Abstract
Affinity peptidomics relies on the successfully proven approach used widely in mass-spectrometry-based protein analysis, where protein samples are proteolytically digested prior to the analysis. Unlike traditional proteomic analyses, affinity peptidomics employs affinity detection instead of, or in addition to, the mass-spectrometry detection. Affinity peptidomics, therefore, bridges the gap between protein microarrays and mass spectrometry and can be used for the detection, identification and quantification of endogenous or proteolytic peptides on microarrays and by MALDI-MS. Phage display technology is a widely applicable generic molecular display method suitable for studying protein–protein or protein–peptide interactions and the development of recombinant affinity reagents. Phage display complements the affinity peptidomics approach when the latter is used, e.g. to characterise a repertoire of antigenic determinants of polyclonal, monoclonal antibodies or other recombinantly obtained affinity reagents or in studying protein–protein interactions. 3D materials such as membrane-based porous substrates and acrylamide hydrogels provide convenient alternatives and are superior to many 2D surfaces in maintaining protein conformation and minimising non-specific interactions. Hydrogels have been found to be advantageous in performing antibody affinity assays and peptide-binding assays. Here we report a range of peptide selection and peptide-binding assays used for the detection, quantification or validation of peptide targets using array-based techniques and fluorescent or MS detection.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Guschin, D., Yershov, G., Zaslavsky, A., Gemmell, A., Shick, V., Proudnikov, D., Arenkov, P. and Mirzabekov, A. (1997) Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal. Biochem. 250, 203–211.
Vasiliskov, A.V., Timofeev, E.N., Surzhikov, S.A., Drobyshev, A.L., Shick, V.V. and Mirzabekov, A.D. (1999) Fabrication of microarray of gel-immobilized compounds on a chip by copolymerization. Biotechniques 27, 592–594.
Lueking, A., Horn, M., Eickhoff, H., Bussow, K., Lehrach, H. and Walter, G. (1999) Protein microarrays for gene expression and antibody screening. Anal. Biochem. 270, 103–111.
MacBeath, G. and Schreiber, S.L. (2000) Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763.
de Wildt, R.M., Mundy, C.R., Gorick, B.D. and Tomlinson, I.M. (2000) Antibody arrays for high-throughput screening of antibody–antigen interactions. Nat. Biotechnol. 18, 989–994.
Arenkov, P., Kukhtin, A., Gemmell, A., Voloshchuk, S., Chupeeva, V. and Mirzabekov, A. (2000) Protein microchips: use for immunoassay and enzymatic reactions. Anal. Biochem. 278, 123–131.
Soloviev, M., Barry, R. and Terrett, J. (2004) Chip based proteomics technology, in Molecular Analysis and Genome Discovery (Rapley R., Harbron S., ed.), John Wiley and Sons Ltd, New York, pp. 217–249.
Scrivener, E., Barry, R., Platt, A., Calvert, R., Masih, G., Hextall, P., Soloviev, M. and Terrett, J. (2003) Peptidomics: a new approach to affinity protein microarrays. Proteomics 3, 122–128.
Barry, R. and Soloviev, M. (2004) Peptidomics approaches to proteomics research. BIOforum Eur. 1, 34–36.
Soloviev, M. and Finch, P. (2005) Peptidomics, current status. J. Chromatogr. B. 815, 11–24.
Soloviev, M. and Terrett, J. (2005) Practical guide to protein microarrays: assay systems, methods and algorithms, in Protein Microarrays (Schena M., ed.), Jones and Bartlett Publishers, Boston, MA, pp. 43–56.
Clarckson, T., Hoogenboom, H.R., Griffiths, A.D. and Winter, G. (1991) Making antibody fragments using phage display libraries. Nature 352, 624–628.
Knappik, A., Ge, L., Honegger, A., Pack, P., Fischer, M., Wellnhofer, G., Hoess, A., Wolle, J., Pluckthun, A. and Virnekas, B. (2000) Fully synthetic human combinatorial antibody libraries (HuCAL). J. Mol. Biol. 296, 57–86.
Binz, K.H. and Plückthun, A. (2005) Engineered proteins as specific binding reagents. Curr. Opin. Biotechnol. 16, 459–469.
Messmer, B.T., Benham, C.J. and Thaler, D.S. (2000) Sequential determination of ligands binding to discrete components in heterogeneous mixtures by iterative panning and blocking (IPAB). J. Mol. Biol. 296, 821–832.
