Fig. 6
From: Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer
Targeted proteomics of saliva proteins. a, b Volcano analyses show log2 ratio of N+/N0 of a proteins and b peptides according to the adjusted P value. Proteins that met the indicated statistical cut-off criteria (Mann−Whitney U test, with P values adjusted for multiple comparisons using the Benjamini−Hochberg FDR method, adjusted P value < 0.05) are colored in red. c The graph demonstrates individually the L/H intensity ratio (not log transformed) of six differentially expressed proteins CSTB, COL6A1, ITGAV, LTA4H, PGK1, and NDRG1 between N+ and N0 saliva samples. *P value < 0.05, Mann−Whitney U test. d Peptide relative quantification (log2 L/H ratio) between N+ and N0 saliva samples. For each protein, 2−3 proteotypic peptides were monitored, with exception for NDRG1, only one proteotypic peptide was monitored. The light peptide (corresponding to the endogenous peptide present in saliva) and the heavy peptide (which corresponds to the synthetic peptide spiked-in saliva) were monitored, and the light/heavy ratio for each of the 14 peptides was obtained by Skyline. Box plots represent the median and interquartile range, whiskers represent the 1–99 percentile, and outliers are represented by empty circles. e Bar plots represent the relationship between MS Discovery analysis of tissue and SRM-MS of saliva in the identification of potential prognostic signatures. The log2 N+/N0 ratio for saliva samples and log2 ITF/inner ratio for neoplastic islands and tumor stroma from microdissected tissues are represented in the graph. f Representative figure illustrates the gradient dynamics of the protein abundance between tissue (ITF and inner tumor) and saliva (N+ and N0), which indicates that the abundance of proteins in saliva and its association with prognosis (N+ and N0) is not necessarily associated with the proximity of the altered oral epithelium. Other components, such as water, electrolytes, DNA, RNA, and microorganisms, were not included. Images in f were adapted from files provided by Servier Medical Art (https://smart.servier.com/, licensed under a Creative Commons Attribution 3.0 Unported License)
