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Protein Analytics - Edman Sequencing

  • Amino acid sequences are reported using single-letter code for the twenty standard proteinogenic amino acids. For a variety of reasons, tryptophans, cysteines and amino acid residues containing side-chain modifications (e.g. phosphorylation) will generally be reported as blanks, as will most of the non-standard amino acids.

  • We often encounter samples containing mixtures of polypeptides.  If a mixture contains two or more polypeptides, we may not be able to unambiguously order their sequences. In order to aid in the separation of such mixed sequences, we provide a very approximate estimate of the picomole yield for each amino acid and we order them in the report according to their relative molar abundances. However, the twenty standard amino acids differ widely in their stability to Edman chemistry, so the given ordering may be misleading.

  • When mixed sequences represent gene-coded proteins, the correct ordering can often be deduced by reference to the known sequence. However, for de novo (i.e. novel) sequences, correctly ordering a mixture of proteins depends upon a clear difference in protein abundance between the components of the mixture. If more than one amino acid is identified at a given cycle the investigator should use caution in assigning a specific amino acid to that position in the sequence.