A new sample preparation method was developed for fresh, whole-cell Gram-positive bacteria to be analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI ToF MS). With fresh, whole-cell Gram-negative bacteria of the Enterobacteriaceae family, we had previously achieved spectra consisting of >50 peaks and mass ranges of 2-25 kDa. Because similar spectral quantity could not be achieved for Gram-positive bacteria, using this same protocol, we investigated an alternative approach that focuses on the thick peptidoglycan layer of the cell wall. Gram-positive bacteria were incubated with 0.05-0.5 mg/ml lysozyme for 30 min prior to being analyzed by MALDI ToF MS. Lysozyme is an enzymatically stable, 14-kDa protein that specifically cleaves between peptidoglycan disaccharide subunits. A significant increase in overall number of peaks (>50) in the 2-14 kDa range was observed without interference from the presence of lysozyme. We show that for four different species (Staphylococcus aureus, S. haemolyticus, Streptococcus pyogenes, and S. agalactiae) reproducible subset of peaks were found within spectra from a reference strain and two unrelated clinical isolates. The data suggests that this sample preparation may be useful for increasing the overall number of peaks within spectra for subsequent development of bacterial identification strategies.