3.2 Proteome summary
All MS/MS spectra were processed using Mascot from six protein samples (M0a, M0b, M0c, M4a, M4b, and M4c). TMT analysis of P. vachellimuscle proteome showed 14,943 unique peptides from 41,278 unique spectra in this database (334,625 total spectra) and resulted in 1,551 unique proteins. All peptide/protein identifications and quantifications are shown in Table S2 . The quality control analysis of the proteome is shown in Table S3 , including mass delta, the distribution diagram of peptide number, peptide length, protein cleavages, and protein mass. All coefficients of variation distribution for proteome showed that a total of 97.36% of the identified proteins displayed a ratio % CV <20%, and proteome project has a good repeatability (Table S3).
A total of 584 differentially expressed proteins ( DEP; fold change > 1.2 andP < 0.05) were reliably quantified using TMT analysis, including 9 upregulated and 575 downregulated proteins undergo hypoxia. KEGG enrichment analysis (P < 0.05) displayed a total of 14 significantly enriched pathways under hypoxia (Fig. 2B ). Muscle function, amino acid and carbohydrate metabolism were the three most represented subclasses. In addition “Alzheimer’s disease”, “Huntington’s disease”, “Parkinson’s disease” containing mitochondrial related proteins was significantly enriched by down DEP. Of note, DEP of carbohydrate metabolism referred to aerobic metabolism mainly centered on “Pyruvate metabolism” (e.g., CS, IDH, DLD, OGDH, SDHa/b, MDH1, down-regulated) and the DEP of amino acid metabolism and human disease involved in amino acid synthesis and muscle dysfunction.