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).