3.1 Protein detection, identification, and primary data
According to TMT data, a total of 33204 spectrum and 22138 unique peptides were identified, and 5681 proteins were detected (Figure S1A and Table S1). The functional annotation of proteins was displayed in Figure S1B. The majority of the identified peptides’ mass error-matching distribution within were 10 ppm (Figure S2A), indicating good accuracy and reliability for the identification of peptides. After sufficient proteolysis, peptides typically contained 6 to 25 amino acids (Figure S2B), showing that the lengths of the peptides was reasonable. Additionally, over 50% of the identified proteins had a molecular weight distribution of 20–80 kDa (Figure S3A), while less than 30% of the identified protein had sequence coverage (Figure S3B). The isoelectric point of identified proteins generally fell between 4.5 and 10. The overall expression trends of all identified proteins are shown in Figure S4.
Three biological replicates were clustered after the PCA analysis, which demonstrated that TH samples from two hosts could be differentiated successfully and had acceptable repeatability (Figure 1A). Figure 1B displayed the correlation between the two sample groups. 533 proteins in total were significantly differentially expressed, 259 of which were up-regulated and 274 of which were down-regulated in TH from FXS (Figure 1C and Table S2).