Protein profile of exhaled breath condensate determined by high resolution mass spectrometry

A method based on liquid chromatography/high resolution tandem mass spectrometry coupled withelectrophoretic separation, for determination and relative quantification of the protein composition ofexhaled breath condensate (EBC), was developed. Application of the procedure to a sample of EBC, pooledfrom nine healthy subjects, resulted in the identification of 167 unique gene products, 113 of which notpreviously reported in EBC samples. The abundance of the protein identified was estimated by meansof the exponentially modified protein abundance index protocol (emPAI). Cytokeratins were by far themost abundant proteins in EBC samples. Many of the identified proteins were associated with multiplecellular location with cytoplasm constituting the largest group. Cytosol, nucleus, membrane, cytoskeletonand extracellular were other abundantly represented locations. No amylase was detected, suggesting theabsence of saliva protein contamination. The profile obtained represents the most comprehensive proteincharacterization of EBC so far reported and demonstrates that this approach provides a powerful tool forinvestigating the protein profile of EBC samples. Compared with analogous investigations, this study alsoshows that the protein profile of EBC is strongly affected by the sampling method adopted.