Infrared (IR) spectroscopy is well established as a valuable technique for assessing protein secondary structure in solutions. One particular form of IR spectroscopy, Fourier transform infrared spectroscopy (FTIR), has become an especially preferred form of IR spectroscopy for the study of protein secondary structure. FTIR has great utility in the rapid determination of secondary structure because it offers accurate, high-resolution spectra with excellent sensitivity & signal-to-noise (S/N) ratios, as compared to other forms of infrared spectroscopy. Over the last thirty years, these properties of FTIR have been increasingly recognized and FTIR has developed into a reliable & accurate technique for the identification of structural features of a variety of samples, including protein secondary structure. The possibility of Fourier transform infrared (FT-IR) spectroscopy to assess the overall molecular composition of microbial cells in a non-destructive manner is reflected in the specific spectral fingerprints highly typical for different microorganisms. With the objective of using FT-IR spectroscopy for discrimination between diverse microbial species and strains on a routine basis, a wide range of chemometrics techniques need to be applied.