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TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
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TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
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Journal Article
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
2016
Overview
TRIC, a cross-run alignment algorithm and software tool, enables reproducible quantification of thousands of peptides across multiple targeted liquid chromatography–tandem mass spectrometry runs.
Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography–tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (
http://proteomics.ethz.ch/tric/
), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ 82/58
/ Biomedical and Life Sciences
/ Biomedical Engineering/Biotechnology
/ Electronic Data Processing - instrumentation
/ Electronic Data Processing - methods
/ Humans
/ Pluripotent Stem Cells - metabolism
/ Protein Precursors - analysis
/ Protein Precursors - metabolism
/ Proteins
/ Proteomics - instrumentation
/ Sequence Alignment - instrumentation
/ Sequence Alignment - methods
/ Sequence Analysis, Protein - instrumentation
/ Sequence Analysis, Protein - methods
/ Software
/ Streptococcus pyogenes - metabolism
/ Studies
