2.4 Differentially expressed proteins (DEP) analysis
TMT-based quantitative proteomic analysis was the same as description in
our previous article, including Protein extraction and digestion,
protein digestion, TMT labeling, low-pH nano-HPLC-MS/MS analysis, and
the database searching (Zhang et
al. 2019). Database searching was conducted using the present RNA-seq
results (Accession codes: SUB7765255) by Mascot.
For protein quantitation, a protein was required to contain at least two
unique peptides. 9 protein ratios were produced by comparing 3 M4 and 3
M0 (i.e., M4a/M0a, M4a/M0b, M4a/M0c, M4b/M0a, M4b/M0b, M4b/M0c, M4c/M0a,
M4c/M0b, M4c/M0c). then the P values were determined using ANOVA
(Student’s t-test) and the 9 ratios.
The mean comparisons of pairs among
the 9 protein ratios calculated fold changes. Finally proteins withP < 0.05 and fold change > 1.2 were
considered to be DEP (Chen et al.2013b; Zhang et al. 2019).