Custom Peptide Synthesis

Frequently Asked Questions for PEPscreen® Peptides

  1. How are PEPscreen peptides synthesized?
  2. What are the capabilities of the synthesis platforms?
  3. Can non-standard residues (NSRs) be used with the PEPscreen platform?
  4. Do the peptides that require modifications need to be the same length?
  5. What quality control (QC) analysis is performed on the PEPscreen peptide libraries?
  6. How do you guarantee the quality of PEPscreen peptides?
  7. What counterions are present in the peptides?
  8. Can I request for HPLC analyses of the peptides?
  9. What average purity can I expect from a PEPscreen peptide set?
  10. How are the peptides quantitated?
  11. How are the peptide sets supplied?
  12. How do I know that there is peptide in the vial?
  13. What does peptide "gross weight" mean? How does it relate to peptide content and peptide purity?
  14. Why does the amount of peptides vary between tubes in a peptide set?
  15. How can we keep track of what peptide is in what position in a plate?
  16. When should I expect to receive my PEPscreen peptide set?
  17. What are the recommended storage conditions for a PEPscreen peptide set?
  18. What are the recommended conditions for re-suspending the peptide set? (253 Kb PDF)


  1. How are PEPscreen peptides synthesized?
    PEPscreen peptides are synthesized on proprietary, state-of-the-art robotic platforms using optimized protocols based on Fmoc-chemistry.

  2. What are the capabilities of the synthesis platforms?
    Each platform can simultaneously synthesize hundreds of peptides and for cost effectiveness we require a minimum of 24 peptides in a set. Each peptide set can have all unique amino acid sequences and varying peptide lengths (8 to 20 residues). Sigma-Genosys has the capability to synthesize and process thousands of peptides each week.

  3. Can non-standard residues (NSRs) be used with the PEPscreen platform?
    Non-standard residues (NSRs) can be incorporated into the peptide sequence, provided that they are commercially available in a form for direct coupling. The NSRs usually include unusual amino acid derivatives, linkers, dyes, affinity ligands, etc.

  4. Do the peptides that require modifications need to be the same length?
    If the modifications involve NSRs that can be incorporated into the sequence like a standard amino acid, the differences in peptide length does not matter. However, if the modifications involve attachment of ligands into certain amino acid side chains, it is recommended that the peptides be of the same length.

  5. What quality control (QC) analysis is performed on the PEPscreen peptide libraries?
    ALL peptides are analyzed by MALDI-TOF mass spectrometry (MS) to confirm its correct molecular weight and the data are stored on a CD as pdf files and sent to the customer with the product. The QC analysis is included in the price of the peptides order.

  6. How do you guarantee the quality of PEPscreen peptides?
    The peptides have to pass both the MS analysis and the final gross weight criteria (>0.5 mg) before shipment. In order for a peptide to pass MS criterion the desired molecular weight must be one of the three major ions by MADI-TOF MS. If the peptide does not meet this QC requirement, it will be re-synthesized. If a peptide fails the additional synthesis attempt it will not be shipped and the customer will not be invoiced for that particular peptide. If a peptide has been re-synthesized and passes only the MS criterion but has a final weight of <0.5 mg, the customer will be given the option to accept the peptide or cancel that particular peptide in a set.

  7. What counterions are present in the peptides?
    Normally, the peptides are supplied with trifluoroacetate counterions. Upon request, the peptides can also be supplied in acetate counterions. However, since there is no purification step, it cannot be guaranteed that the peptide is free of trifluoroacetate counterions. If the peptide set had been supplied in trifluoroacetate, most of the trifuloroacetate counterions can be exchanged to acetate counterions by resuspending the peptides in 200 ml of neat HOAc, followed by re-lyophilization. This procedure is repeated one more time. Finally, the peptides are re-dissolved in 50% acetic acid in water and then re-lyophilized. The residual trifluoroacetate concentration is usually too low to be a factor in most research applications.

