Computational protocol: iTRAQ-based quantitative proteomic analysis reveals the distinct early embryo myofiber type characteristics involved in landrace and miniature pig

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Protocol publication

[…] The cellular component (CC), molecular function (MF) and biological process (BP) of the proteins identified by iTRAQ were annotated by the Blast2GO software (https://www.blast2go.com/); GO functional classification and enrichment analysis were also performed to identify GO terms that were significantly enriched in DEPs using DAVID analysis (http://david.abcc.ncifcrf.gov/). The myogenic DEPs and predicted protein interaction network was illustrated by STRING (http://string-db.org/) and Cytoscape 3.1.0 (http://www.cytoscape.org/). Relative expression of proteins was based on the ratio of the reporter ions of peptides using Mascot software. T-test was used to analyze the p-value. Moreover, the protein with the 1.5-fold change as well as the p value less than 0.05 was designated the DEPs. Statistical analyses were conducted with SPSS 10.0. […]

Pipeline specifications

Software tools Blast2GO, DAVID
Application MS-based targeted proteomics
Organisms Sus scrofa, Homo sapiens