SWATH label-free proteomics for cystic fibrosis research

Clarissa Braccia, Valeria Tomati, Emanuela Caci, Nicoletta Pedemonte, Andrea Armirotti

Research output: Contribution to journalArticlepeer-review


BACKGROUND: Label-free proteomics is a powerful tool for biological investigation. The SWATH protocol, relying on the Pan Human ion library, currently represents the state-of-the-art methodology for this kind of analysis. We recently discovered that this tool is not perfectly suitable for proteomics research in the CF field, as it lacks assays for several proteins crucial for the CF biology, including CFTR.

METHODS: We extensively investigated the proteome of a very popular model for in vitro research on CF, CFBE41o-, and we used the corresponding data to improve the power of SWATH proteomics for CF investigation. We then used this improved tool to explore in depth the proteome of primary bronchial epithelial (BE) cells deriving from four CF individuals compared with that of four corresponding non-CF controls. By means of advanced bioinformatics tools, we outlined the presence of a number of protein networks being significantly altered by CF.

RESULTS: Our analysis on patients' BE cells identified 154 proteins dysregulated by the CF pathology (94 upregulated and 60 downregulated). Some known CFTR interactors are present among them, but our analysis also revealed the alteration of other proteins not previously known to be related with CF.

CONCLUSIONS: The present work outlines the power of SWATH label free proteomics applied to CF research.

Original languageEnglish
Pages (from-to)501-506
Number of pages6
JournalJournal of Cystic Fibrosis
Issue number4
Publication statusPublished - Jul 2019


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