Peptide Purification Services

Preparative & analytical purification built around real impurity profiles — aligned with GLP / ISO 13485 quality systems (non-GMP).

Purification is not a single method — it’s a sequence-specific strategy. We select separation mechanisms, tune selectivity to isolate your target from near-neighbor impurities, and deliver documentation that supports ISO 90001 /ISO 13485 / GLP aligned

RP-HPLC (prep & analytical) Ion-exchange (IEX) HILIC for polar peptides SEC desalting & polishing Fit-for-purpose QC + COA GLP / ISO 90001 & 13485 aligned

Overview

Why peptide purification matters

Synthetic peptides often contain truncated sequences, deletion products, incomplete deprotection remnants, and modification byproducts. These can distort biological readouts and weaken reproducibility. Purification isolates the desired peptide fraction while controlling look-alike impurities that can co-elute or mimic activity.

  • Cleaner signal and better assay confidence
  • Improved lot-to-lot consistency
  • Reduced risk from near-neighbor impurities
  • Clear documentation for regulated non-GMP workflows

Quality statement: Services are aligned with GLP / ISO 9001 & 13485 quality systems.

How we work (in practice)

We treat purification as method development with a measurable goal: separate target from the most risk-relevant impurities, maintain yield, and provide verification data that matches your intended use.

Orthogonal selectivity Scalable workflows Impurity-focused strategy Traceable reporting
  • Review: sequence, modifications, constraints, intended application
  • Screen: conditions that resolve target vs key impurities
  • Purify: preparative fraction collection with tracking
  • Confirm: analytical HPLC purity + MS identity verification
  • Report: COA + supporting data package (project-defined)
Peptide purification laboratory with preparative chromatography systems and technicians performing sample handling

Purification Methods (Educational)

Different methods separate peptides by different physical principles. The strongest results often come from orthogonal steps when a single mode cannot fully resolve the impurity set.

Reversed-Phase HPLC (RP-HPLC)

The primary workhorse for peptides, separating mainly by hydrophobicity. Selectivity is tuned by stationary phase choice, gradient shape, temperature, and mobile phase conditions.

  • Best for: most synthetic peptides; truncations; deletion products
  • Strength: high resolution, scalable prep & analytical modes
  • Note: closely related impurities may require an orthogonal step
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Ion-Exchange (IEX)

Separates by charge at a chosen pH. Useful when target and impurities behave similarly in RP but differ in net charge.

  • Best for: charge variants; terminal heterogeneity; deamidation-related shifts
  • Strength: orthogonal selectivity vs RP
  • Note: pH selection is the strategy lever
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HILIC

Designed for polar analytes. Helps when peptides are too hydrophilic for strong RP retention or when RP selectivity is limited.

  • Best for: highly polar peptides; difficult RP retention
  • Strength: alternative selectivity; strong orthogonal pairing with RP
  • Note: method screening is typically worth it for tough polar sequences
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Size-Exclusion (SEC)

Separates by size rather than chemistry. Often used for desalting/buffer exchange and polishing, not primary look-alike impurity resolution.

  • Best for: desalting; small molecule removal; certain aggregate checks
  • Strength: gentle, non-binding separation
  • Note: limited resolution for closely sized peptide impurities
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When multi-step purification is the right answer

If the main risk is “near neighbor” impurities that co-elute (or partially co-elute), forcing a single method can waste time and yield. A deliberate two-step approach typically wins.

Problem Recommended strategy Why it works
Co-elution in RP IEX pre-fractionation → RP polish Charge selectivity separates what hydrophobicity cannot
Very polar peptide HILIC capture → RP polish HILIC improves retention/selectivity; RP finalizes purity
Need clean final matrix RP purification → SEC/desalting SEC removes salts/small molecules with minimal stress

Method Selection Guide

Fast rules that usually hold
  • Default: start with RP-HPLC unless there’s a known reason not to.
  • Charge-driven issues: add IEX when RP selectivity is insufficient.
  • Polar peptides: screen HILIC early to avoid RP dead-ends.
  • Matrix cleanup: SEC or desalting after chromatographic purification.
  • Hard impurity set: plan orthogonal steps up front.
What to send us (minimum)
  • Sequence + modifications
  • Target quantity (mg/g) and preferred format
  • Purity expectation (or intended use so we can recommend one)
  • Known issues (solubility, oxidation, sticky behavior)
  • Timeline and shipping destination

If you don’t know the “right” purity target, share the downstream assay/application and we’ll recommend a fit-for-purpose specification.

How we outperform generic purification pages
Impurity-first planning

We optimize separation against the impurities that matter most, not just “a peak.”

Clear documentation

Chromatograms + MS confirmation + a COA that actually answers what you need.

Scientist-to-scientist support

Direct technical communication for fast troubleshooting and decision-making.

Deliverables & Fit-for-Purpose QC

Representative deliverables
  • Analytical HPLC chromatogram(s) + purity assessment
  • Mass spectrometry identity verification (project-appropriate)
  • Fraction map / pooling rationale (what was collected and why)
  • Yield and handling notes
  • Certificate of Analysis (COA) with results summary

Deliverables can be tailored to your internal reporting requirements (templates, naming, traceability).

Quality system alignment
  • Controlled documentation and traceability
  • Instrument maintenance and method recordkeeping
  • Sample custody and labeling discipline
  • Change awareness when conditions must be adjusted

Services are aligned with GLP / ISO 13485 quality systems for regulated non-GMP needs.

Example purification workflow
Step Purpose Outcome
Condition screening Identify separation conditions that resolve target vs key impurities Shortlist of conditions with measurable resolution
Preparative collection Collect fractions using defined criteria and tracking Target-enriched fractions with documented windows
Analytical verification Confirm purity and identity of pooled fraction(s) HPLC + MS confirmation for the final pool
Finalize + report Provide COA and agreed data package Delivered material + documentation aligned to your program

Request a Quote

What to provide
  • Peptide sequence + any modifications (e.g., labels, cyclization, phosphorylation)
  • Starting material details (crude peptide amount, solvent, any prior cleanup)
  • Target quantity (mg/g) and preferred final format (lyophilized, solution)
  • Purity expectation (or downstream application so we can recommend a target)
  • Known challenges (solubility, oxidation, co-elution, aggregation)
  • Deadline and shipping destination

If you’re unsure about purity requirements, tell us the assay or use-case. We’ll recommend a fit-for-purpose target and workflow.

Share your sequence and project constraints. Our scientists will recommend a purification strategy, expected selectivity risks, and an analytical plan aligned to your program requirements.

Fastest path

For faster routing, include: sequence, modifications, amount, and deadline in your email.

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.