Kay, B.K., Kasanov, J. and Yamabhai, M. (2001) Screening phage-displayed combinatorial peptide libraries. Methods 24, 240–246.
Noren, K.A. and Noren, C.J. (2001) Construction of high-complexity combinatorial phage display peptide libraries. Methods 23, 169–178.
Smith, G.P. (1985) Filamentous fusion phage: novel expression vectors that display clones antigens on the virion surface. Science 228, 1315–1317.
Ditzel, H.J., Barbas, S.M., Barbas, C.F., 3rd and Burton, D.R. (1994) The nature of the autoimmune antibody repertoire in human immunodeficiency virus type 1 infection. Proc. Natl Acad. Sci. USA. 91, 3710–3714.
Scott, J.K. and Smith, G.P. (1990) Searching for peptide ligands with an epitope library. Science 249, 386–390.
Cwirla, S.E., Peters, E.A., Barrett, R.W. and Dower, W.J. (1990) Peptides on phage: a vast library of peptides for identifying ligands. Proc. Natl Acad. Sci. USA. 87, 6378–6382.
Devlin, J.J., Panganiban, L.C. and Devlin, P.E. (1990) Random peptide libraries: a source of specific protein binding molecules. Science. 249, 404–406.
Barry, R., Scrivener, E., Soloviev, M. and Terrett, J. (2002) Chip-based proteomics technologies. Int. Genomic Proteomic Technol. Feb, 14–22.
Quanjun, L., Wei, Z., Hong, W., Jujun, Z., Yujie, Z. and Zuhong, L. (2002) Detection YMDD mutation of HBV with a polyacrylamide film immobilized molecular beacon array. 8th International conference on Electronic Materials, IUMRS-ICEM 2002, Xi’an, China, pp. 387–39.2
Brueggemeier, S.B., Kron, S.J. and Palecek, S.P. (2004) Use of protein-acrylamide copolymer hydrogels for measuring protein concentration and activity. Anal. Biochem. 329, 180–189.
Burnham, M.R., Turner, J.N., Szarowski, D. and Martin, D.L. (2006) Biological functionalization and surface micropatterning of polyacrylamide hydrogels. Biomaterials 27, 5883–5891.
Salata, O. (2007) Nanotechnology in therapeutics: hydrogels and beyond. J. Nanobiotechnol. 5, 5.
Jacchetti, E., Emilitri, E., Rodighiero, S., Indrieri, M., Gianfelice, A., Lenardi, C., Podestà, A., Ranucci, E., Ferruti, P. and Milani, P. (2008) Biomimetic poly(amidoamine) hydrogels as synthetic materials for cell culture. J. Nanobiotechnol. 6, 14.
Tang, J. and Xiao, P. (2009) Polymerizing immobilization of acrylamide-modified nucleic acids and its application. Biosens. Bioelectron. 24, 1817–1824.
Barbas, C.F., 3rd, Kang, A.S., Lerner, R.A. and Benkovic, S.J. (1991) Assembly of combinatorial antibody libraries on phage surfaces: the gene III site. Proc. Natl Acad. Sci. USA. 88, 7978–7982.
Hoogenboom, H.R., Griffiths, A.D., Johnson, K.S., Chiswell, D.J., Hudson, P. and Winter, G. (1991) Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Nucleic Acids Res. 19, 4133–4137.
Griffiths, A.D., Williams, S.C., Hartley, O., Tomlinson, I.M., Waterhouse, P., Crosby, W.L., Kontermann, R.E., Jones, P.T., Low, N.M., Allison, T.J., Prospero, T.D., Hoogenboom, H.R., Nissim, A., Cox, J.P.L., Harrison, J.L., Zaccolo, M., Gherardy, E. and Winter, G. (1994) Isolation of high affinity human antibodies directly from large synthetic repertoires. EMBO J. 13, 3245–3260.
Vaughan, T.J., Williams, A.J., Pritchard, K., Osbourn, J.K., Pope, A.R., Earnshaw, J.C., McCafferty, J., Hodits, R.A., Wilton, J. and Johnson, K.S. (1996) Human antibodies with sub-nanomolar affinities isolated from a large non-immunized phage display library. Nat. Biotechnol. 14, 309–314.
Rai, A.J., Gelfand, C.A., Haywood, B.C., Warunek, D.J., Yi, J., Schuchard, M.D., Mehigh, R.J., Cockrill, S.L., Scott, G.B., Tammen, H., Schulz-Knappe, P., Speicher, D.W., Vitzthum, F., Haab, B.B., Siest, G. and Chan, D.W. (2005) HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5, 3262–3277.
