Crude peptide (revision 11)

Crude peptide is the material obtained immediately after cleavage from the solid support, before any chromatographic purification. It contains the target peptide together with every by-product that accumulated during assembly and cleavage.^[1]

Its purity is highly variable and is largely determined by sequence. An easy 10-residue sequence may cleave at high purity; a difficult 40-residue sequence may cleave at well under half. That figure sets the cost and difficulty of everything that follows.^[1]

Crude peptide is sold as such in some markets, principally where the purchaser intends to purify it. Material described only as "crude" is not a defective product; it is an intermediate, and describing it accurately is what distinguishes it from a purified one.^[2]

The dominant impurities are sequence-related: deletion sequences missing one or more residues where a coupling failed, truncated sequences where a chain was capped, and any peptide bearing residual protecting groups where cleavage was incomplete.^[1][3]

Cleavage adds its own. Strongly acidic conditions release reactive cations from the protecting groups, which can alkylate tryptophan, methionine and cysteine unless scavengers capture them; oxidation and, for susceptible sequences, aspartimide formation also occur.

Non-peptide material is present too: scavengers, residual cleavage reagent, and trifluoroacetate. A crude figure quoted as a percentage is normally a chromatographic area percent, so it says nothing about how much of the solid is peptide at all. See Peptide content.^[2]

Preparative chromatography separates the target from the closely related impurities, and the yield of that step falls as crude purity falls: more material must be discarded to reach a given specification.^[1]