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

Wingren, Christer LU ; James, Peter LU and Borrebaeck, Carl LU (2009) In Proteomics 9(6). p.1511-1517
Abstract
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Proteomics
volume
9
issue
6
pages
1511 - 1517
publisher
John Wiley & Sons
external identifiers
  • wos:000264890400009
  • pmid:19235165
  • scopus:63049087845
ISSN
1615-9861
DOI
10.1002/pmic.200800802
language
English
LU publication?
yes
id
545b5200-87c6-4e17-ad3b-6058caff0f91 (old id 1302297)
date added to LUP
2009-03-27 13:14:34
date last changed
2017-10-22 03:53:03
@article{545b5200-87c6-4e17-ad3b-6058caff0f91,
  abstract     = {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.},
  author       = {Wingren, Christer and James, Peter and Borrebaeck, Carl},
  issn         = {1615-9861},
  language     = {eng},
  number       = {6},
  pages        = {1511--1517},
  publisher    = {John Wiley & Sons},
  series       = {Proteomics},
  title        = {Strategy for surveying the proteome using affinity proteomics and mass spectrometry.},
  url          = {http://dx.doi.org/10.1002/pmic.200800802},
  volume       = {9},
  year         = {2009},
}