Solid-phase peptide synthesis
In short Solid-phase peptide synthesis is the standard method for making peptides chemically. The chain grows one amino acid at a time on a solid resin support.
Each cycle couples one building block and then removes its protecting group so that the next can follow. Excess reagents are washed out without the growing peptide leaving the resin.
At the end the finished chain is cleaved from the support and purified, usually by preparative HPLC. This step is also the source of the counterion that later stays attached to the molecule.
Because every cycle has a small error rate, the yield falls as the chain gets longer. That is why long peptides take more work and cost more than short ones.
The process consists of three recurring steps: remove the temporary protecting group at the end of the chain, couple the next amino acid in excess, and wash out everything left over. Because the growing chain is anchored to the resin, a rinse is enough to separate it, instead of a full purification.
No cycle runs to completion. If a coupling fails on one bead, the chain carries on growing without that link, and the result is a molecule very close to the target in mass. These deletion sequences are the main reason why purity never reaches one hundred per cent.
Cleavage is usually done with trifluoroacetic acid, which also removes the side-chain protecting groups and stays on the molecule as a counterion. The whole process, with figures, is described in how a peptide is made.