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Automated Selected Reaction Monitoring Software for Accurate Label-Free Protein Quantification.

Teleman, Johan LU ; Karlsson, Christofer LU ; Waldemarson, Sofia LU ; Hansson, Karin M LU ; James, Peter LU ; Malmström, Johan LU and Levander, Fredrik LU (2012) In Journal of Proteome Research 11(7). p.3766-3773
Abstract
Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide... (More)
Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Proteome Research
volume
11
issue
7
pages
3766 - 3773
publisher
The American Chemical Society
external identifiers
  • pmid:22658081
  • wos:000306049800021
  • scopus:84863624355
ISSN
1535-3893
DOI
10.1021/pr300256x
language
English
LU publication?
yes
id
1d135957-d015-4c4a-8100-26dadc5396c5 (old id 2859864)
date added to LUP
2012-07-10 11:27:37
date last changed
2017-10-01 03:33:06
@article{1d135957-d015-4c4a-8100-26dadc5396c5,
  abstract     = {Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.},
  author       = {Teleman, Johan and Karlsson, Christofer and Waldemarson, Sofia and Hansson, Karin M and James, Peter and Malmström, Johan and Levander, Fredrik},
  issn         = {1535-3893},
  language     = {eng},
  number       = {7},
  pages        = {3766--3773},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Automated Selected Reaction Monitoring Software for Accurate Label-Free Protein Quantification.},
  url          = {http://dx.doi.org/10.1021/pr300256x},
  volume       = {11},
  year         = {2012},
}