Table 1.

Quantification of neoantigens through MANA-SRM

Cell lineTransfectedEndogenous HLA A allelesTotal # of cells (million)Enriched by W6/32 antibodyEnriched by isotype control antibodyPredicted binding peptide by NetMHC 4.0Predicted binding affinity by NetMHC 4.0 (unit: nmol/L, the lower value the stronger binding)Detected abundance (femtomole)Detected copy number per cell
COS-7HLA-A3 + KRAS G12C vectorN/A285.3YESNOVVGACGVGK (9-mer)221.43N/DN/D
N/AVVVGACGVGK (10-mer)375.53N/DN/D
COS-7HLA-A3 + KRAS G12D vectorN/A270.9YESNOVVGADGVGK (9-mer)1,172.0864 ± 6.3196 ± 19.3
N/AVVVGADGVGK (10-mer)938.86 ± 0.5321 ± 1.9
COS-7HLA-A3 + KRAS G13D vectorN/A286.7YESNOVVGAGDVGK (9-mer)1,552.0426 ± 3.775 ± 10.7
N/AVVVGAGDVGK (10-mer)936.842.2 ± 0.57 ± 1.6
COS-7HLA-A2 + KRAS G12C vectorN/A261.9YESNON/AN/AN/DN/D
COS-7HLA-A2 + KRAS G12D vectorN/A300.3YESNON/AN/AN/DN/D
COS-7HLA-A2 + KRAS G13D vectorN/A276.6YESNON/AN/AN/DN/D
COS-7HLA-A1 + KRAS WT vectorN/A290.2YESNOILDTAGQEEY86.69N/DN/D
COS-7HLA-A1 + KRAS Q61H vectorN/A254.9YESNOILDTAGHEEY185.91178 ± 12.2583 ± 40.0
COS-7HLA-A2 + KRAS Q61H vectorN/A266.2YESNON/AN/AN/DN/D
COS-7HLA-A1 + KRAS Q61L vectorN/A267.6YESNOILDTAGLEEY66.03136 ± 13.5512 ± 50.8
COS-7HLA-A2 + KRAS Q61L vectorN/A269.6YESNON/AN/AN/DN/D
COS-7HLA-A1 + KRAS Q61R vectorN/A261.9YESNOILDTAGREEY322.2340 ± 3.5127 ± 11.1
COS-7HLA-B7 + IDH2 R140Q vectorN/A273.3YESNOSPNGTIQNIL228.618 ± 1.325 ± 4.1
COS-7HLA-B7 + IDH2 R140Q vectorN/A289.2NOYESN/AN/AN/DN/D
COS-7HLA-A3 + IDH2 R140Q vectorN/A268.6YESNON/AN/AN/DN/D
RPMI-6666Not transfectedA*02:01, A*03:012,100YESNON/AN/AN/DN/D
HHNot transfectedA*01:01, A*01:012,000.0YESNON/AN/AN/DN/D
CFPAC-1_G12D knock-inNot transfectedA*02:01, A*03:0183.1YESNOVVGADGVGK (9-mer)1,172.084 ± 0.540 ± 5.0
HS578.TNot transfectedA*03:01, A*24:0270.4YESNOVVGADGVGK (9-mer)1,172.086 ± 0.671 ± 7.1
HL-60Not transfectedA*01:01, A*01:011,990.1YESNOILDTAGLEEY66.0310 ± 1.04 ± 0.4
SW948Not transfectedA*01:01, A*01:01326.1YESNOILDTAGLEEY66.036 ± 0.715 ± 1.75
RDNot transfectedA*01:01, A*01:01412.9YESNOILDTAGHEEY185.914 ± 0.38 ± 0.6
Hs940.TNot transfectedA*01:01, A*01:01131.3YESNOILDTAGREEY322.230.2 ± 0.021 ± 0.1
  • Abbreviations: N/A, not available; N/D, not detectable.