A new method is proposed for the elimination of the spectral contribution of two atmospheric gases (CO<sub>2</sub> and H<sub>2</sub>O) in Fourier transform infrared (FT-IR) spectra of clinical samples. The algorithm is based on the measurement of reference spectra of H<sub>2</sub>O followed by an automatic calculation of the spectral contribution of the above-mentioned gases to the sample spectra. Then this contribution is compensated by spectral subtraction. Attenuated total reflectance FT-IR spectra of serum and urine samples in the presence of atmospheric gases were corrected and compared with spectra obtained with an N<sub>2</sub> purge. Visual inspection of the spectra as well as calculated noise levels confirmed that the method compensated for the contribution of CO<sub>2</sub> and H<sub>2</sub>O to serum and urine spectra to a great extent. As compared with the correction performed by a commercial software package, the proposed method clearly improved the correction of CO<sub>2</sub> and provided similar results for H<sub>2</sub>O compensation. Correlation values between corrected spectra and those obtained under N<sub>2</sub>-purged conditions in the fingerprint region were higher than 0.995, and noise values in regions where samples did not absorb confirmed the suitability of the correction. The proposed method is fast, easy, and extensible to other gaseous interferences, devices, and acquisition conditions.

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