Analyses were performed by injecting 2 µg in quadruplicate into the mass spectrometry platform consisting of an Ultimate 3000 nano LC connected to an Orbitrap Fusion Tribrid MS (Thermo Fisher Scientific, Waltham, MA, USA). Peptides were eluted over two hours by mixing buffer A (99.9% water, 0.1% formic acid) with increasing concentrations of buffer B (99.9% acetonitrile, 0.1% formic acid). This universal method was used with the settings described [36 (link)].
A total of 88 raw data files were entered into MaxQuant version 1.6.6.0 for LFQ analysis [37 (link)] and searched against the Uniprot Sus scrofa database and the Homo sapiens database downloaded on 8 November 2020. Generally, the default settings were used in MaxQuant, including a false discovery rate (FDR) of 0.01 for protein identification and peptide spectrum matches. Digestion with Trypsin was used instead of Trypsin/P, an LFQ minimum ratio count was set to 1, and the match between the runs function was used.
A total of 88 raw data files were entered into MaxQuant version 1.6.6.0 for LFQ analysis [37 (link)] and searched against the Uniprot Sus scrofa database and the Homo sapiens database downloaded on 8 November 2020. Generally, the default settings were used in MaxQuant, including a false discovery rate (FDR) of 0.01 for protein identification and peptide spectrum matches. Digestion with Trypsin was used instead of Trypsin/P, an LFQ minimum ratio count was set to 1, and the match between the runs function was used.
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