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...

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

10.1038/nmeth.3954