Provided herein are methods and systems for nanopore-based identification and sequencing of modified amino acids. In some aspects, a method for processing a modified amino acid comprises providing the modified amino acid comprising a polymerizable molecule and a plurality of monomers; incorporating a monomer into or adjacent to the polymerizable molecule to generate a partially polymerized modified amino acid; and translocating the partially polymerized modified amino acid through a nanopore. In some embodiments, signals measured at or adjacent to the nanopore under one or more applied voltages are used to identify amino acid types.