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Introduction: Particles in Exhaled Air (PExA) is a relatively new method for non-invasive sampling of the small airways. It seeks to count and capture the aerosols that are exhaled after a breathing maneuver specifically designed to expel them. The aim of this study was to optimize the extraction of proteins from such PExA samples, specifically complement protein C3, utilizing the new sample Punch Out Technique (sPOT). To accomplish this, two filters for PExA sample collection and seven buffers for PExA sample extraction were selected and compared. Method: The method used to gather the samples was PExA, with the sPOT technique to prepare the sample for analysis. To identify C3 in the samples an automatic Western blot called Wes was used. Results: The extraction process that seemed to yield the most of other proteins was a Millipore PTFE filter extracted in RIPA-buffer. With the monoclonal antibody for C3 selected, Wes was unable to detect any C3 in the PExA samples. Albumin, IgG and transferrin were however detectable. Discussion: Seeing as other proteins were detectable in the extracted PExA-samples, such as albumin, transferrin, and IgG, the extraction process was successful. This means C3 either has too low of a concentration to be detectable in PExA samples, or perhaps there is some interference during the extraction process.