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.
At a glance
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- Supplementary Text and Figures (2,802 KB)
Supplementary Notes 1–7
- Supplementary Software (1,023 KB)
- Supplementary Table 1 (5,888 KB)
Result table describing the manually picked peptides with retention times and peak boundaries.
- Supplementary Table 2 (140 KB)
Significant proteins from the S. pyogenes analysis without any alignment.
- Supplementary Table 3 (166 KB)
Significant proteins from the S. pyogenes analysis with TRIC alignment.
- Supplementary Table 4 (569 KB)
Degradation rates for the iPSC as determined by SWATH-MS analysis on the peptide level.
- Supplementary Table 5 (89 KB)
Degradation rates for the iPSCs as determined by SWATH-MS analysis on the protein level.
- Supplementary Table 6 (32 KB)
GO-enrichment analysis using Gorilla.