After searching online for peptide mapping to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand the protein being analyzed.

Does this method operate in "sequence space" then? If so, what exactly is the relation of the two?

  • $\begingroup$ I slightly edited the question for clarity. Feel free to roll back. $\endgroup$ – AliceD May 21 '15 at 15:09

Shimadzu explains peptide mapping as follows:

Peptide mapping involves selectively cleaving the individual target [proteins] using an appropriate enzyme or chemical and analyzing the peptide fragments obtained using HPLC [high-performance liquid chromatography] or another suitable method. [... I]dentification of the peptide fragments separated by LC [...] [can be done] using amino acid composition analysis, N-terminal amino acid sequence analysis, or mass spectrometry.

As such, it does not provide a sequence of amino acids. Instead, you get a specific set of peptides of different sizes, dependent on the method used, that in turn can be used for protein fingerprinting.

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