Research Paper Volume 16, Issue 3 pp 2194—2231

Figure 3. Proteomics of pathological tissue sections in psoriatic skin and normal skin. (A) Schematic diagram of the quantitative proteomics sequencing process for formalin-fixed and paraffin-embedded (FFPE) pathology sections. (I) Formalin-fixed and paraffin-embedded (FFPE) pathology section. (II) Enzymatic digestion and extraction of proteins. (III) Schematic diagram of LC-MS/MS. (IV) Label-free quantification. (B) Clinical information on patients: 9 patients with psoriasis and 6 specimens of normal skin. (C) Principal component cluster analysis for protein quantification of all clinical samples, with the degree of aggregation representing the magnitude of inter-sample variability. The results show that the normal and psoriatic samples clustered to form two major groups, indicating the heterogeneity that exists between the samples and a true reflection of the differences between the two groups. (D) Correlation analysis between all samples. The colours and numbers represent the strength of the correlation. (E) Peptide length distribution in pathological histological sections of psoriatic skin and normal skin. The vertical axis represents the ratio of charged particle mass to charge, i.e. the mass-to-charge ratio (m/z), and the horizontal axis represents the peptide length, with each point indicating a different peptide segment and the colour indicating a different charge gradient. The bar graph represents the charge. (F) Protein identification analysis. Total spectrums: the number of secondary spectra generated by mass spectrometry. Matched spectrums: the number of valid spectra, the number of spectra matching the theoretical secondary spectrum. Peptides: the number of identified peptides, the number of peptide sequences resolved by matching. Unique peptides: the number of identified unique peptides, the number of unique peptide sequences resolved by matching. Identified proteins: number of identified proteins, number of proteins resolved by specific peptides. Quantifiable proteins: number of proteins quantified by specific peptides. (G) Distribution of the number of peptides. (H) Protein molecular weight distribution. (I) Protein coverage distribution. Most proteins have less than 30% coverage. In a shotgun (bottom-up) technique based on mass spectrometry, the mass spectra scan for peptides with a greater abundance preference. Thus, protein coverage and abundance in the sample are positively correlated. (J) Quality classification of differential proteins and their KEGG analysis. The quality of differentially expressed proteins is divided into four levels (see Supplementary Table 7 for details). Light purple indicates Q1, light green indicates Q2, pink indicates Q3, light blue indicates Q4. (K) The KEGG pathway of the differential proteins after classification into different groups. Dark red indicates the level of pathway activity. The classical IL-17 pathway is observed in the higher quality Q4 group, which also contains cytokine receptor interactions, further supporting the molecular hypothesis of the follicular psoriasis axis.