Whereas peptide libraries are mixtures of peptides with (partially) randomised sequences, a peptide array is simply a larger collection of peptides such that parallel synthesis becomes a cost effective strategy. These sequences could be completely independing, but more often they are related. The Alanine scan peptide array is one example, and arrays for epitope mapping is another. Peptide length, amount and purity may vary depending on your application, but 10-20 amino acids, 1 mg, desalted is a common specification for screening purposes. Since these peptides typically are low purity material for screening purposes, reagent quality and synthesis strategy may be defining for the outcome of the project.
The main issue with poor synthesis reagents is that a comparatively large percentage lacks the FMOC protection group. This means that one ends up with material for which a large population has inadvertently doubly added amino acids.
The single most important thing to include in the synthesis strategy is the use of a capping cycle for each amino acid coupling step. For reasons of saving money, this step is often omitted, but this will result in deletion sequences. Deletion sequences are such sequences for which a given amino acid coupling step did not work. If the intended sequence was ACDEFGH and D failed you have ACEFGH. This is a difference that can have a serious impact on the usability in your application. With the acetylation however, the peptide is effectively terminated resulting in a truncation instead. In this case it would be EFGH, as peptides are grown from C-terminus to N-terminus.
Since peptide arrays are often low purity (perhaps only desalted), there is a lot to gain if these impurities can be avoided by just using high quality reagents and a good synthesis strategy. While it is true that these troublesome sequences can be removed to some extent by HPLC purification, it is not the whole truth. We are discussing this further in our text describing the production of high quality peptides. Here it suffices to conclude that by doing things right, even without HPLC purification, you will have material where all peptides have the correct sequence, albeit truncated for some of them.
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.
Examples of references of customers using our custom peptide arrays include;
Trulsson M, Yu H, Gisselsson L, Chao Y, Urbano A, et al. 2011
HAMLET Binding to α-Actinin Facilitates Tumor Cell Detachment.
PLoS ONE 6(3): e17179. doi:10.1371/journal.pone.0017179
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