Pretoimics_fullset_FOT_r8150c312_randomfloor.csv

A total of 312 LC-MS/MS datasets were generated under a data-dependent acquisition mode (DDA) using different platforms. MS raw files were searched against the National Center for Biotechnology Information’s (NCBI) human Refseq protein database (updated on 04-07-2013, 32,015 entries) using Firmiana 1.0 enabled with Mascot 2.3 (Matrix Science Inc). False discovery rate (FDR) by using a target-decoy strategy was set to 1% for both proteins and peptides. Proteins were then quantified using the label-free iBAQ approach. The fraction-of-total (FOT) is used to represent the normalized abundance of a particular protein, which was defined as a protein’s iBAQ value divided by the total iBAQ of all identified proteins within one sample.