Differences between Spectral Clustering clusters in salivary lysozyme and chitinase activity compared using one-way ANOVA and Games-Howell post-hoc tests.

<p>The magnitude of the inter-cluster differences is quantified using Cohen’s <i>d</i> measure of effect size (<i>i</i>.<i>e</i>. the difference between the two means divided by the standard deviation of the data).</p

Boxplots stratified on the 4 clusters showing peak intensities across the sample population for the 9 peaks determining the clustering structure.

<p>X-axis contains the 4 clusters. Y-axis contains the peak intensity, scaled from 0 (minimum detection level) to 100 (maximum detected intensity of any peak across all samples and peaks). Peaks are listed in decreasing order of their importance for the clustering, same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156707#pone.0156707.t002" target="_blank">Table 2</a>. (A) P-C peptide, Fr. 15–44. (B) P-C peptide, Fr. 1–25. (C) unidentified peak (m/z = 5980). (D) P-C peptide (1+ charge). (E) unidentified peak (m/z = 2725). (F) Cystatin B, Fr. 1–53. (G) P-C peptide, Fr. 15–35. (H) P-C peptide (2+ charge). (I) II-2 basic proline-rich protein, phosphorylated.</p

Peaks identified by Unsupervised Feature Selection to be determining the subgroups found by Spectral Clustering. Peaks are listed in decreasing order of their effect on the clustering.

<p>Peaks identified by Unsupervised Feature Selection to be determining the subgroups found by Spectral Clustering. Peaks are listed in decreasing order of their effect on the clustering.</p

Putative identities for peaks in the MALDI-TOF MS spectra of saliva from healthy volunteers.

<p>Putative identities for peaks in the MALDI-TOF MS spectra of saliva from healthy volunteers.</p

Spectral Clustering co-occurrence plot.

<p>Participants are ordered along both X- and Y-axis according to the co-occurrence score (i.e. the more similar the peptide profiles of any two participants, the higher their tendency to cluster together and the closer they are placed on the axis). Co-occurrence score values range from 0 (for participants who never cluster together) to 1.0 (for participants who always cluster together). The horizontal bar delimits the four clusters.</p

PCA scores plot.

<p><b>(A) PCA based on all 80 peaks compared to (B) PCA scores plot based solely on the 9 peaks resulting from the Feature Selection procedure.</b> Individuals are color labeled according to their cluster. The proportion of variance explained was as follows: (A) PC1–17.4%, PC2–8.8% (26.2% cumulative). (B) PC1–39.5%, PC2–26.3% (65.8% cumulative).</p