The challenge of deriving quantitative information from the infrared spectra of proteins arises from the large number of secondary-structures and amino acid side-chain functional groups that all contribute to the spectral intensity, such as within the Amide-I band (1600-1700 cm -1 ). The band is invariably heavily convoluted from overlapping spectral features thereby making interpretation difficult such that deconvolution is usually required. This work critically examines the methods available to deconvolute the spectra and assesses the commonly used methods and algorithms applied to vibrational spectra for smoothing and peak identification. We show that unless their spectra have very high signal-to noise ratios, quantitative analysis to decipher protein constituents is not feasible. The advantages and disadvantages of spectral smoothing using Adjacent-Averaging (AA), the Savitsky-Golay (SG) filter and the Fast Fourier Transform (FFT) filter are examined in detail. The use of derivative spectra to identify peaks is described with particular reference to the influence and reduction of interfering water bands in the Amide-I region. The reliability of band narrowing techniques such as second-derivative analysis or Fourier deconvolution that lead to the identification of the contributing protein peaks are investigated. Both methods are shown to be limited in their capacity to resolve features with very similar frequencies. Additionally, the presence of narrow bands arising from high frequency noise whether from atmospheric water vapour, acoustic vibrations or electrical interference, results in both methods becoming increasingly unusable as narrow bands are preferentially enhanced at the expense of broad ones such as the Amide-I bands. An optimal strategy is critically developed to allow accurate determination and quantification of protein constituents and their conformations. Additionally, quantitative methods are proposed to account for baseline-shifts which would otherwise introduce significant errors in similarity indices.