Peptide Synthesis Reagents

Peptide synthesis reagents can be sorted into several smaller categories, namely coupling reagents, protecting/labeling reagents and deprotection/ cleavage reagents. Coupling reagents are the largest subset of peptide synthesis reagents and the most important. 

Peptide Coupling Reagents

Peptide coupling reagents activate the acid group of the protected amino acids for forming a new peptide amide bond.  These reagents are also often used to attach the first amino acid of a peptide sequence to the peptide synthesis resin.  The most peptide coupling reagents belong to one of these catagories:

  • Carbodiimides
  • Phosphonium salts
  • Amidium Salts
  • Uronium Salts
  • Additives


Carbodiimides are usually used with an additive such as HOBt to form activated ester intermediates.  Ureas are the byproducts formed from carbodiimides.  N,N'-dicyclohexylurea, the byproduct from DCC (N,N'-dicyclohexylcarbodiimide), is not soluble in most organic solvents and forms a precipitate when DCC is used.  DCC is useful in manual synthesis, but is not suitable for automated peptide instruments.  The urea byproduct of DIC (N,N'-diisopropylcarbodiimide) is soluble in peptide synthesis solvents and DIC can be utilized in automated peptide synthesizers.  EDC and its urea byproduct are water soluble and are often used to conjugate smaller molecules to proteins. 

AAPPTec supplies:

Phosphonium Salts

Some of the first coupling reagents developed were phosphonium salts.  Phosphonium salts and related phosphorus compounds are very efficient, highly reactive and cause very little racemization.  PyAOP and PyBrOP are the recommended reagents for coupling to N-methyl amino acids and alpha, alpha-disubstituted glycines.

AAPPTec offers:

Aminium Salts

When these reagents were introduced, they were believed to have a uronium structure.  Later structure studies revealed that these reagents actually have aminium structure.  They are very efficient peptide coupling reagents with little racemization.  Coupling reactions are complete in as little as six minutes and when HOBt is added, racemization can be reduced to insignificant levels.

AAPPTec offers:

Uronium Salts

Uronium salts are very efficient coupling reagents.  They are not as widely utilized as HBTU and HATU, but are used in special applications, especially in difficult reactions or where racemization must be minimized.

AAPPTec provides:

Coupling Additives

When used with carbodiimide reagents, these compounds form activated esters.  Used with other coupling reagents, they suppress racemization.

AAPPTec supplies:

 Protecting/Labelling Reagents

Protecting groups are temporarily applied to keep reactive functional groups on the amino acids and peptides from interfering in the peptide synthesis reactions and producing unwanted side products.  At the approriate point in the synthesis, the protecting groups are removed to expose the functional group.

Labels are small molecules attached to a peptide to assist in later identification or manipulation of the peptide.  Typical labels are  dye or fluorescent compounds.

AAPPtec supplies:

Deprotection/Cleavage Reagents

Primarily two types of deprotection reagents are used in solid phase peptide synthesis.  The first type are N-deprotection reagents.  These remove only the N-terminal protection group of the peptide attached to the resin.  These are trifluoroacetic acid (TFA) in Boc chemistry and piperidine in Fmoc chemistry.  DBU may also be used to selectively remove Fmoc groups when deprotection with piperidine is sluggish.

Cleavage reagents are the secon type of deprotection reagents utilized in solid phase peptide synthesis.  Cleavage reagents typically cleave the peptide product from the resin and at the same time, remove all of the side chain protection groups producing the free peptide.  In Boc chemistry, typical cleavage reagents are HF, TFMSA and TMSOTf.  In Fmoc chemistry, TFA is utilized.

AAPPTec offers:

All AAPPTec peptide synthesis reagents are available in bulk.  Please send an e-mail to for a quotation.

  • Quantities and Prices

    To obtain a quotation for custom peptide synthesis, click HERE or contact AAPPTec by e-mail at
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  • About Us

    AAPPTec, located in Louisville, KY, USA, offers custom peptides in quantities from mg to kg, in purities from crude to 98%, all at an affordable price. In addition to standard peptides, we also provide custom peptides with modifications such as cyclization, phosphorylation, acetylation, fluorescent labels, etc.

    Our Production Team has decades of experience in preparing high quality peptides, including long peptides, difficult peptides and peptides with special modifications.

    Our Customer Support Team has many years of experience in the peptide business and they are ready to help you with questions, orders, etc.

    AAPPTec continually strives to provide the latest technology, the most competitive prices and the highest standard of customer support to peptide chemists worldwide.

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  • FAQ

    1. How do I request a quote for my peptide?

    To request an instant quote, please sign up a free account with us and proceed to the peptide order page. If you do not have an account with us yet and would like to receive a quote for your peptide(s), please email us: or call us at 1-888-692-9111 and ask for a peptide service representative.

    2. What type of chemistry do you use?

    AAPPTec generally utilizes Fmoc chemistry for most peptide production.

    3. How do you generally purify your peptides?

    Our peptides are generally purified by preparative reversed phase HPLC, using trifluoroacetic acid (TFA) modified buffers at pH 2. Buffer A is 0.1 % TFA deionized water and buffer B is 0.1 % TFA in acetonitrile (ACN) at pH 2. Peptides are dissolved in either straight buffer A, or some amount of buffer B then diluted with buffer A.

    Sometimes it is necessary to use an organic polar solvent like (formic acid or acetic acid) in DMSO or DMF to aid in the dissolving of hydrophobic peptides but this is done on a case-by-case basis depending on the sequence analysis. The separation is monitored by UV at 214 nm and fractions are collected and analyzed by mass spectrometry for product identity and by reversed phase analytical HPLC for purity.

    The fractions are then lyophilized to remove the solvents. The fractions that meet the specifications of the order are then combined into one vial. Next, we run a final mass spectrum and analytical HPLC on the combined material.

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