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Peptide Isolation & Purification
Peptides sit between small molecules and proteins, so they need their own purification approach. Planta Analytica builds peptide-specific methods for targets up to 5 kDa, whether they start in a fermentation broth, a dried pellet, a crude extract or a crude synthetic batch. We scale from milligrams up to kilograms.
Peptide types we handle
Fermentation-derived peptides
Targets recovered from fermentation broth or dried pellets, including mixtures from exploratory fermentations.
Crude synthetic peptides
Synthesis batches cleaned up to remove side products and close-eluting impurities.
Botanical & natural peptides
Peptides isolated from crude extracts and other complex natural sources.
RiPPs & modified bioactive peptides
Ribosomally synthesized and post-translationally modified peptides and other bioactive peptides from natural product discovery.
The challenge
Most chromatography workflows were designed for small molecules or for proteins. Peptides fall in between, so standard methods often lose selectivity or yield. Exploratory fermentations rarely produce a single clean product. Synthetic batches carry side products that must be removed. Impurities often share the target peptide’s charge, polarity and size, so telling them apart takes mass spectrometry. Highly polar or labile peptides add another layer of difficulty.
We build each peptide method around the feedstock, the peptide’s ionic behavior and the purity your application actually needs.
Peptide purification techniques
| Technique | Best for | Typical use |
|---|---|---|
| Reverse-phase HPLC (C18, C8, C4) | High-resolution separation of individual peptides from complex mixtures | Our most common peptide purification step. Mobile phases and buffers (e.g. ammonium acetate, ammonium formate, potassium phosphate) are tuned to each peptide's ionic nature. |
| Ion-exchange chromatography | Separating charged peptides from a neutral matrix at high loading capacity | Extraction and high-throughput processing of larger quantities of product |
| Size-exclusion chromatography | Separating peptides from components of different molecular size | Complementary clean-up step within a multi-stage purification |
| Counter-current chromatography, incl. pH-zone refining | Peptides that differ only slightly in pKa, and highly polar peptides | pH-zone refining for close pKa differences, or strongly buffered solvent systems to stabilize phases and improve retention |
| Unconventional solid & mobile phases | Difficult cases: very polar peptides or poor solubility | Novel solid-phase applications and modified mobile phases to retain polar peptides or raise loading capacity |
In-house analytics: HPLC and mass spectrometry are run in-house, with NMR available through partner labs. Identity is confirmed primarily by MS, and every delivery comes with a certificate of analysis.
Purity matched to your application
Early screening and bioactivity work, where an enriched fraction is enough to move forward.
Product and process development that needs a cleaner, more consistent peptide.
Analytical reference standards and work that needs a well-characterized peptide.
You set the target, and we purify to it. Every delivery includes a COA stating purity / wt%.
Who we help
Pharmaceutical
Fermentation & biotech
Botanical & nutraceutical
Natural product & discovery research
Research & development teams
How it works
Share what you have
Complete our submission questionnaire with your feedstock, any chromatograms, the expected molecular weight and a possible structure, even if the details are incomplete.
NDA if needed
Working with a confidential peptide? We sign a non-disclosure agreement before you share the details.
Formal quote
We review your request and send a formal quote. For larger projects, the first step is a 1–2 week feasibility study.
PO & sample shipment
When your PO arrives, we arrange shipping of your material to our lab.
Sample review & LIMS intake
On arrival we check your material and register it in our LIMS, so you can follow progress from your client dashboard.
Purification & delivery
We run the peptide method, verify identity by MS, and ship the purified peptide with its certificate of analysis.
What to send us
- Fermentation broth or dried pellets
- Crude extracts, or material you have already extracted or fractionated
- Crude synthetic peptide batches
- Starting raw material, and we can help you source it for the isolation
- Whatever data you have: chromatograms, feedstock details, molecular weight, possible structure
Typical timelines
Routine peptide purifications: about 5 business days in most cases.
More complex purifications: usually 3–4 weeks.
Specialty work: timing agreed for each project.
Large projects: usually begin with a 1–2 week feasibility study.
Quality
We are not ISO or GLP certified or accredited at this time. Our lab operates according to GLP principles and ISO/IEC 17025 practices while we pursue formal ISO/IEC 17025 accreditation.
What you receive
- Purified peptide — in quantities from milligrams up to kilograms
- Certificate of analysis — COA reporting purity / wt%
- Identity confirmation — primarily by mass spectrometry; further structural information on request
- Full traceability — documented handling from intake to delivery
Frequently asked questions
We isolate and purify peptides up to 5 kDa. For small molecules up to about 3,000 Da, see our Compound Purification service.
Fermentation broth, dried pellets, crude extracts, crude synthetic peptides, and already extracted or fractionated material. We can also support raw material procurement. Projects range from milligrams up to kilograms.
Purity is set by your request and application. We deliver anything from enriched products (around 20%) up to 98%+ pure standards, and every delivery comes with a certificate of analysis stating purity / wt%.
In our experience, reverse-phase HPLC (C18, C8 and C4 phases) is the most common technique for peptide purification. For extraction and high-throughput processing, ion-exchange chromatography separates charged peptides from the neutral matrix with high loading capacity. We also use size-exclusion chromatography and counter-current chromatography, including pH-zone refining for peptides that differ only slightly in pKa. Identity is confirmed primarily by mass spectrometry, and HPLC and NMR are also available in-house.
Pricing is project dependent. Routine purifications are typically turned around in about 5 business days, complex purifications typically take 3–4 weeks, and lead times for specialty projects are determined per project. Larger projects usually start with a 1–2 week feasibility study that de-risks the project, estimates its scope and develops the method.
Yes. If your project involves confidential IP, we can put a non-disclosure agreement in place before you share details.
Yes. Once your sample is received and reviewed, it is entered into our LIMS, and you can track your order in your online client dashboard.
Peptide isolation and purification certainly pose many challenges. (1) Side products produced during peptide synthesis must be removed to obtain pure peptides. (2) The impurities present in complex peptide mixtures often have similar physiochemical properties to the target peptide, necessitating the use of specialized analytical techniques, such as mass spectrometry. (3) Target peptides obtained from natural sources are present in extremely complex mixtures, which requires highly selective isolation techniques. (4) Optimization of parameters can often be time-consuming; not only can column parameters be altered, but mobile phase composition, pH, temperature, and flowrate may affect your selectivity and yields.
The most commonly used mobile phase in general is water and acetonitrile, with trifluoroacetic acid as a pH modifier. This holds true with peptides; however, their ionic nature often requires departure from the convention. Replacement of acetonitrile partially or entirely with alcohols can offer unique selectivity and favorable peak shape.
Control of the pH using different modifiers and buffers can greatly improve the selectivity as well as ensuring a more stable environment in which to purify the peptides. The most commonly used buffers include ammonium acetate, ammonium formate, and mono-basic and di-basic potassium phosphate.
The polarity of a peptide mainly determines its solubility. The majority of peptides are soluble in water. However, some peptides do not completely dissolve. Acidic solutions dissolve basic peptides, while basic solutions dissolve acidic peptides. A small volume of an organic solvent (e.g., DMSO, DMF, acetonitrile, methanol, or isopropanol) may dissolve very hydrophobic peptides. Water is then utilized to dilute the solution up to the desired concentration.
Have a peptide that needs purifying?
Tell us about your feedstock and target, and we’ll propose a peptide-specific method and a quote.