除Cbz保护基外，叔丁氧羰基（Boc）是目前多肽合成中广泛使用的氨基保护基，特别是在固相合成中，一般用Boc而不用Cbz。Boc 对于催化氢解不敏感, 对碱和亲核试剂有一定的稳定性。Boc-氨基酸除个别外都能得到结晶；易于酸解除去，但有具有一定的稳定性，Boc-氨基酸能较长期的保存而不分解；酸解时产生的是叔丁基阳离子再分解为异丁烯，它一般不会带来副反应；对碱水解、肼解,催化氢解和大多数亲核试剂稳定，但比Cbz对酸敏感。当Boc和Cbz同时存在时，可以用催化氢解脱去Cbz，而Boc保持不变; 或用酸解脱去Boc, 而Cbz不受影响，因而两者能很好地搭配。

叔丁氧羰基(Boc)导入

游离氨基酸在用NaOH 或NaHCO3 控制的碱性条件下用二氧六环和水的混合溶剂中很容易与同Boc2O反应得到N-叔丁氧羰基氨基酸化合物。这是氨基酸引入Boc常用方法之一，它的优点是其副产物很容易除去。有时对一些亲核性较大的胺，一般可在甲醇中和Boc酸酐直接反应即可，无须其他的碱，其处理也方便。对水较为敏感的氨基衍生物，采用Boc2O/Et3N/MeOHor DMF 在40~50oC下进行，因为这些无水条件下用于保护O17标记的氨基酸而不会由于与水交换使O17丢失。有空间位阻的氨基酸而言，用Boc2O/Me4NOH.5H2O/CH3CN是十分有利的。

和Boc2O一样， 2-(叔丁氧甲酰氧亚氨基)-2-苯基乙腈 (Boc-ON)是相对稳定的结晶混合物,也可以用于氨基酸的保护. 另外, 在Boc2O存在下使用催化量的羟胺得到的Boc-ONH2与胺的反应比Boc2O快1.5~2.5倍。

而Curtius Reaction通过叔丁醇也可以引入Boc。 同时在催化氢化和Boc2O存在的条件下, 也容易将苄基或Cbz等保护基可氢解除去而转化为Boc保护; 同样, 在KF/Et3N/Boc2O/DMF条件下, 室温也可以将Fmoc保护基除去而转化为Boc保护。

氨基酸Boc2O引入Boc保护示例：

A 4-L, four-necked, round-bottomed flask, equipped with an efficient stirrer, a dropping funnel, reflux condenser, and thermometer is charged with a solution of 44 g (1.1 mol) of sodium hydroxide in 1.1 L of water. Stirring is initiated and 165.2 g (1 mol) of L-phenylalanine 1 is added at ambient temperature, and then diluted with 750 mL of tert-butyl alcohol. To the well-stirred, clear solution is added dropwise within 1 hr, 223 g (1 mol) of di-tert-butyl dicarbonate. A white precipitate appears during addition of the di-tert-butyldicarbonate. After a short induction period, the temperature rises to about 30~35°C. The reaction is brought to completion by further stirring overnight at room temperature. At this time, the clear solution will have reached a pH of 7.5~8.5. The reaction mixture is extracted two times with 250 mL of pentane, and the organic phase is extracted three times with 100 mLof saturated aqueous sodium bicarbonate solution. The combined aqueous layers are acidified to pH 1~1.5 by careful addition of a solution of 224 g (1.65 mol) of potassium hydrogen sulfate in 1.5 L of water. The acidification is accompanied by copious evolution of carbondioxide. The turbid reaction mixture is then extracted with four 400-mL portions of ethyl ether.The combined organic layers are washed two times with 200 mL of water, driedover anhydrous sodium sulfate or magnesium sulfate, and filtered. The solvent is removed under reduced pressure using a rotary evaporator at a bath temperature not exceeding 30°C. The yellowish oil that remains is treated with 150 mL of hexane and allowed to stand overnight. Within 1 day the following portions of hexane are added with stirring to the partially crystallized product: 2 × 50 mL, 4 × 100 mL, and 1 × 200 mL.The solution is placed in a refrigerator overnight; the white precipitate is collected on a Büchner funnel and washed with cold pentane. The solid is dried under reduced pressure at ambient temperature to constant weight to give a first crop. The mother liquor is evaporated to dryness leaving yellowish oil, which is treated in the same manner as described above, giving a second crop. The total yield of pure white N-tert-butoxycarbonyl-L-phenylalanine 2 is 207~230 g (78~87% yield), mp 86~88°C。