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The non-target fraction is mostly synthesis-related: deletion and truncation sequences, plus residual water and counter-ion. What it is made of matters more than the percentage.
A purity figure of 99% says one percent of the detected material was something else. It does not say what. Those are different questions with different consequences, and the second one is the one a reader usually cares about without realising it is missing from the headline number.
Solid-phase synthesis builds a chain one residue at a time, and each coupling step is efficient rather than perfect. A step that fails on a fraction of chains produces molecules missing one residue — deletion sequences — or chains that stopped early, truncations. These dominate the impurity profile of most synthetic peptides and are closely related to the target molecule, which is exactly why they are hard to separate from it.
If each coupling succeeds on the same proportion of chains, the proportion of fully correct molecules falls with every residue added. A long or difficult sequence can therefore assay several points lower than a short one from the same facility on the same day, with nothing wrong at either. Comparing purity figures across compounds of very different lengths is comparing two different difficulties.
Lyophilised peptides retain residual water and typically carry a counter-ion from the purification step. Both contribute to the mass in the vial without being the target compound, and neither necessarily appears in a chromatographic purity figure because they may not be detected by the method. This is one of the clearer reasons a content or mass test is not interchangeable with a purity test.
Impurities from synthesis are present from the start. Degradation products appear over time, driven by moisture, heat, light and oxygen. A report cannot always distinguish them, but the pattern across a series can: a profile that is stable across lots points at process, while one that worsens with the age of the sample points at handling or storage.
Two vials can both report 98% and be quite different: one with a single related impurity at two percent, another with a dozen unidentified peaks totalling the same. A report that publishes the chromatogram lets you see which. One that publishes only the percentage has discarded the distinction before you got to read it.
Prefer reports that show the trace rather than only the number. Where only numbers are available, prefer a series over a single reading, because a consistent figure across lots implies a consistent profile even when you cannot see it. And treat a modest purity figure on a long, difficult sequence as ordinary rather than alarming.
None of the above lets a reader identify what the impurities in a specific vial are. It lets you ask better questions of a document and interpret a number more accurately. Identifying impurities requires analysis you are not in a position to perform, and any page suggesting you can tell from a percentage is overstating what the figure contains.
The claims on this page about what makes up the non-target fraction, and why its composition matters can be checked against sources outside this site: