3.3. The use of PCA in MALDI-TOF MS for chicken feces E. coli
A general PCA analysis (I. Phyloproteomic study) of 122 CFEC isolates was performed, and a dendrogram profile and a 2D scattering profile was formed (Figure 1). Also, the variance values were automatically calculated and shown on the dendrogram in Figure 1A. With these three analyses (dendrogram, scattering profile, and variance), rough preliminary information was obtained according to the cluster formation of the most distant and the farthest and closest ones among 35 isolates among 122 CFECs and the scattering of these isolates. These two profiles and variance values were evaluated together. As seen in Figures 1A and 1B, seven CFEC isolates that are far from the main cluster as they have some differences are separated from other CFECs in the dendrogram profile and settled into separate clusters. For example, CFEC-38 (CFEC-ESBL-38), CFEC-90 (CFEC-ESBL-90), and CFEC-19 isolates with the highest variance (PC1) of 31% in this analysis were placed on the far right in a separate cluster. Also, three E.coli CFEC-108, CFEC-69, and CFEC-35 are separated by a separate line although they appear to be part of the larger cluster by the second variance value (PC2: 14%) (Fig. 1A and B). Consistent with the results in the dendrogram, the scattering profile in Figure 1C also shows that these seven isolates scatter far from the large cluster.