Fragmentation / deletion Δm -42.0218 severity: low-moderate

Deguanidination of Arg

Arg's guanidino group is split off, leaving Ornithine in place of Arg. -42 Da. Common with Pmc/Mtr protection, much rarer with Pbf.

Affected residue(s): R

Why it happens (mechanism)

Strong acid (TFA, HF, or TFMSA) protonates the guanidinium, and the C-N bond to the δ-carbon undergoes hydrolysis or solvolysis, ejecting urea-related fragments. Net: side chain goes from -NH-C(=NH)-NH₂ to -NH₂, i.e., Arg → Orn.

When it strikes (triggers)

Pmc or Mtr-protected Arg under prolonged TFA. Old protocols. Hot acid. HF cleavage. Less common with modern Pbf protection (more electron-rich, slower deguanidination).

How to spot it (MS signature)

-42.02 Da from full-length. Note: same Δm as loss of an acetyl, so confirm identity by location of effect (only when Arg present in the sequence).

How to prevent it

Use Fmoc-Arg(Pbf)-OH, not Pmc / Mtr. Pbf is more electron-rich and resists deguanidination.
TFA cleavage at room temperature, ≤2 h, with adequate scavenger (TIS or H₂O).
For peptides with multiple Arg, monitor cleavage time empirically — first-Arg loss is often visible by HPLC before second-Arg.

If it already happened (salvage)

Cannot be re-guanidinated cleanly under standard peptide conditions. Re-synthesize.

Source

Yi Yang, Side Reactions in Peptide Synthesis (Elsevier, 2016), Chapter 1, §1.9.