  8. Can I request for HPLC analyses of the peptides?
    Yes, analytical RP-HPLC or HPLC-ESI/MS analyses can be performed for a nominal fee. The analytical HPLC is typically run on a 4.6 mm x 250 mm C18 column using a 25-min gradient.

  9. What average purity can I expect from a PEPscreen peptide set?
    Since all PEPscreen peptides are supplied without purification, the purity of the individual peptides in a set varies considerably. The average purity of the peptides in a set depends on both the amino acid sequence and the peptide length. Controlled experiments showed that sets of 96 unique sequences containing 10, 15, and 20 residues gave average purities of 80±13%, 65±18%, and 50±20%, respectively. The performance of the synthesis platforms are constantly monitored by synthesizing the ACP control peptide (a 10-mer) to yield a minimum purity of 92±5%.

  10. How are the peptides quantitated?
    Each peptide is weighed and the gross weight is reported and supplied as part of the QC documentation.

  11. How are the peptide sets supplied?
    The peptide set is supplied to the customer as lyophilized film coated at the bottom of 1-ml tubes arranged in a 96-tube plate and individually sealed with silicon rubber lids. Individual tubes are used to allow re-sorting of the peptides in a plate, if necessary, as well as to prevent cross contamination since adjacent tubes are not in contact with each other like in well-plates. The peptide is supplied in coated film to prevent the peptide from sticking to the upper sides and the lid of the tubes during handling and transit.

  12. How do I know that there is peptide in the vial?
    The coated peptide film is really difficult to see and at best appears as a translucent film on the lower 1/3 of the tube.

  13. What does peptide “gross weight” mean? How does it relate to peptide content and peptide purity?
    Peptide "gross weight" refers to the actual weighed weight of the peptide. The gross weight includes the correct peptide, residual water, as well as peptide and non-peptide impurities that may be present and contribute to the weight.

    "Peptide content" is more specific and refers to the amount of correct peptide relative to everything else that contributes to the gross weight of the sample, such as residual water, peptide impurities, and non-peptide impurities. "Peptide content" is not obtained from weighing the sample. Instead, it is estimated from the combined data from amino acid analysis and from peptide purity. Peptide content is affected by the amount of water and salts present in the peptide sample.

    "Peptide purity" refers to the amount of correct peptide relative to all peptide and non-peptide impurities (except water and salts) that are detected by the assay method. Normally, peptide purity is determined by analytical RP-HPLC and detected by the absorbance at 215 nm. Peptide purity is then estimated from the percentage of the peak area of the correct peptide relative to the combined areas of all peaks present, whether these peaks are derived from peptide or non-peptide impurities. Peptide purity is not affected by the presence of water and salts because these species are generally not detected by the assay method.

  14. Why does the amount of peptides vary between tubes in a peptide set?
    The final gross weight of the peptides in a set is a result of different factors, such as the length of the peptide sequence, the types of amino acid residues used, the efficiency of each coupling step, their solubility in different solvents used in the production process, and their ability to retain water in lyophilized form. These factors are acting together, but the contributions of each are impossible to assess.

  15. How can we keep track of what peptide is in what position in a plate?
    Each tube is individually labeled with the peptide number, the amino acid sequence, and a 2D barcode.

  16. When should I expect to receive my PEPscreen peptide set?
    If the peptide set does not require re-synthesis, the peptides may be shipped in as short as four business days. If re-synthesis is required, the order will typically ship in 7 business days. Delivery time can also depend on the size of the peptide set being ordered.

  17. What are the recommended storage conditions for a PEPscreen peptide set?
    The lyophilized peptide and peptide solutions should be stored at –20 °C when not in use. For long-term storage (over one year), it is recommended that peptides be stored at –80 °C. Lyophilized powders are generally more stable than peptide solution. In addition, freeze-thaw cycles should be minimized, especially for peptide solutions. For periodic use of the peptides, it is highly recommended to prepare aliquots of peptide solutions and thaw only the aliquots needed to for experiment.

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