The peptide which was synthesized using solid phase peptide synthesizer have Trt protected cysteine and Boc-protected Lysine, we have used a cocktail 80:5::5:10 TFA: Phenol: Water: Tips.In this condition, the deprotection has happened properly but the cysteine is again getting re alkylate with tBu (25-30% conversion by LCMS).So We need cocktail which can avoid this re alkylation and other oxidation of product cysteine and disulfide formation, Indirectly we need free cysteine after cleavage
@Neelesh
I agree with Anthony above. Anisole or thioanisole may be a better π-nucleophile than phenol, and therefore more likely to intercept the t-Butyl cation before it S-alkylates the deprotected cysteine. The t-Butylated byproducts may be more soluble in diethyl ether (i.e., easier to remove from your peptide by precipitation and trituration) because they lack the hydroxy group. Also, I would use this ratio to make the deprotection cocktail: TFA/anisole/water/TIPS = 80/8/2/10 (less water than before, more π-nucleophile). Water is not an optimal nucleophile in reactions involving large hydrophobic cations (e.g., Trt or t-Bu). Also, in the presence of water (pKa 16), thiols (pKa 9 to 10) are likely to be deprotonated (and therefore more reactive towards alkylating agents). Water in peptide deprotection cocktails also helps to hydrolyze residual TFAA (trifluoroacetic anhydride) in the TFA (unopened fresh bottles), which could unintentionally acylate the N-terminus, lysine/ornithine sidechain amine, or tryptophan sidechain indole.
Below is an earlier ResearchGate thread on a similar topic, with more recommendations from the scientific forum. Hope these help!
https://www.researchgate.net/post/What_are_appropriate_scavengers_in_the_t-butyl_group_deprotection_in_peptide_synthesis
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