Why am I getting unexpected peaks in my chromatogram?

Peaks that appear in your chromatogram but do not correspond to your expected analytes can come from several sources. Identifying the cause depends on when and where the peaks appear.

Contamination from the previous run

If compounds from a previous injection are still in the column when the next run starts, they elute during the new run and appear as unexpected peaks. This is called carryover. It is most common when running samples at very different concentration levels or when the column has not fully cleared between runs.

To check, run a blank (no sample injected) after a high-concentration sample. If the peaks appear in the blank, carryover is the cause. Increasing the final hold temperature or extending the hold time between runs usually resolves it.

Septum bleed

Septa degrade over time, particularly at high injector temperatures. Fragments of septum material can fall into the liner and vaporise, producing peaks in the chromatogram. These peaks are typically small, broad, and appear consistently across multiple runs.

Replace the septum regularly. Use low-bleed septa rated for your injector temperature.

Liner contamination

Non-volatile residues can accumulate in the inlet liner over time, particularly from dirty sample matrices. These residues can partially vaporise during subsequent runs and produce unexpected peaks.

Inspect and replace the liner periodically. Use a liner appropriate for your injection mode (split, splitless, or on-column).

Column degradation

As a column ages, stationary phase breakdown products can produce peaks in addition to the rising baseline associated with column bleed. If unexpected peaks persist after ruling out contamination sources, the column may need replacing.

System contamination

If the carrier gas supply contains impurities, or if there is a leak allowing air into the system, oxidation products can form on the column and produce peaks. Check gas purity, replace gas line filters, and leak-test the system.

How to diagnose the source

Run a blank with no injection to check for system contamination. Run a solvent blank to check for contamination from the solvent or syringe. Compare the retention times of the unexpected peaks across multiple runs. Consistent retention times suggest a repeatable contamination source. Shifting retention times suggest carryover or degradation.