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

Nat Methods. 2016 Sep;13(9):777-83. doi: 10.1038/nmeth.3954. Epub 2016 Aug 1.


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 (, 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.

MeSH terms

  • Algorithms
  • Electronic Data Processing / instrumentation
  • Electronic Data Processing / methods*
  • Humans
  • Mass Spectrometry
  • Peptides / analysis*
  • Peptides / metabolism
  • Pluripotent Stem Cells / metabolism
  • Protein Precursors / analysis
  • Protein Precursors / metabolism
  • Proteolysis
  • Proteomics / instrumentation
  • Proteomics / methods*
  • Reproducibility of Results
  • Sequence Alignment / instrumentation
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / instrumentation
  • Sequence Analysis, Protein / methods*
  • Software*
  • Streptococcus pyogenes / metabolism


  • Peptides
  • Protein Precursors