass Spectrom. 19, 103-110. [PUBMED][PDF] [Abstract...]

Structure and asparagine deamidation

Rivers J, McDonald L, Edwards IJ, Beynon RJ. (2008) Asparagine deamidation and the role of higher order protein structure. J. Proteome Res. 7, 921-7. [PUBMED][PDF] [Abstract...]

Urinary lipocalins

Beynon, RJ, Hurst, JL, Turton, MJ , Robertson, DHL , Armstrong, SD, Cheetham, SA, Simpson, D, MacNicoll, A, Humphries, RE  (2008) Urinary lipocalins in rodenta: is there a generic model? Chemical Signals in Vertebrates 11, 37-49 [PDF] [Abstract...]

First paper on a systematic analysis of MUP expression

Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG, Harrow JL. (2008) Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. [PUBMED][PDF] [Abstract...]

Designer genes for mass spectrometry

Eyers CE, Simpson DM, Wong SC, Beynon RJ, Gaskell SJ. (2008) QCAL-a Novel Standard for Assessing Instrument Conditions for Proteome Analysis. J Am Soc Mass Spectrom. 19, 1275-1280 [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...]

Biomarkers of ragwort poisoning in horses

Moore RE, Knottenbelt D, Matthews JB, Beynon RJ, Whitfield PD. (2008) Biomarkers for ragwort poisoning in horses: identification of protein targets.BMC Vet Res. 4:30. [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...]

Phosphorylation stoichiometry

Rigorous determination of the stoichiometry of protein phosphorylation using mass spectrometry (2009) Johnson H, Eyers CE, Eyers PA, Beynon RJ, Gaskell SJ. J Am Soc Mass Spectrom. 20, 2211-2220 [PUBMED][PDF] [Abstract...]

MUP variation in lab mouse strains

Cheetham SA, Smith AL, Armstrong SD, Beynon RJ, Hurst JL. (2009) Limited variation in the major urinary proteins of laboratory mice. Physiol Behav. 96, 253-261 [PUBMED][PDF] [Abstract...]

Dynamic SILAC for global assessment of proteome turnover

Doherty, M.K., Hammond, D., Clague, M. J., Gaskell, S.J. & Beynon, R.J. (2009) Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J. Proteome Res. 8, 104-112 [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...]

Even the smallest of hamsters have lipocalins in their urine.

Turton MJ, Robertson DH, Smith JR, Hurst JL, Beynon RJ. Roborovskin, a Lipocalin in the Urine of the Roborovski Hamster, Phodopus roborovskii. Chem Senses. 2010 Jun 24. [PUBMED][PDF] [Abstract...]

It is a truth, universally acknowledged, that a mouse in possession of darcin must be in want of a mate.

Nominated as 'Exceptional' by Etienne Joly in Faculty1000 Biology (
Roberts SA, Simpson, Armstrong, Davidson, Robertson, McLean, Beynon & Hurst JL (2010) Darcin: a male pheromone that stimulates female memory and sexual attraction to an individual male's odour. BMC Biology 8:75. [PUBMED][PDF] [Abstract...]