Proteome epitope tags and methods of use thereof in protein modification analysis

A method for detecting the presence or absence of a post-translational modification at a location on a target protein within a sample, comprising:

• (1) computationally analyzing an amino acid sequence of said target protein to identify one or more potential sites for said post-translational modification;
• (2) computationally identifying an amino acid sequence of at least one fragment of said target protein, said fragment predictably resulting from a treatment of said target protein within said sample, and said fragment comprising at least one of said potential post-translational modification sites and, separate therefrom, a PET (proteome epitope tag) unique to said fragment within said sample;
• (3) generating a capture agent that specifically binds said PET separate from said post-translational modification on said fragment, and immobilizing said capture agent to a support;
• (4) subjecting said sample to the treatment to produce said fragment, rendering said fragment soluble in solution, and contacting said fragment with said capture agent to bind said fragment, at said PET, to said capture agent;
• (5) detecting, on said fragment bound to said capture agent, the presence or absence of said post-translational modification by using a secondary capture agent specific for said post-translational modification separate from said PET on said fragment, wherein said secondary capture agent is labeled by a detectable moiety.