Purification is the step that turns a crude synthesis mixture into a peptide preparation suitable for research. Because synthesis can generate closely related byproducts (e.g., deletion sequences), purification often relies on chromatography to separate the target peptide from impurities based on charge, hydrophobicity, binding affinity, or size.
At a glance
- Purification is selective separation of the desired peptide from synthesis byproducts.
- One method may be enough for some peptides; others benefit from a “capture + polish” approach.
- Scale, resolution, and recovery are the key trade-offs.
Where impurities come from
During peptide synthesis, each coupling and deprotection step can introduce side products. Common impurity classes include truncated sequences, protected fragments, and chemically modified variants (for example oxidation-sensitive residues under certain conditions).
A typical workflow: capture, then polish
- Capture step: removes the bulk of small-molecule and major byproducts, improving the mixture substantially.
- Polishing step: a second, complementary separation that targets closely related peptide variants and improves final purity.
Common purification strategies
Reversed-phase chromatography (RP)
Separates primarily by hydrophobic interactions. Often provides strong resolution for many peptides and is widely used in peptide purification workflows.
Ion-exchange chromatography (IEX)
Separates based on net charge. Useful when charge differences between target and impurities are pronounced or when RP selectivity is insufficient.
Size-exclusion / gel filtration (SEC/GF)
Separates by size. Often used for desalting or removing aggregates rather than resolving very similar peptides.
Affinity approaches (when applicable)
Leverages specific binding to a ligand or matrix. Highly selective when the peptide system is designed for it, but not universally applicable.
What impacts purification success
- Loading: too much sample can flatten resolution.
- Gradient and solvents: influence separation selectivity and peak shape.
- Flow rate and temperature: can improve or degrade resolution depending on the setup.
- Fraction pooling criteria: determines the balance between purity and yield.
What buyers should request or verify
- Chromatogram(s) from the final purification/analysis method.
- MS data supporting identity.
- Clear labeling of the peptide form (salt/counterion where applicable).
Trusted Peptides aims to make purification outcomes legible—so you’re not guessing what “purified” means for your sequence.
