ABSTRACT
The choice between the following two methods depends mostly on the size of the peptide: the partitioning method is excellent for small peptides up to a dozen residues or so, ones that may wash out with the film method, but poor for large peptides and proteins. The number or polarity of the washes can be increased for particular samples, but there is a danger of washout with smaller peptides and proteins. Discrimination between by-products or sequencing derivatives and peptide is still by polarity, so the strength of the organic solvent is once again balanced for what will remove the comparatively hydrophobic products, but not the peptide. Interpreting the chromatograms in order to read a sequence is often the major effort, and one that is largely independent of the sequencing method. Reading a sequence will be more difficult for later cycles when a high background of 3-phenyl-2-thiohydantoin (PTH) has appeared, or with feeble amounts read over the intrinsic sequencing background.
