enterica proteins: PduC (2, 3); PduP (5, 6); PduD (8); PduB (9, 10); PduB' (11, 12); PduK (13, 14); PduT (15); PduU (18); PduH, and PduJ (20). Although the sequence coverages for spot 4 provided by MS-Fit and Profound were 15 and 1600 respectively, the comparison of its spectra with those of spots 5 and 6 indicated that all three of these spots are the PduP protein. The low sequence coverage may be attributed to the quantity of protein used for analysis since spot 4 was visibly less in amount than either spots 5 or 6 and only 6 peptides were matched compared to 15 in spots 5 and 6. Some disparities were noted between the results of the two mass fingerprinting programs and these differences are most likely a result of the different databases searched by MS-Fit or differences in the programs themselves. Using MS-Fit, only searches conducted with the spectra for spots 7, 13, and 14 returned significant matches for Pdu proteins found in the NCBJ-nr database. Matches for the remainder of the proteins were found primarily using the Genpept database except for spots 9,11, and 18, which had significant matches in the Swiss-Prot database. Interestingly, Profound was able to find a significant match for each of the Pdu proteins using only the NCBI-nr database. Also of note is the finding that PduH was not identified using MS-Fit, however a theoretical digest of the protein using MS-digest (http://prospector.ucsf.edu) and a manual comparison of the resulting peptide fragments and the spectra resulted in a match of 4 peptides and a sequence coverage of 4000. In several instances more than one protein spot corresponded to the same pdu protein indicating that some organelle proteins existed in different forms during electrophoresis. This could have resulted from incomplete denaturation of the polyhedral organelles prior to isoelectric focusing, from the tight association of lipids or proteins, or from covalent modification. To break down possible non-covalent interactions, dodecyl-