Deletion Sequence

A deletion sequence arises when a coupling does not go to completion: the amine at a fraction of the resin sites stays unreacted, the next cycle acylates it anyway, and those chains continue to the end one residue short. The product is a peptide with the correct terminal residues and an internal gap, lighter than the target by exactly the mass of what is missing. It is distinct from a truncated sequence, where the chain stopped growing altogether.

The mass shifts are diagnostic: a missing glycine is fifty-seven daltons lighter, alanine seventy-one, leucine or isoleucine one hundred and thirteen, tryptophan one hundred and eighty-six. Deletions cluster in hydrophobic or beta-sheet-forming stretches where the resin-bound chain aggregates and buries its own reactive terminus. Capping after each coupling converts would-be deletions into terminated, acetylated chains, which are shorter, chemically different, and far easier to separate.

Deletions matter more than other impurity classes for a chromatographic reason: a peptide missing one internal residue out of thirty has nearly the same length, charge and hydrophobicity as the target and can co-elute with it under an ordinary gradient. A high area purity therefore does not exclude them. Mass spectrometry does, because the mass difference is unambiguous, provided the analysis has the resolution and the analyst looks below the base peak.

The specification that invites the error reports only that molecular weight was confirmed, with a single observed mass. That confirms a species of the right mass is present; it does not exclude a companion peak a few tens of daltons lighter carrying much of the material. A related misconception treats deletions as evidence of age or poor storage. They are built in at synthesis, so a freshly made vial contains exactly as many as one that has sat for a year.