DMF (dimethylformamide), DCM (dichlormethane),
diisopropylether,
piperidine and TIPS (triisopropylsilane) were purchased from Sigma-Aldrich. NMM (4-methylmorpholine) and TFA (2,2,2-trifluoroacetic acid) were acquired from Fisher Scientific;
Fmoc-protected Wang-resins,
Fmoc-protected amino acids, and HCTU (
O-(6-chloro-1-hydrocibenzotriazol-1-yl)-1,1,3,3-tetra -methyluronium hexafluorophosphate) were obtained from AAPPTEC. An
Overture robotic solid phase peptide synthesizer (Protein Technologies, Tucson, USA) was used to synthesize peptides on a 20 µmol scale utilizing 10-fold excess of
Fmoc-protected amino acids (200 mM) relative to the Fmoc-Wang-resin. Deprotection by 20%
piperidine in
DMF for 2×5 min. Double coupling was performed in a conservative manner of 2×15 min rotations with a ratio of 1∶1∶2 (200 mM amino acid, 200 mM HCTU, 400 mM NMM) in
DMF.
DMF washing was applied for 5×30 sec after deprotection and double coupling. Automated cleavage was applied for 2 h with 95% vol.+2.5% vol.+2.5% vol. (TFA, H
2O, TIPS), after multiple washing steps with DCM (3×30 sec). Using ice-cold
diisopropylether, the peptides were precipitated from the final TFA-peptide solution and rewashed. All peptide products were analyzed on an
LC-20A HPLC instrument (Shimadzu) using an rpC18, 110 Å, 5 µm, 150×3 mm column (Macherey-Nagel), with a linear gradient of 5–70% ACN/H
2O (0.1% TFA) over 25 min with a flow rate of 0.5 ml×min
−1; UV-VIS detection at 210 nm. Masses were detected between 300–1500 Da with a Shimadzu
LCMS-2020 single-quad mass spectrometer (ESI+). UV
210 purity of all products: >98%. Peptide sequences are denoted with the calculated molecular weight (
mw, unit: Da), observed retention times (
Rt, unit: minutes) and masses (
m+); some peptides exhibited water clusters (*): SII (
mw = 331.40,
Rt = 9.87,
m+ = 332.15, 333.15, 663.4, 664.4), IIN (
mw = 358.43,
Rt = 6.86,
m+ = 359.15, 360.15, 719.40, 717.45, 718.45), INF (
mw = 392.45,
Rt = 10.15,
m+ = 393.15, 394.10, 786.30, 785.4, 1175.75), NFE (
mw = 408.41,
Rt = 7.66,
m+ = 408.10, 409.95, 817.35), FEK (
mw = 422.48,
Rt = 6.45,
m+ = 432.20, 424.20), EKL (
mw = 388.46,
Rt = 7.59,
m+ = 389.15, 390.15, 777.45), SIIN (
mw = 445.51,
Rt = 8.86,
m+ = 446.25, 447.25, 891.55, 892.50), IINF (
mw = 505.61,
Rt = 10.36,
m+ = 527.35*, 528.25*, 529.30*, 957.30*, 958.40*), INFE (
mw = 521.57,
Rt = 9.77,
m+ = 522.25, 523.20, 1043.55, 1044.55, 1045.50), NFEK (
mw = 536.59,
Rt = 6.93, m+ = 537.25, 538.25, 539.25), FEKL (
mw = 534.63,
Rt = 9.39,
m+ = 536.35, 537.25, 538.20, 1071.65, 1072.60), SIINF (
mw = 592.68,
Rt = 11.99,
m+ = 593.30, 594.35, 596.25, 1184.85, 1185.75, 1186.70, 1187.70), IINFE (
mw = 634.72,
Rt = 10.76,
m+ = 635.35, 636.30, 637.30, 1269.70, 1270.80), INFEK (
mw = 649.74,
Rt = 8.84,
m+ = 325.75, 650.35, 651.35, 652.35), NFEKL (
mw = 649.74,
Rt = 9.59,
m+ = 650.35, 651.35, 652.30, 1300.85), SIINFE (
mw = 721.79,
Rt = 11.5,
m+ = 722.40, 723.40, 724.30, 1443.9, 1444.90, 1445.90), IINFEK (
mw = 762.89,
Rt = 9.77, m+ = 382.35, 763.40, 764.40, 765.40), INFEKL (
mw = 762.89,
Rt = 10.84,
m+ = 382.30, 763.45, 764.4, 957.45, 965.45, 965.45), SIINFEK (
mw = 849.97,
Rt = 10.51,
m+ = 425.80, 850.50, 851.45, 852.45), IINFEKL (
mw = 876.05,
Rt = 11.51,
m+ = 438.95, 876.55, 877.50, 878.50).
Koch C.P., Perna A.M., Pillong M., Todoroff N.K., Wrede P., Folkers G., Hiss J.A, & Schneider G. (2013). Scrutinizing MHC-I Binding Peptides and Their Limits of Variation. PLoS Computational Biology, 9(6), e1003088.