2.6. Proteomics Data Analysis

Protein identification and label-free quantification normalization of MS/MS data were performed using MaxQuant v1.5.2.8 (http://www.maxquant.org, accessed on 20 May 2015). The Andromeda search algorithm incorporated in the MaxQuant software was used to correlate MS/MS data against the Homo sapiens UniProt reference proteome database (release 2016_11) and a contaminant sequence set provided by MaxQuant. Perseus v.1.5.6.0 (www.maxquant.org/, accessed on 1 June 2016) was used for data analysis, processing, and visualization. Normalized label-free quantification intensity values were used as the quantitative measurement of protein abundance for subsequent analysis. The data matrix was filtered for the removal of contaminants and peptides identified by site. Label-free quantification intensity values were log2 transformed.