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Strategy for surveying the proteome using affinity proteomics and mass spectrometry.

  • Christer Wingren
  • Peter James
  • Carl Borrebaeck
Publishing year: 2009
Language: English
Pages: 1511-1517
Publication/Series: Proteomics
Volume: 9
Issue: 6
Document type: Journal article
Publisher: John Wiley & Sons

Abstract english

Antibody-based microarrays is a rapidly evolving technology that has gone from the first proof-of-concept studies to more demanding proteome profiling applications, during the last years. Miniaturized microarrays can be printed with large number of antibodies harbouring predetermined specificities, capable of targeting high- as well as low-abundant analytes in complex, nonfractionated proteomes. Consequently, the resolution of such proteome profiling efforts correlate directly to the number of antibodies included, which today is a key limiting factor. To overcome this bottleneck and to be able to perform in-depth global proteome surveys, we propose to interface affinity proteomics with MS-based read-out, as outlined in this technical perspective. Briefly, we have defined a range of peptide motifs, each motif being present in 5-100 different proteins. In this manner, 100 antibodies, binding 100 different motifs commonly distributed among different proteins, would potentially target a protein cluster of 10(4) individual molecules, i.e. around 50% of the nonredundant human proteome. Notably, these motif-specific antibodies would be directly applicable to any proteome in a specie independent manner and not biased towards abundant proteins or certain protein classes. The biological sample is digested, exposed to these immobilized antibodies, whereby motif-containing peptides are specifically captured, enriched and subsequently detected and identified using MS.


  • Immunology in the medical area


  • ISSN: 1615-9861
Carl B
Carl Borrebaeck
E-mail: carl [dot] borrebaeck [at] immun [dot] lth [dot] se


Department of Immunotechnology




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