2.8.3. Data Analysis

A Swiss-Prot database search for protein and peptide identification matched with *Charadrius vociferus* species was performed using the Spectrum Mill MS Proteomics Workbench (Agilent Technologies, Santa Clara, CA, USA). Carbamidomethylation was selected as the fixed modification parameter and trypsin as the digestive enzyme, with the maximum number of cleavage equal to 2. Auto-validation was set for MS searches at a false discovery rate (FDR) of 1.2% and data export to Mass Profiler Professional (MPP v 14.9.1, Agilent Technologies, Santa Clara, CA, USA) for further analysis. The software confirmed the identified protein and the post-translation modifications if present, and the data files were then processed by principal component analysis (PCA) using the MPP software.
