A manufacturing method comprises collecting a sample from a cell culture used by a manufacturing application, and controlling a Raman spectrometer to collect a Raman spectrum of a targeted volume within the sample. The method further comprises obtaining reference spectra uniquely associated with a known cell line, which comprise at least two of: spectral measurements of mycoplasma by itself, a contaminated cell line, and a pure cell line. Moreover, the method comprises comparing the reference spectra to the collected spectrum, and identifying whether there is at least one unnatural molecular composition within the collected spectrum based upon the comparison of the reference spectra to the collected spectrum. An indication is provided as to whether mycoplasma is detected in the collected Raman spectrum where at least one unnatural molecular composition is identified within the collected spectrum, and the manufacturing application is stopped where mycoplasma is detected in the collected Raman spectrum.