Table IV Estimated extent of the alterations induced in the B*51 peptidome by ERAP1 and/or ERAP2 depletion
Role ofComparisonsVolcano analysesaAltered featuresbP2LengthPC
NSignificant% AlteredTotalIR>1.5 (Σ)Δ (%)% alteredΔ (%)% alteredΔ (%)% altered
ERAP1 (E2+)WT/E1KO112728425.21842136427.720.51410.419.214.2
ERAP1 (E2−)E2KO/E1E2KO #1101248648.01925159538.131.61915.78.57.0
E2KO/E1E2KO #19107753850.01948161648.240.013.411.17.86.5
ERAP2 (E1+)WT/E2KO118830125.318731193N.S.N.S.29.118.5127.6
ERAP2 (E1−)E1KO/E1E2KO #1105336234.41808142224.919.
E1KO/E1E2KO #19111441637.31843129835.925.311.
ERAP1 + 2WT/E1E2KO #191737641.01888157233.227.610.99.112.410.3
WT/E1E2KO #1996243945.61940157441.533.75.54.511.39.2
  • aVolcano analyses (supplemental Fig. S2): N, total peptides compared, including only peptides found in both cell lines and identified in more than one of the biological triplicates of each cell line; Significant and % altered indicate total peptides and percent relative to N, respectively, showing statistically significant expression differences between the cells compared. As a control, the % altered peptides between E1E2KO clones #1 and #19 in this comparison was to 12.3%.

  • bAltered features (Fig. 35): Total, number of peptides shared between the two cell lines compared plus peptides found only in each one of the two cell lines; IR>1.5 (Σ), added peptides from the IR>1.5 subsets from each cell line, including peptides found only in one of the cell lines; Δ (%), percent of peptide differences found in the comparison between the IR>1.5 subsets, as shown in Fig. 35. Only those features showing statistical significance were included. N.S.: not significant. % altered, % of the total peptidome altered in each given feature.