Field	Value
Level_1_data_methods	Curated peptide list from 74 proteins quantified in iPSCs; an extracted subset of the the total number of quantified proteins from these DIA-MS analyses of whole proteome extracts of 6 human iPSC lines. A Skyline document of these peptides is available in Panorama to look at raw parent and transition ion signals of these 74 proteins.
Level_1_data_QC_methods	
Level_2_data_methods	Pre-normalized protein and peptide quantitative values acquired from transition level signal of DIA-MS data acquisitions. DIA-MS data files were seached by OpenSWATH to generate lists of transition ion intensitied when searched against a sample specific ion library generated from DDA analyzes of iPSC pooled samples. The transition level OpenSWATH output was submitted to mapDIA in order to generate peptide and protein level signals from the transition level quantitation. This data set includes 38 MS data files of 6 iPSC lines in biological and technicle replicates. 
Level_2_data_QC_methods	
Level_3_data_methods	Normalization of transition level signal was performed by summing intensites of all transitions identifed within a sample and dividing each transition ion by the total signal. The protein and peptide quantitative values are generated in MapDIA from normalized OpenSWATH transition level signals of the DIA-MS data acquisitions. This data set includes 38 MS data files of 6 iPSC lines in biological and technicle replicates. 
Level_3_data_QC_methods	
Level_4_data_methods	Curated list of 74 proteins quantified in iPSCs. Normalized protein signals were averaged for all biological and technical replicates analyzed per cell line and log2 transformed. 
Level_4_data_QC_methods	
