The methods and apparatus 100, disclosed herein are of use for sequencing 150 and/or identifying 160 proteins 230, 310, polypeptides 230, 310 or peptides 230, 310. Proteins 230, 310 containing labeled amino acid residues may be synthesized and passed through nanopores 255, 330. A detector 257, 345 operably coupled to a nanopore 255, 330 may detect labeled amino acid residues as they pass through the nanopore 255, 330. Distance maps 140 for each type of labeled amino acid residue may be compiled. The distance maps 140 may be used to sequence 150 and/or identify 160 the protein 230, 310. In different embodiments of the invention, amino acid residues labeled with luminescent labels 235, 245 or nanoparticles 315 may be detected using photodetectors 257 or electrical detectors 345. Apparatus 100 of use for protein 230, 310 sequencing 150 and/or identification 160 are also disclosed herein.