1. 18 DTLC(+57Da)IGYHA 26 HA N-terminus HA C-terminus 557 DGSLQC(+57Da)RIC(+57Da)I 566 ( A ) ( B ) 1 MNPNQKIITIGSVC 14 (+57Da) NA N-terminus ( C ) NA C-terminus 456 SWPDGAELPFTIDK 469 Fig. S1 200 400 600800 m/z 227.05 y2y2 390.21 y3y3 447.26 y4y4 560.36 y5y5 720.36 y 6 +57Da 833.44 y 7 +57Da 490.12 b 4 +57Da 603.24 b 5 +57Da 660.30 330.12 b3b3 b 6 +57Da 823.27 b 7 +57Da 960.49 b 8 +57Da MS/MS 525.24 50% 100% 0 [b 9 +114Da] 2+ 200400600 800 1000 m/z 292.16 405.24 545.77 561.34 930.46 849.46 962.48 1090.51 661.34 817.50 y 2 +57Da y 3 +57Da b 9 +114Da y 7 +114Da b 8 +57Da y 6 +114Da 721.45 y 5 +114Da y 4 +57Da b 6 +57Da MS/MS 611.29 50% 100% 0 ( D ) y 12 2+ y 12 1200 400 600800 1000 m/z1400 274.10 545.79 651.89 1429.54 1314.48 1302.54 720.37 833.56 962.45 1090.51 1205.48 y 10 2+ b2b2 y6y6 y7y7 y8y8 y 10 y 11 b 12 b 13 MS/MS 788.39 50% 100% 0 b 10 40060080010001200 1400 278.01 422.16 535.18 636.21 665.39 749.37 826.35 939.39 1040.43 1153.47 1210.49 1297.48 1396.55 y 2 +57Da y 4 +57Da y 5 +57Da y 6 +57Da [y 12 +57Da] 2+ y 7 +57Da b7b7 b8b8 b9b9 b 11 b 12 b 13 MS/MS 787.88 50% 100% 0 m/z

2. [121xp_HA] MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK 60 [X181A_HA] MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK 60 [121xp_HA] LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETS SSDNGTCYPG DFIDYEELRE 120 [X181A_HA] LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETS SSDNGTCYPG DFIDYEELRE 120 [121xp_HA] QLSSVSSFER FEIFPNTSSW PNHDSNKGVT AACPHAGAKS FYKNLIWLVK KGNSYPKLSK 180 [X181A_HA] QLSSVSSFER FEIFPKTSSW PNHDSDKGVT AACPHAGAKS FYKNLIWLVK KGNSYPKLSK 180 [121xp_HA] SYINDKGKEV LVLWGIHHPS TSADQQSLYQ NADAYVFVGS SRYSKKFKPE IAIRPKVRGQ 240 [X181A_HA] SYINDKGKEV LVLWGIHHPS TSADQQSLYQ NADAYVFVGS SRYSKTFKPE IAIRPKVRDR 240 [121xp_HA] EGRMNYYWTL VEPGDKITFE ATGNLVVPRY AFAMERNAGS GIIISDTPVH DCNTTCQTPK 300 [X181A_HA] EGRMNYYWTL VEPGDKITFE ATGNLVVPRY AFAMERNAGS GIIISDTPVH DCNTTCQTPK 300 [121xp_HA] GAINTSLPFQ NIHPITIGKC PKYVKSTKLR LATGLRNVPS IQSRGLFGAI AGFIEGGWTG 360 [X181A_HA] GAINTSLPFQ NIHPITIGKC PKYVKSTKLR LATGLRNVPS IQSRGLFGAI AGFIEGGWTG 360 [121xp_HA] MVDGWYGYHH QNEQGSGYAA DLKSTQNAID EITNKVNSVI EKMNTQFTAV GKEFNHLEKR 420 [X181A_HA] MVDGWYGYHH QNEQGSGYAA DLKSTQNAID EITNKVNSVI EKMNTQFTAV GKEFNHLEKR 420 [121xp_HA] IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRSQL KNNAKEIGNG 480 [X181A_HA] IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRSQL KNNAKEIGNG 480 [121xp_HA] CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREEIDGV KLESTRIYQI LAIYSTVASS 540 [X181A_HA] CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREEIDGV KLESTRIYQI LAIYSTVASS 540 [121xp_HA] LVLVVSLGAI SFWMCSNGSL QCRICI 566 [X181A_HA] LVLVVSLGAI SFWMCSNGSL QCRICI 566 Fig. S2 [121xp_NA] MNPNQKIITI GSVCMTIGMA NLILQIGNII SIWISHSIQL GNQNQIETCN QSVITYENNT 60 [X181A_NA] MNPNQKIITI GSVCMTIGMA NLILQIGNII SIWISHSIQL GNQNQIETCN QSVITYENNT 60 [121xp_NA] WVNQTYVNIS NTNFAAGQSV VSVKLAGGSS LCPVSGWAIY SKDNSVRIGS KGDVFVIREP 120 [X181A_NA] WVNQTYVNIS NTNFAAGQSV VSVKLAGNSS LCPVSGWAIY SKDNSVRIGS KGDVFVIREP 120 [121xp_NA] FISCSPLECR TFFLTQGALL NDKHSNGTIK DRSPYRTLMS CPIGEVPSPY NSRFESVAWS 180 [X181A_NA] FISCSPLECR TFFLTQGALL NDKHSNGTIK DRSPYRTLMS CPIGEVPSPY NSRFESVAWS 180 [121xp_NA] ASACHDGINW LTIGISGPDN GAVAVLKYNG IITDTIKSWR NNILRTQESE CACVNGSCFT 240 [X181A_NA] ASACHDGINW LTIGISGPDN GAVAVLKYNG IITDTIKSWR NNILRTQESE CACVNGSCFT 240 [121xp_NA] VMTDGPSNGQ ASYKIFRIEK GKIVKSVEMN APNYHYEECS CYPDSSEITC VCRDNWHGSN 300 [X181A_NA] VMTDGPSNGQ ASYKIFRIEK GKIVKSVEMN APNYHYEECS CYPDSSEITC VCRDNWHGSN 300 [121xp_NA] RPWVSFNQNL EYQIGYICSG IFGDNPRPND KTGSCGPVSS NGANGVKGFS FKYGNGVWIG 360 [X181A_NA] RPWVSFNQNL EYQIGYICSG IFGDNPRPND KTGSCGPVSS NGANGVKGFS FKYGNGVWIG 360 [121xp_NA] RTKSISSRNG FEMIWDPNGW TGTDNNFSIK QDIVGINEWS GYSGSFVQHP ELTGLDCIRP 420 [X181A_NA] RTKSISSRNG FEMIWDPNGW TGTDNNFSIK QDIVGINEWS GYSGSFVQHP ELTGLDCIRP 420 [121xp_NA] CFWVELIRGR PKENTIWTSG SSISFCGVNS DTVGWSWPDG AELPFTIDK 469 [X181A_NA] CFWVELIRGR PKENTIWTSG SSISFCGVNS DTVGWSWPDG AELPFTIDK 469

