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Nat Methods. 2011 Nov 6;8(12):1041-3. doi: 10.1038/nmeth.1770.

Rapid empirical discovery of optimal peptides for targeted proteomics.

Author information

1
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.

Abstract

We report a method for high-throughput, cost-efficient empirical discovery of optimal proteotypic peptides and fragment ions for targeted proteomics applications using in vitro-synthesized proteins. We demonstrate the approach using human transcription factors, which are typically difficult, low-abundance targets and empirically derived proteotypic peptides for 98% of the target proteins. We show that targeted proteomic assays developed using our approach facilitate robust in vivo quantification of human transcription factors.

PMID:
22056677
PMCID:
PMC3227787
DOI:
10.1038/nmeth.1770
[Indexed for MEDLINE]
Free PMC Article

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