LC-MS/MS Analysis of Kyse450 Proteome

LC-MS/MS analysis and label-free based MS quantification of proteins in Kyse450 cells were performed as previously described^{23 (link)}. A Firmiana proteomics workstation was used to process the raw MS data. Kyse450 lysates were digested into peptides with trypsin, then subjected to MS analysis on a Fusion Lumos instrument (Thermo Fisher Scientific). Raw MS data were used to interrogate the NCBI human Refseq protein database (released on 04-07-2013, 32,015 entries) with the Mascot search engine (version 2.3, Matrix Science Inc.) with a false discovery rate < 1% at the peptide and protein level. The intensity-based label-free quantification (iBAQ) algorithm was used for protein quantification. The iBAQ value was transferred into a fraction of total protein iBAQ amount per experiment (FOT). Then the FOT values were multiplied by 10⁶ and log₁₀ transformed to obtain the FOT values for low abundance proteins.