Truncated Sequence

A truncated sequence is a chain that stopped growing before the synthesis finished. In Fmoc solid-phase chemistry, where assembly runs from the C-terminus outward, the resulting impurity lacks residues from the N-terminal end but is otherwise a continuous stretch of the correct sequence. That distinguishes it from a deletion sequence, which is missing an internal residue while both flanking regions remain present and correctly ordered.

Truncations are partly deliberate. Capping, meaning the acetylation of any chain that failed to couple in a given cycle so that it cannot react again, is standard practice precisely because it converts what would have become deletion impurities into terminated ones. That trade is worth making because the mass difference is large, often hundreds of daltons, so truncations are conspicuous by mass spectrometry and usually well separated by reversed-phase chromatography.

The distinction changes what a crude profile is telling you. A crude dominated by truncations reflects poor coupling efficiency and costs yield, but the impurities are removable. A crude carrying deletions reflects incomplete deprotection or capping and costs purity, because a molecule one residue short can differ from the target by less than the resolving power of the analytical method. Reading only a purity number collapses that difference into nothing.

Two assumptions to avoid. Truncated fragments are not inert by default: shortened analogues of receptor ligands sometimes retain partial agonism or behave as antagonists, and any novel fragment is a candidate immunogen. And a truncation-free claim is only as good as the chromatographic window it was made in, since very short fragments can elute near the void volume and fall outside the integrated region altogether.