Protecting-group residue / loss Δm +242.1096 severity: low-moderate

Trt protecting-group residue on Asn/Gln/Cys/His

Incomplete Trt removal from N(Trt), Q(Trt), C(Trt), or H(Trt). +242 Da. Indicates short cleavage time or insufficient scavenger.

Affected residue(s): N Q C H

Why it happens (mechanism)

Trt cleaves under mild TFA but the trityl cation is stabilized — it can re-add to the side chain if not effectively scavenged. Insufficient time → equilibrium not reached.

When it strikes (triggers)

TFA cleavage <90 min. Cold cleavage. No TIS in cocktail (TIS specifically scavenges Trt cation). Multiple Trt-protected residues compete for scavenger.

How to spot it (MS signature)

+242.11 Da. Multiple residues → ladder pattern.

How to prevent it

Always include TIS (2.5%) in cleavage cocktail — it's a near-specific Trt cation scavenger.
Cleave for ≥2 h at RT for peptides with ≥3 Trt-protected residues.
Use TFA ≥92%.

If it already happened (salvage)

Re-treat with TFA/TIS/H₂O for 1 h. Effective in most cases.

Source

Yi Yang, Side Reactions in Peptide Synthesis (Elsevier, 2016), Chapter 1, Appendix I.