AffinityProteome publications

The following 36 publications appeared during the period of the project and acknowledged project funding:

Alhamdani, M.S., Schröder, C. & Hoheisel, J.D. (2010). Analysis conditions for proteomic profiling of mammalian tissue and cell extracts with antibody microarrays. Proteomics 10, 3203-3207

Alhamdani MS, Youns M, Buchholz M, Gress TM, Beckers MC, Maréchal D, Bauer A, Schröder C, Hoheisel JD (2012) Immunoassay-based proteome profiling of 24 pancreatic cancer cell lines. J Proteomics. 2012 May 8. [Epub ahead of print]

Blokzijl A, Friedman M, Pontén F, Landegren U. (2010) Profiling protein expression and interactions: proximity ligation as a tool for personalized medicine. J Intern Med. 268:232-45

Bradbury AR, Sidhu S, Dübel S, McCafferty J. (2011) Beyond natural antibodies: the power of in vitro display technologies. Nat Biotechnol. 29:245-54.

Darmanis S, Nong RY, Hammond M, Gu J, Alderborn A, Vänelid J, Siegbahn A, Gustafsdottir S, Ericsson O, Landegren U, Kamali-Moghaddam M. (2010) Sensitive plasma protein analysis by microparticle-based proximity ligation assays. Mol Cell Proteomics 9:327-35

Dübel S, Stoevesandt O, Taussig MJ, Hust M. (2010) Generating recombinant antibodies to the complete human proteome. Trends Biotechnol. 28:333-9.

Düvel J, Bertinetti D, Möller S, Schwede F, Morr M, Wissing J, Radamm L, Zimmermann B, Genieser HG, Jänsch L, Herberg FW, Häussler S. (2012) A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa. J Microbiol Methods. 88:229-36.

Erlbruch A, Hung CW, Seidler J, Borrmann K, Gesellchen F, König N, Kübler D, Herberg FW, Lehmann WD, Bossemeyer D. (2010) Uncoupling of bait-protein expression from the prey protein environment adds versatility for cell and tissue interaction proteomics and reveals a complex of CARP-1 and the PKA Cbeta1 subunit. Proteomics. 10:2890-900.

Friedrich A, Hoheisel JD, Knemeyer JP, Marmé N. (2011) A universally applicable process for preparing stoichiometrically 1:1 labeled functional proteins Proteomics. 11:3757-60.

Gold L et al. (2010) Aptamer-based multiplexed proteomic technology for biomarker discovery. PloS One 2010 5:e15004.

Gu G, Friedman M, Jost C, Johnsson K, Kamali- Moghaddam M, Plückthun A, Landegren U, Söderberg O (2012) Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation. New Biotechnology (in press)

Hanke SE, Bertinetti D, Badel A, Schweinsberg S, Genieser HG, Herberg FW. (2011) Cyclic nucleotides as affinity tools: phosphorothioate cAMP analogs address specific PKA subproteomes. N Biotechnol. 28:294-301.

Hust M, Meyer T, Voedisch B, Rülker T, Thie H, El-Ghezal A, Kirsch MI, Schütte M, Helmsing S, Meier D, Schirrmann T, Dübel S. (2011) A human scFv antibody generation pipeline for proteome research. J Biotechnol. 152:159-70

Hust M, Steinwand M, Al-Halabi L, Helmsing S, Schirrmann T, Dübel S. (2009) Improved microtitre plate production of single chain Fv fragments in Escherichia coli. N Biotechnol. 25:424-8.

Hust M, et al (2012) Generating recombinant antibodies for research, diagnostics and therapy using phage display. Current Biotechnology 1: 33-41

Landegren U, Vänelid J, Hammond M, Nong RY, Wu D, Ulleros E, Kamali-Moghaddam M. (2012) Opportunities for sensitive plasma proteome analysis. Anal Chem. 84:1824-30.

Liu Y, Gu J, Hagner-McWhirter A, Sathiyanarayanan P, Gullberg M, Söderberg O, Johansson J, Hammond M, Ivansson D, Landegren U. (2011) Western blotting via proximity ligation for high performance protein analysis. Mol Cell Proteomics. 10:O111.011031.

Lolicato M, Nardini M, Gazzarrini S, Möller S, Bertinetti D, Herberg FW, Bolognesi M, Martin H, Fasolini M, Bertrand JA, Arrigoni C, Thiel G, Moroni A. (2011) Tetramerization dynamics of C-terminal domain underlies isoform-specific cAMP gating in hyperpolarization-activated cyclic nucleotide-gated channels. J Biol Chem. 286:44811-20.

