The Rockefeller University Proteomics Resource Center

Peptide Synthesis Frequently Asked Questions

1. At what scale are peptides synthesized?

Currently custom peptides can be synthesized at 0.025, 0.05, and 0.1 mmol scale. Larger scales are possible through manual synthesis. Contact the peptide synthesis staff for more information (email here). FMOC based peptide synthesis chemistries are used in conjunction with manual organic chemistry protocols. High throughput synthesis of peptide libraries can be performed at lower scales of 0.005 and 0.010 mmol scales in addition to the scales above.

2. What is the difference between Custom synthesis and High throughput synthesis?

Custom synthesis involves optimizing or "customizing" synthesis conditions for individual peptides for best quality and yield. This involves an initial evaluation of the sequence for potential "trouble spots" and modification of the synthesis protocols to accommodate the difficult regions. If the initial product is not of sufficient purity, a resynthesis is attempted after analysis of the product and readjustment of the synthesis conditions to accommodate the additional information. Generally HPLC purification is usually requested in order to ensure product of the highest quality.

High throughput synthesis is designed for the economical, quicker synthesis of large numbers of related peptides at one time. In order to accomplish the quicker turnaround time, compromises are made in the synthesis protocols and only minimal "customizing" of synthesis conditions are possible. However, there are savings in terms of cost and time and this type of synthesis is well suited for production of libraries and mixtures of peptides where the purity of individual peptides is not crucial. An example of this type of library would be one used for epitope mapping, where a contiguous sequence of protein is synthesized in relatively short, overlapping peptide segments. Since any particular short sequence would be represented in more than one peptide the purity of any particular peptide is not critical. High throughput synthesized peptides are not HPLC purified due to restrictions of time and cost.

3. How much do peptides cost?

For complete pricing on Peptide Synthesis or or on all the PRC's prices click on the appropriate link.

4. How long does it take to get my peptide(s)?

Typically, routine peptide orders can be completed within 10 working days. However, the time to completion may be longer depending on the current backlog of orders. Peptides longer than 25 residues and modified peptides will also take longer due to the increased complexity of synthesis. Requests for additional material from an earlier synthesis can usually be completed within two weeks or less. Purification will also increase the delivery time.

Delivery time for high throughput peptides will vary widely depending on the number of peptides, scale, sequences and current backlog. Please contact us for more information.

5. How much material can I expect to receive?

This depends on length, sequence and scale. For example, the yield of a typical 17mer at 0.025 mmol scale would be about 30 to 40 mg of crude peptide. Different scales, lengths and sequences will yield proportionally more or less material. If HPLC purification is desired, this will reduce the yield by at least 50% or more, depending on the initial peptide sequence purity of the crude product Unlike most commercial labs, the PRC does not charge on a per milligram basis. We have a flat fee pricing system in which we will return to you as much material as is recovered from one cleavage and subsequent purifications. In most cases this works to your advantage.

6. What types of phospho- or other modified peptides can be synthesized?

Currently the PRC is regularly synthesizing peptides with phosphorylated forms of serine, threonine, and tyrosine. These peptides can be as long as 20 amino acids, although at this length yields can begin to drop. Peptides with more than one phosphorylated residue can be manufactured. Other modifications such as biotinylation, acetylation, methylation, dye labelling, fatty acid labelling and other modifications of the N-teminus or lysine epsilon amino groups can also be performed. Recovery amounts vary dramatically depending on the particular sequence of each peptide.

Important rules to consider when designing your modified peptide:

Success is highly sequence dependent. The largest factor appears to be steric hinderance during the addition of the modified amino acid. Surrounding the modification site with hindered residues such as histidine, arginine, cysteine, etc., can cause problems.
Yields and purity can vary dramatically for modified peptides compared to the unmodified versions.
Show us your sequence! Constant innovations in chemistries and protocols are allowing us to synthesize longer and more complex modified peptides.

7. I noticed that the order form only goes up to 30 amino acids. Can you (will you) make longer peptides?

The theoretical limit for an "ideal" peptide (couplings of at least 98% efficiency) on our instrument would be approximately 70 amino acids for an overall yield of about 24% of the desired peptide. A yield lower than this would be impossible to purify. However, the chances for sequence related synthesis failure also increases with peptide length. Therefore careful consideration of the particular sequence is a must. We have successfully synthesized peptides of over 41 amino acids in length with good yield and purity and others have synthesized peptides of over 70 amino acids on similar instruments. We are always willing to consider the synthesis of challenging peptides and would be happy to discuss your particular requirements!

8. I don't see a price listing for High Throughput peptides. How do I find out how much it will cost?

Although the per peptide costs for high throughput synthesis is significantly lower than for custom synthesis, the total cost for the entire library can be significant due to the large number of peptides. For this reason, please contact us for a customized quote and suggestions for sequence selection strategies.

Do you have a question that's not answered here? Send it to us and we'll post it on the FAQ page!

This page last updated on December 12, 2005

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