J O U R N A L O F P R O T E O M I C S 8 8 ( 2 0 1 3 ) i v – v

Contents

Editorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Plenary Speaker:- Peter Roepstorff2D gels still have a niche in proteomics

A. Rogowska-Wrzesinska, M.-C. Le Bihan, M. Thaysen-Andersen, and P. Roepstorff (Denmark, France) . . . . . . . . . . . . . . 4

Poster Prize winner:- Shabaz MohammedBenchmarking stable isotope labeling based quantitative proteomics

A.F.M. Altelaar, C.K. Frese, C. Preisinger, M.L. Hennrich, A.W. Schram, H.Th.M. Timmers, A.J.R. Heck, and S. Mohammed(The Netherlands) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Young Investigator winner:- Michaela D. Filiou15N metabolic labeling: Evidence for a stable isotope effect on plasma protein levels and peptide chromatographicretention times

C. Webhofer, Y. Zhang, J. Brusis, S. Reckow, R. Landgraf, G. Maccarrone, C.W. Turck, and M.D. Filiou (Germany) . . . . . . . 27

Roundtable ReportsPlant proteomics: Current status and future prospects

R.G. Uhrig, and G.B. Moorhead (Canada). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Clinical proteomics stretch goals: EuPA 2012 roundtable report

S.E. O'Neil, M.J. Palviainen, S. Ten Have, M. Filiou, A. Gonzalez, K. Hodge, S. Surinova, D. Penque, and M.S. Baker(Sweden, Finland, United Kingdom, Germany, Switzerland, Portugal, Australia) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software developmentS.F. Martin, H. Falkenberg, T.F. Dyrlund, G.A. Khoudoli, C.J. Mageean, and R. Linding (UK, Germany, Denmark) . . . . . . . . 41

Food SecurityProteomics as a tool to explore human milk in health and disease

P. Roncada, L.H. Stipetic, L. Bonizzi, R.J.S. Burchmore, and M.W. Kennedy (Italy, UK) . . . . . . . . . . . . . . . . . . . . . . . . . . 47Muscle and meat: New horizons and applications for proteomics on a farm to fork perspective

G. Paredi, M.-A. Sentandreu, A. Mozzarelli, S. Fadda, K. Hollung, and A.M. de Almeida (Italy, Spain, Argentina, Norway,Portugal) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Food Peptidomics: Large scale analysis of small bioactive peptides — A pilot studyS.L. Lahrichi, M. Affolter, I.S. Zolezzi, and A. Panchaud (Switzerland) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Data HandlingCleaning up the masses: Exclusion lists to reduce contamination with HPLC-MS/MS

K. Hodge, S. Ten Have, L. Hutton, and A.I. Lamond (United Kingdom) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92ProteoCloud: A full-featured open source proteomics cloud computing pipeline

T. Muth, J. Peters, J. Blackburn, E. Rapp, and L. Martens (Belgium, Germany, South Africa) . . . . . . . . . . . . . . . . . . . . . 104

doi:10.1016/S1874-3919(13)00358-8

Ava i l ab l e on l i ne a t www.sc i enced i r ec t . com

www.e l sev i e r. com/ loca te / j p ro t

OthersPerformance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer forproteomics research

C.R. Weisbrod, M.R. Hoopmann, M.W. Senko, and J.E. Bruce (United States) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers

L. Fischer, Z.A. Chen, and J. Rappsilber (United Kingdom, Germany) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120The effect of organelle discovery upon sub-cellular protein localisation

L.M. Breckels, L. Gatto, A. Christoforou, A.J. Groen, K.S. Lilley, and M.W.B. Trotter (UK, Spain) . . . . . . . . . . . . . . . . . . . 129Optimised ‘on demand’ protein arraying from DNA by cell free expression with the ‘DNA to Protein Array’ (DAPA) technology

R. Schmidt, E.A. Cook, D. Kastelic, M.J. Taussig, and O. Stoevesandt (UK) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

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