3. Fig. S3 281 C(+144Da)YPDSSEITC(+57Da)VC (+57Da)R 293 280 SC(+57Da)YPDSSEITC(+57Da)VC (+57Da)R 293 ( A ) 334 S(+72Da)C(+144Da)GPVSSNGAN(+1Da)GYK 347 332 TGSC(+57Da)GPVSSN(+1Da)GAN(+1Da)GYK 347 ( B ) 1000 400 800 600 1200 14001600m/z 335.16 434.28 411.09 594.29 662.51 695.34 743.94 808.37 937.44 1024.45 1111.45 1226.46 1323.49 1399.31 1559.33 1486.53 y 2 +57Da y 3 +57Da b 3 +57Da y 4 +114Da y 5 +114Da [y 12 +114Da] 2+ [y 11 +114Da] 2+ y 6 +114Da y 7 +114Da y 8 +114Da y 9 +114Da y 10 +114Da y 11 +114Da y 12 +114Da b 12 +114Da b 13 +171Da MS/MS 867.35(2+) 50% 100% 0 1000 400 800 600 1200 1400 200 m/z 303.25 417.34 545.22 624.94 659.35 737.70 834.36 948.31 1030.63 1087.53 1247.20 1346.36 y3y3 y 4 +1Da y 6 +1Da y 7 +2Da y 9 +2Da y 11 +2Da y 12 +2Da y 13 +59Da [b 14 +59Da] 2+ b 15 +59Da MS/MS 747.33(2+) [b 16 +59Da] 2+ 50% 100% 0 b 10 +58Da b 14 +59Da

4. HA(PDB: 3LZG) Cys21 Cys107 Cys153 Cys492 NA(PDB: 3NSS) Cys124 Cys129 Cys231 Cys233 Cys238 Cys290 Cys318 Cys417 Cys421 Cys84 Cys481 Cys72 Cys320 Cys161 Cys92 Cys184 Cys281 Cys292 Cys446 Cys279 Cys59 Cys488 Fig. S4 Cys335 Cys292 Cys296

5. Fig. S5 39 FYIQM 44 C(+72Da)TELK 48 CH 2 S O O H 1000 400 800 600 1200 200 m/z 311.07 424.05 552.24 665.37 490.24 796.32 924.37 1037.41 1201.35 283.18 742.75 872.78 b2b2 b3b3 b4b4 y4y4 y 5 +72Da y 6 +72Da y 7 +72Da y 8 +72Da b 10 +72Da MS/MS 674.32(2+) C+72Da 50% 100% 0

6. Fig. S6 ( A ) ( B ) NYMC-X181A-HA: 384 STQNAID(+144Da)EITNKVNSVIEK 402 y 12 y 13 b6b6 NIBRG-121xp-NA: 181 ASAC(+57Da)HD(+144Da)GINWL 191 b5b5 b6b6 y5y5 1000 400 800 600 1200 m/z 502.22 615.24 687.18 738.09 817.20 873.72 909.21 965.95 1030.25 1085.93 b5b5 b6b6 y 12 2+ [y 13 +144Da] 2+ [y 14 +144Da] 2+ [y 15 +144Da] 2+ [y 16 +144Da] 2+ [y 17 +144Da] 2+ D+144 DaIAN Q 50% 100% 0 200 MS/MS 750.05(3+) 1000 400 800 600 1200 m/z 301.16 318.13 432.11 527.20 628.82 685.54 786.24 843.19 956.31 1070.35 1256.34 y2y2 y3y3 [b 11 +201Da] 2+ b 5 +57Da b 6 +201Da b 7 +201Da b 8 +201Da b 9 +201Da b 10 +201Da [b 10 +201Da] 2+ y 5 2+ D+144 Da G I N W 50% 100% 0 200 MS/MS 694.31(2+)