mass spect data MHC I- vs MHC I+ ANOVA outputs all raw data 2peptides.xlsx

Mass spectroscopy was performed on NK cells isolated from splenocytes using murine NK Isolation Kit II (Miltenyi Biotech). As described in Lei et al the NK cells were obtained from splenocytes of MHC class I- mice (beta 2 ug KO and H2Kb, H2Db and beta 2 ug KO "triple knockout" TKO mice). The protein database searches were analyzed using Scaffold (ver. 4.4.8) and proteins were identified using the Protein Prophet algorithm with protein and peptide thresholds at 1% false discovery rate (FDR)

and 0.1 % FDR respectively. Quantification of relative protein abundance was performed using spectral counting with P values generated in Scaffold (ver. 4.0) using a Fischer’s exact test. The

minimum spectral count value was set to 1 and proteins with at least 5 or greater spectral counts were used to quantify changes in protein abundances. Non-hierarchical clustering of proteins within the “Natural Killer Cell Mediated Cytotoxicity” and “PI3 Kinase-AKT Signaling Pathway” as defined by Scaffold was performed to evaluate levels of signaling intermediates downstream from surface activating receptors.