Peptide libraries

A peptide library is a mixture of peptides, typically of a fixed length of sequences partly randomised, whereas a peptide arrays is a collection of separate peptides. Since the peptide library is a mixture of peptides, the material is always a desalted crude preparation. An example library could look like this:

NH₂ D-G-X-X-X-X-X-X -amide

Where the first two amino acids are fixed, Asp and Gly, and the following six residues (X) are any random amino acid, except Cys. The theoretical and ideal size of the library would be a mixture of 19⁶ different peptide sequences.

It should be noted that a common strategy for adding the Xs is to add all the amino acids at different concentrations coupling them all together in one tube. The problem with this strategy is that there will not be an equal distribution of the random sequences. The reason for this is that there is competition for the available amino acid incorporation sites, and some couplings occur considerably more often - or less - than others.What should be done in order to get closer to the ideal library is to add each amino acid separately, mix the resins, acetylate and then de-protect FMOC, and then weigh them out into 19 tubes to add the next amino acid. This certainly is more work, but in this way, and in conjunction with having an acetylation cycle for each amino acid coupling step, you are assured that the amino acids are present in the expected amounts.

Having the capping (acetylation) cycle also means that libraries that have fixed amino acids at certain positions, are guaranteed to have these in place. If we expand on the example in the above and say that amino acid #5 always should be Proline:

NH₂ D-G-X-X-P-X-X-X -amide

Without the capping cycle, there will be deletion sequences, which causes the library to contain sequences where the Proline is out of position. Conversely, using poor quality synthesis reagents will cause a high rate of inadvertently doubly added amino acids, which also causes Proline to shift out of position.

Since peptide libraries are only desalted, there is a lot to gain if deletion sequences and doubly added amino acids can be avoided by using high quality reagents and a good synthesis strategy. In fact, it is always a good idea to do things this way, as explained in our text describing the production of high quality peptides.

Additional information

Custom production

Innovagen has serviced the research community since 1992. Over the years we have been providing thousands of synthetic peptides, and we know how just choosing the right synthesis strategy can make a world of difference for the final product. But our commitment goes beyond this as we believe that quality always pays off and we will go that extra mile for the benefit of your project. Please take a few moments to read about our view on the production of high quality peptides.

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