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.