Abstract : We show that the origin of the spectral fluctuations frequently observed in tip enhanced Raman spectroscopy (TERS) experiments can be mainly related to the presence of surface-contaminating amorphous carbon- based species. We have monitored the spectral fluctuations originating from the sharp metallic tips used as apertureless near field probes, as well as from commonly used noble metal substrates. A correlation between the tip surface roughness and the carbon-based spectral fluctuations has been revealed. An Au-(1 1 1) bare substrate has been mapped with sub-wavelength resolution by TERS, evidencing the localization of the carbon contaminants on the surface steps and grain boundaries.