Custom Peptide Synthesis: How It Works and What to Ask

PEPMAKE Research Team (Synthesis & Business Team)
⏱️ 7 min read
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Custom Peptide Synthesis: How It Works and What to Ask

Short answer

Custom peptide synthesis is a service that builds a specific amino acid sequence for a researcher, then purifies and tests it. Most peptides are made with solid-phase peptide synthesis (SPPS), which attaches amino acids one by one to a solid resin.

What is solid-phase peptide synthesis?

Solid-phase peptide synthesis (SPPS) is the standard method for making peptides in the laboratory. First described in the 1960s, it attaches the first amino acid to a solid resin bead, then adds the remaining amino acids one at a time. When the chain is complete, the peptide is cleaved from the resin and purified [1].

The main steps are:

  • Sequence design - the customer provides the amino acid sequence.
  • Coupling - amino acids are added step by step on the resin.
  • Cleavage - the finished chain is removed from the resin.
  • Purification - reversed-phase HPLC removes truncated and side products.
  • Characterization - mass spectrometry confirms identity and HPLC confirms purity.
  • Lyophilization - the purified peptide is freeze-dried into a stable powder [2].
  • Why labs use custom synthesis

  • Any sequence - from short fragments to 50+ amino acid chains.
  • Modifications - acetylation, amidation, biotin labels, fluorescent tags, D-amino acids and more.
  • Controlled scale - from milligrams for assays to grams for larger studies.
  • Documentation - batch-specific COA with HPLC and MS data.
  • Purity grades explained

    GradeTypical HPLC purityBest for
    Crude60-80%Screening and method development
    Standard85-95%Most cell-based and biochemical assays
    High purity95-98%Structure-activity studies
    Research grade99%+Sensitive assays and analytical work

    Higher purity costs more and takes longer, so choose the grade that matches your experiment rather than always ordering the maximum.

    What to ask a synthesis supplier

  • Do you provide a COA per batch? - including HPLC chromatogram and MS spectrum.
  • What is the actual net peptide content? - peptides contain salts and water; ask for the peptide content percentage.
  • What modifications are supported? - confirm your specific modification before ordering.
  • What is the realistic timeline? - including purification and QC, not just coupling.
  • What is the failure/repeat policy? - what happens if QC fails?
  • Is the sequence kept confidential? - important for proprietary sequences.
  • Compliance and labeling

    Custom peptides intended for laboratory use should be labeled for research use only (RUO) and should not be marketed with clinical claims. If your project needs documentation for your institution, ask for full batch traceability.

    PEPMAKE offers custom peptide synthesis with sequence submission, purity selection, quantity selection and batch-level HPLC/MS documentation.

    FAQ

    What is custom peptide synthesis?

    A service that builds a specific amino acid sequence and delivers purified, tested peptide material.

    How long does it take?

    Typically 1-3 weeks for short peptides, including QC and shipping.

    What purity can I request?

    From crude to 99%+ HPLC purity, depending on the sequence and scale.

    What information do I need to provide?

    The sequence, quantity, purity, modifications and any labeling requirements.

    References

  • Solid phase protein chemical synthesis: a review of methods for producing and purifying polypeptides. PubMed entry
  • Peptides as therapeutic agents: challenges and opportunities, including synthesis and quality considerations. Molecules (2023). PMC article
  • Looking for Certified Research Peptides?

    All PEPMAKE compounds are synthesis-verified by independent third-party HPLC & ESI-MS testing with guaranteed ≥99% purity.

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