Protein identification was performed using the Homo sapiens taxonomy (20,200 sequences) setting of the Swiss-Prot database (SwissProt_2015_06) with Proteome Discoverer 2.1 (version 2.1.1.21, Thermo Scientific) as previously described (53 (link)). Quantification of MS1 precursor ions was analyzed using the Proteome Discoverer 2.1 (version 2.1.1.21, Thermo Scientific). A relative quantification approach was used for deamidation measurement as follows: The ratio of a deamidated peptide/total peptide was used to represent the abundance of the deamidated peptide. The ratio of a specific deamidated peptide across the samples was standardized (z score); the mean standardized values of the peptides derived from one protein were used to represent the level of deamidated protein abundance.