Met alkylation by DODT scavenger

DODT (3,6-dioxa-1,8-octanedithiol), an EDT alternative, can alkylate Met thioether under TFA. +117 Da. Sometimes overlooked.

Why it happens (mechanism)

DODT under TFA loses thiol to give a sulfonium intermediate that adds to Met's S, giving a sulfonium adduct. The ether-rich backbone of DODT is what makes it +117 (vs. +76 for EDT).

When it strikes (triggers)

DODT-containing cleavage cocktails on Met-rich peptides. Common in cocktails marketed as 'odorless EDT alternative'.

How to spot it (MS signature)

+117 Da on Met residue. Specific to DODT.

How to prevent it

• Switch back to EDT or thioanisole if Met is in the sequence.
• Or use Fmoc-Met(O)-OH building block (sulfoxide protection prevents alkylation), reduce post-cleavage.

If it already happened (salvage)

• Sulfonium can sometimes be removed by reductive treatment, but yields are poor. Re-synthesize.

Source

Yi Yang, Side Reactions in Peptide Synthesis (Elsevier, 2016), Chapter 3, §3.10.