Method of protein analysis

A method for interpreting the mass spectrum of a test peptide or a test polypeptide comprising:

• (A) providing a population of Tryptic fragments of the test peptide or the test polypeptide having carboxy-terminal lysine or arginine residues and ionizing said fragments to produce doubly charged gas phase ions;
• (B) obtaining the mass spectra, and calculating molecular weights there from, for the fragments and for a population of daughter ions of incremental molecular weight, which population of daughter ions results substantially from fragmentation of the amide backbone of said fragments;
• and
• (C) determining at least a portion of the sequence of the test peptide or the test polypeptide by comparing differences in molecular weights between said gas phase ions and daughter ions to the molecular weight of amino acids.

A method for determining the sequence of a test peptide or a test polypeptide comprising:

• (A) cleaving the amide backbone of the test peptide or the test polypeptide by treatment with Trypsin to form a sub-population of fragments having carboxy-terminal lysine or arginine residues;
• (B) ionizing, by ion evaporation ionization, said fragments to produce doubly charged gas phase ions;
• (C) further fragmenting the gas phase ions under conditions which produce a population of daughter ions of incremental molecular weight utilizes collision-induced dissociation with a collision voltage of less than one kilovolt, which population of daughter ions results substantially from fragmentation of the amide backbone of said fragments;
• (D) determining the molecular weight of said gas phase ions and daughter ions by mass spectrometry;
• and,
• (E) determining the sequence of at least a portion of the test peptide or the test polypeptide from the determined molecular weights.