Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy are analytical techniques employed for the analysis of protein secondary structure. The use of CD spectroscopy is limited to low protein concentrations (<2mg ml1), while FTIR spectroscopy is commonly used in a higher concentration range (>5mg ml1). Here we introduce a quantum cascade laser (QCL)-based IR transmission setup for analysis of protein and polypeptide secondary structure at concentrations as low as 0.25mg ml1 in deuterated buffer solution. We present dynamic QCL-IR spectra of the temperature-induced -helix to -sheet transition of poly-L-lysine. The concentration dependence of the - transition temperature between 0.25 and 10mg ml1 was investigated by QCL-IR, FTIR and CD spectroscopy. By using QCL-IR spectroscopy it is possible to perform IR spectroscopic analysis in the same concentration range as CD spectroscopy, thus enabling a combined analysis of biomolecules secondary structure by CD and IR spectroscopy.