For years mass spectrometrists have sought to develop rapid and accurate means of detecting and characterizing microorganisms. Recently taxonomic identification of pure bacteria has become possible through the use of matrixassisted laser desorption/ionization (MALDI) mass spectrometry, directly detecting abundant proteins and other components that comprise cells during rapid cellular growth. The resultant mass measurement of whole cell bacteria derives primarily from desorbed, intact proteins and lipid components, specific to cells in culture. MALDI mass spectra appear as characteristic profiles that are comprised of biomarkers, unique within particular classes of microorganisms that are sometimes referred to as "fingerprint patterns." These biomarkers, mass to charge observations unique to an organism, are not always assigned as specific proteins or lipids. Rather, low-resolution MALDI spectra are treated as "fingerprints." Subtle changes in either growth of the cell colony or MALDI sample preparations can cause fluctuations in recorded mass fingerprints, distorting biomarkers and complicating microorganism identification. However, reproducibility is sufficiently good that differences in mass fingerprints allows researchers to characterize and identify species of microorganisms. Recently MALDI Fourier transform mass spectrometry (FTMS) of environmental samples has proved its advan-