Barry, R., Diggle, T., Terrett, J. and Soloviev, M. (2003) Competitive assay formats for high-throughput affinity arrays. J. Biomol. Screen. 8, 257–263.
Heo, J. and Crooks, R.M. (2005) Microfluidic biosensor based on an array of hydrogel-entrapped enzymes. Anal. Chem. 77, 6843–6851.
Zubtsov, D.A., Savvateeva, E.N., Rubina, A.Y., Pan’kov, S.V., Konovalova, E.V., Moiseeva, O.V., Chechetkin, V.R. and Zasedatelev, A.S. (2007) Comparison of surface and hydrogel-based protein microchips. Anal. Biochem. 368, 205–213.
Thomas, G., El-Giar, E.M., Locascio, L.E. and Tarlov, M.J. (2006) Hydrogel-immobilized antibodies for microfluidic immunoassays: hydrogel immunoassay. Methods Mol. Biol. 321, 83–95.
Parker, L.L., Brueggemeier, S.B., Rhee, W.J., Wu, D., Kent, S.B., Kron, S.J. and Palecek, S.P. (2006) Photocleavable peptide hydrogel arrays for MALDI-TOF analysis of kinase activity. Analyst 131, 1097–1104.
Rubina, A.Y., Dyukova, V.I., Dementieva, E.I., Stomakhin, A.A., Nesmeyanov, V.A., Grishin, E.V. and Zasedatelev, A.S. (2005) Quantitative immunoassay of biotoxins on hydrogel-based protein microchips. Anal. Biochem. 340, 317–329.
Tanaka, H., Hanasaki, M., Isojima, T., Takeuchi, H., Shiroya, T. and Kawaguchi, H. (2009) Enhancement of sensitivity of SPR protein microarray using a novel 3D protein immobilization. Colloids Surf. B Bioint. 70, 259–265.
Dyukova, V.I., Dementieva, E.I., Zubtsov, D.A., Galanina, O.E., Bovin, N.V. and Rubina, A.Y. (2005) Hydrogel glycan microarrays. Anal. Biochem. 347, 94–105.
Charles, P.T., Taitt, C.R., Goldman, E.R., Rangasammy, J.G. and Stenger, D.A. (2004) Immobilization strategy and characterization of hydrogel-based thin films for interrogation of ligand binding with staphylococcal enterotoxin B (SEB) in a protein microarray format. Langmuir 20, 270–272.
Hofmann, H.J. and Hädge, D. (1987) On the theoretical prediction of protein antigenic determinants from amino acid sequences. Biomed. Biochim. Acta 46, 855–866.
Pellequer, J.L. and Westhof, E. (1993) PREDITOP: a program for antigenicity prediction. J. Mol. Graph. 11, 204–210.
Ponomarenko, J.V. and Bourne, P.E. (2007) Antibody–protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct. Biol. 7, 64.
Flower, D.R. (2007) Immunoinformatics and the in silico prediction of immunogenicity. An introduction. Methods Mol. Biol. 409, 1–15.
El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2008) Predicting linear B-cell epitopes using string kernels. J. Mol. Recognit. 21, 243–255.
Chen, J., Liu, H., Yang, J. and Chou, K.C. (2007) Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 33, 423–428.
Ponomarenko, J., Bui, H.H., Li, W., Fusseder, N., Bourne, P.E., Sette, A. and Peters, B. (2008) ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9, 514.
Van Regenmortel, M.H. and Pellequer, J.L. (1994) Predicting antigenic determinants in proteins: looking for unidimensional solutions to a three-dimensional problem?. Pept. Res. 7, 224–228.
Hopp, T.P. and Woods, K.R. (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl Acad. Sci. USA. 78, 3824–3828.
Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105–312.
Hopp, T.P. (1993) Retrospective: 12 years of antigenic determinant predictions, and more. Pept. Res. 6, 183–190.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Zhang, F., Dulneva, A., Bailes, J., Soloviev, M. (2010). Affinity Peptidomics: Peptide Selection and Affinity Capture on Hydrogels and Microarrays. In: Soloviev, M. (eds) Peptidomics. Methods in Molecular Biology, vol 615. Humana Press. https://doi.org/10.1007/978-1-60761-535-4_23
Download citation
DOI: https://doi.org/10.1007/978-1-60761-535-4_23
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-534-7
Online ISBN: 978-1-60761-535-4
eBook Packages: Springer Protocols