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J Proteome Res. 2012 Jul 6;11(7):3766-73. doi: 10.1021/pr300256x. Epub 2012 Jun 14.

Automated selected reaction monitoring software for accurate label-free protein quantification.

Author information

1
Protein Technology, Department of Immunotechnology, Lund University, BMC D13, 22184 Lund, Sweden.

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.

PMID:
22658081
PMCID:
PMC3426189
DOI:
10.1021/pr300256x
[Indexed for MEDLINE]
Free PMC Article

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