Bacteria/Mass Spectrometry Table 3. Settings for weighted-pattern matching algorithm. Species Specific mass signal (m/z) E.a. 1232 E.a. 273 E.a. IL6 E.a. MR1 E.p. Ejp557 E.p. 16/96 3750 4361 8725 8842 9510 9554 7594 8244 8287 4092 5561 8186 7696 4722 9445 7235 1000 1000 1000 1000 5000 1000 1000 1000 5000 1000 1000 1000 1000 2500 5000 5000 2000 5000 5000 5000 5000 5000 5000 5000 5000 To differentiate between the various E. amylovora (E.a.) and E. pyrifoliae (E.p.) sub-species, a weighted-pattern matching algorithm as described in the Methods section was applied. For sub-species identification specific masses in the reference spectra that allow differentiation between sub-species are given an overemphasized value. For E. amylovora unspecific mass signals were set to zero except for the mass signals listed in the table. E. pyrifoliae sub-species can be determined by changing the weight values for the mass signals given in the Table. By summation of all these values each entry in the library acquires a specific number. doi:10.1371/journal.pone.0002843.t003 Figure 6. SNP genoytyping. We genotyped a SNP in the galE gene by MALDI-MS to distinguish E. amylovora strains of North American origin (E. amylovora 273) from that of European/Mediterranean origin such as E. amylovora 1/79 (DSM 17948) and CFBP1430. Masses detected in the spectra correspond to an A-allele (theoretical mass: 1225 m/z) or a C-allele (theoretical mass: 1201 m/z). doi:10.1371/journal.pone.0002843.g006 PLoS ONE | www.plosone.org 8 July 2008 | Volume 3 | Issue 7 | e2843