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TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
Open accessAbstract
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.
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Metadata
- Authors
- Röst, H. L., Liu, Y., D'Agostino, G., Zanella, M., Navarro, P., Rosenberger, G., Collins, B. C., Gillet, L., Testa, G., Malmström, L., & Aebersold, R.
- Venue
- Nature Methods
- Published
- 2016-08-01
- Volume
- 13
- Issue
- 9
- Pages
- 777-783
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2498136312
- Cited by
- 175
- References
- 23
- FWCI
- 8.69
- Type
- journal article
- Language
- en
- Open access
- green
- Licence
- www.springer.com/tdm (tdm)
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