Peptide mapping, an identity test for proteins, is an essential analytical method for elucidating the primary amino acid structure of proteins. For recombinant protein pharmaceuticals, such as monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs), peptide mapping is used for proof of identity, primary structural characterization, and quality assurance (QA). Regulatory agencies issued ICH Q6B guidance which specifies the use of peptide mapping as a critical quality test procedure for drug characterization used to confirm desired product structure for lot release purposes. Peptide mapping involves enzymatic treatment of a protein, resulting in the formation of peptide fragments, followed by separation and identification of the resultant fragments by LC-MS/MS in a reproducible manner. It can identify single amino acid changes resulting from events such as errors in the reading of complementary DNA (cDNA) sequences or point mutations.

Poochon developed a standardized platform for peptide mapping of purified proteins using protease digestion and liquid chromatography tandem-mass spectrometry (LC-MS/MS).