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.

TRIC : An automated alignment strategy for reproducible protein quantification in targeted proteomics / H.L. Röst, Y. Liu, G. D'Agostino, M. Zanella, P. Navarro, G. Rosenberger, B.C. Collins, L. Gillet, G. Testa, L. Malmström, R. Aebersold. - In: NATURE METHODS. - ISSN 1548-7091. - 13:9(2016), pp. 777-783. [10.1038/nmeth.3954]

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

G. D'Agostino;M. Zanella;G. Testa;
2016

Abstract

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.
biotechnology; molecular biology; biochemistry; cell biology
Settore BIO/11 - Biologia Molecolare
Settore BIO/13 - Biologia Applicata
Settore INF/01 - Informatica
Settore BIO/10 - Biochimica
Settore BIO/18 - Genetica
Article (author)
File in questo prodotto:
File Dimensione Formato  
Roest et al Nature Methods 2016.pdf

accesso riservato

Tipologia: Publisher's version/PDF
Dimensione 782.25 kB
Formato Adobe PDF
782.25 kB Adobe PDF   Visualizza/Apri   Richiedi una copia
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/445912
Citazioni
  • ???jsp.display-item.citation.pmc??? 62
  • Scopus 106
  • ???jsp.display-item.citation.isi??? 102
social impact