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Background As a part of development of medicine for extreme situations, we determined, for the first time, the protein composition of the exhaled breath condensate (EBC) of cosmonauts before and after long-lasting orbital flights on the International Space Station (ISS). The purpose of the experiment "Protocon" was the study of the EBC proteome and metabolome changes for Russian cosmonauts, who are members of the main crew of International Space Station (ISS). We started working on this topic in April 2013, with expedition #35 to the ISS. At the moment we have 13 complete sets of samples (before/after flight to ISS). Methods The analysis was performed by electrospray ionization ion cyclotron resonance mass spectrometry. The pattern of variation of the protein composition of the exhaled air during preflight preparation, at the time of landing, and seven days after landing was elucidated. Results Forty-four proteins that appeared in the exhaled breath condensate of the cosmonauts after a long orbital flight and landing and were absent before the flight were detected. These proteins included the immune response proteins, indicating cell and blood vessel damage. Several protein markers of early lung cancer (POTEE, Cep290, and TBC1D1) were found in several EBC samples of crew members post flight, while these markers were absent from the preflight samples and control samples collected from the crew members half year after landing. These landing samples were located in “grey” (undefined) zone in the predictive model for lung cancer based on EBC samples of 130 donors with different pulmonary disorders, while other samples of cosmonauts were located in “green” non-cancer zone (Roc auc score: 0.99. F1 score: 0.93). Conclusions A dynamic observation of changes in EBC composition revealed a dramatic increase in the amount of exhaled proteins at landing. The appearance and subsequent elimination of the cancer markers may be indicative of both potential risk for cancer due to spaceflight factors and overloading (stress and radiation) and the human body potential to restore the normal functions and to prevent cell malignant transformation. Keywords Spaceflight; proteomics; extreme conditions; human proteome; exhaled breath condensate