Mustafa SA, Hoheisel JD, Alhamdani MS. (2011) Secretome profiling with antibody microarrays. Mol Biosyst. 7:1795-801.

Parizek P, Kummer L, Rube P, Prinz A, Herberg FW, Plückthun A. (2012) Designed Ankyrin Repeat Proteins (DARPins) as Novel Isoform-specific Intracellular Inhibitors of c-Jun N-terminal Kinases. ACS Chem Biol. 2012 May 8. [Epub ahead of print]

Marschall, A., Frenzel, A., Schirrmann, T., Schüngel, M. and Dübel, S. (2011) Targeting antibodies to the cytoplasm. MAbs. 2011 3:3-16. Review.

Schirrmann T, Meyer T, Schütte M, Frenzel A, Hust M. (2011) Phage display for the generation of antibodies for proteome research, diagnostics and therapy. Molecules. 16:412-26. Review.

Schmidt J, Müsken M, Becker T, Magnowska Z, Bertinetti D, Möller S, Zimmermann B, Herberg FW, Jänsch L, Häussler S. (2011) The Pseudomonas aeruginosa chemotaxis methyltransferase CheR1 impacts on bacterial surface sampling. PLoS One. 6:e18184.

Schmidt, R., Jacak, J., Schirwitz, C., Stadler, V., Michel, G., Marmé, N., Schütz, G.J., Hoheisel, J.D. & Knemeyer, J.-P. (2010). Single-molecule detection on a protein-array assay platform for the exposure of a tuberculosis antigen. J. Proteome Res., 10:1316-1322

Schröder C et al. (2010) Antibody microarrays for expression analysis. Antibody Engineering 2: 429-445

Schröder C, Alhamdani MS, Fellenberg K, Bauer A, Jacob A, Hoheisel JD. (2011) Robust protein profiling with complex antibody microarrays in a dual-color mode Methods Mol Biol. 785:203-21.

Sill M, Schröder C, Hoheisel JD, Benner A, Zucknick M (2010) Assessment and optimisation of normalisation methods for dual-colour antibody microarrays. BMC Bioinformatics. 11:556.

Søberg K, Larsen AC, Diskar M, Backe PH, Bjørås M, Jahnsen T, Laerdahl JK, Rognes T, Herberg FW, Skålhegg BS. (2012) Identification and Characterization of Novel Mutations in the Human Gene Encoding the Catalytic Subunit Calpha of Protein Kinase A (PKA). PLoS One. 7:e34838

Stoevesandt O, Vetter M, Kastelic D, Palmer EA, He M, Taussig MJ. (2011) Cell-free expression put on the spot: advances in repeatable protein arraying from DNA (DAPA). New Biotechnol. 28:282-90.

Stoevesandt O (2012) Protein arraying by cell-free expression and diffusion across a fluid-filled gap. New Biotechnol. Apr 24. [Epub ahead of print]

Stoevesandt O, Taussig M (2012) Affinity Proteomics: The Role of Specific Binding Reagents in Human Proteome Analysis. Expert Revs Proteomics, in press.

Stoevesandt O, He M, Taussig MJ. (2011) Protein microarrays printed from DNA microarrays. Methods Mol Biol. 671:95-106.

Tavoosidana G, Ronquist G, Darmanis S, Yan J, Carlsson L, Wu D, Conze T, Ek P, Semjonow A, Eltze E, Larsson A, Landegren UD, Kamali-Moghaddam M. (2011) Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer. Proc Natl Acad Sci U S A. 108:8809-14.

Yepes D, Jacob A, Dauber M, Costina V, Hofheinz R, Neumaier M, Findeisen P (2011) Substrate optimization and clinical validation of reporter peptides for MS-based protease profiling in serum specimens: a new approach for diagnosis of malignant disease. Int J Oncol. 39:145-54

Zieba A, Grannas K, Söderberg O, Nilsson M, Landegren U (2012) Molecular tools for companion diagnostics. New Biotechnology (in press)

Zieba A, Pardali K, Soderberg O, Lindbom L, Nystrom E, Moustakas A, Heldin CH, Landegren U. (2012) Intercellular variation in signaling through the TGF-beta pathway and its relation to cell density and cell cycle phase. Mol Cell Proteomics. [Epub ahead of print]