Why does capping after coupling improve results during solid phase peptide synthesis (SPPS)?
The Case: I have conducted a lab experiment where we coupled three Fmoc-protected amino acids, and did a final capping (acetylate) at the end of the synthesis. However, I was told that one can theoretically cap after every single amino acid coupling to ensure that the final product is correct. That is, one can "eliminate" or terminate the synthesis of peptides where the amino acids are innocently coupled (?).
I don't really understand why, because if you cap then you "block" all of the peptides that you are synthesizing (?). Therefore, how can you add further onto the chain if you cap after each amino acid? This seems counterintuitive, or I might be a bit confused. If you are able to de-protect the cap to further couple on more amino acids, then what is the point of capping?
Is there someway that capping only “caps” onto amino acids that are not coupled or that did not couple the previous amino acid somehow?