Abstract
Sequential Window Acquisition of all THeoretical fragment ion spectra (SWATH) is a data independent acquisition mode used to accurately quantify thousands of proteins in a biological sample in a single run. It exploits fast scanning hybrid mass spectrometers to combine accuracy, reproducibility and sensitivity. This method requires the use of ion libraries, a sort of databases of spectral and chromatographic information about the proteins to be quantified. In this chapter, a typical workflow of SWATH experiment is described, from the sample preparation to the analysis of proteomics data.
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Acknowledgments
The help of Dr. Valeria Tomati, from Gaslini Children Hospital, Genova, is gratefully acknowledged. This work was supported by Fondazione Italiana Ricerca Fibrosi Cistica (grant FFC#1-2019 to AA).
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Braccia, C., Liessi, N., Armirotti, A. (2021). Quantification of Changes in Protein Expression Using SWATH Proteomics. In: Cecconi, D. (eds) Proteomics Data Analysis. Methods in Molecular Biology, vol 2361. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1641-3_5
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DOI: https://doi.org/10.1007/978-1-0716-1641-3_5
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