Rapid identification of microorganisms using matrix assisted laser desorption/ionization (MALDI) is a rapidly growing area of research due to the minimal sample preparation, speed of analysis and broad applicability of the technique. This approach relies on expressed biochemical markers, often proteins, to identify microorganisms. Therefore, variations in culture conditions that affect protein expression may limit the ability of MALDI-MS to correctly identify an organism. We have expanded our efforts to investigate the effects of culture conditions on MALDI-MS signatures to specifically examine the effects of pH, growth rate and temperature. Continuous cultures maintained in bioreactors were used to maintain specific growth rates and pH for E. coli HB 101. Despite measurable morphological differences between growth conditions, the MALDI-MS data associated each culture with the appropriate library entry (E. coli HB 101 generated using batch culture on a LB media), independent of pH or growth rate. The lone exception was for a biofilm sample collected from one of the reactors which had no appreciable degree of association with the correct library entry. Within the data set for planktonic organisms, variations in growth rate created the largest variation between fingerprints. The effect of varying growth temperature on Y. enterocolitica was also examined. While the anticipated effects on phenotype were observed, the MALDI-MS technique provided the proper identification.