Restrepo-Pérez, L., Joo, C. & Dekker, C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).
Dorey, A. & Howorka, S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat. Chem. 16, 314–334 (2024).
Lu, C., Bonini, A., Viel, J. H. & Maglia, G. Toward single-molecule protein sequencing using nanopores. Nat. Biotechnol. 43, 312–322 (2025).
Aebersold, R. & Mann, M. Mass-spectrometric exploration of proteome structure and function. Nature 537, 347–355 (2016).
Gregorich, Z. R. & Ge, Y. Top-down proteomics in health and disease: challenges and opportunities. Proteomics 14, 1195–1210 (2014).
Edman, P. A method for the determination of amino acid sequence in peptides. Arch. Biochem. 22, 475 (1949).
Shuken, S. R. An introduction to mass spectrometry-based proteomics. J. Proteome Res. 22, 2151–2171 (2023).
Timp, W. & Timp, G. Beyond mass spectrometry, the next step in proteomics. Sci. Adv. 6, eaax8978 (2020).
Alfaro, J. A. et al. The emerging landscape of single-molecule protein sequencing technologies. Nat. Methods 18, 604–617 (2021).
Zhao, Y. et al. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. Nat. Nanotechnol. 9, 466–473 (2014).
Ohshiro, T. et al. Detection of post-translational modifications in single peptides using electron tunnelling currents. Nat. Nanotechnol. 9, 835–840 (2014).
Shrestha, P. et al. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. Nat. Nanotechnol. 16, 1362–1370 (2021).
Zheng, L., Sun, Y., Hein, L. A., Eisenstein, M. & Hyongsok, T. S. Single-molecule peptide sequencing through reverse translation of peptides into DNA. Nat. Biotechnol. https://doi.org/10.1038/s41587-026-03061-z (2026).
Swaminathan, J. et al. Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat. Biotechnol. 36, 1076–1082 (2018).
Reed, B. D. et al. Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device. Science 378, 186–192 (2022).
Filius, M. et al. Full-length single-molecule protein fingerprinting. Nat. Nanotechnol. 19, 652–659 (2024).
Püntener, S. & Rivera-Fuentes, P. Single-molecule peptide identification using fluorescence blinking fingerprints. J. Am. Chem. Soc. 145, 1441–1447 (2023).
Yan, S. et al. Single molecule ratcheting motion of peptides in a Mycobacterium smegmatis porin A (MspA) nanopore. Nano Lett. 21, 6703–6710 (2021).
Brinkerhoff, H., Kang, A. S. W., Liu, J., Aksimentiev, A. & Dekker, C. Multiple rereads of single proteins at single-amino acid resolution using nanopores. Science 374, 1509–1513 (2021).
Motone, K. et al. Multi-pass, single-molecule nanopore reading of long protein strands. Nature 633, 662–669 (2024).
Luo, R. Y. et al. Exploration of semiconductor chip-based single-molecule protein sequencing for identification of hemoglobin variants. Anal. Chem. 98, 3458–3465 (2026).
Cherf, G. M. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat. Biotechnol. 30, 344–348 (2012).
Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–353 (2012).
Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016).
Garalde, D. R. et al. Highly parallel direct RNA sequencing on an array of nanopores. Nat. Methods 15, 201–206 (2018).
Chen, Z. et al. Controlled movement of ssDNA conjugated peptide through Mycobacterium smegmatis porin A (MspA) nanopore by a helicase motor for peptide sequencing application. Chem. Sci. 12, 15750–15756 (2021).
Nova, I. C. et al. Detection of phosphorylation post-translational modifications along single peptides with nanopores. Nat. Biotechnol. 42, 710–714 (2024).
Chen, X. et al. Resolving sulfation posttranslational modifications on a peptide hormone using nanopores. ACS Nano 18, 28999–29007 (2024).
Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 31, 247–250 (2013).
Nivala, J., Mulroney, L., Li, G., Schreiber, J. & Akeson, M. Discrimination among protein variants using an unfoldase-coupled nanopore. ACS Nano 8, 12365–12375 (2014).
Zhang, S. et al. Bottom-up fabrication of a proteasome-nanopore that unravels and processes single proteins. Nat. Chem. 13, 1192–1199 (2021).
Martin-Baniandres, P. et al. Enzyme-less nanopore detection of post-translational modifications within long polypeptides. Nat. Nanotechnol. 18, 1335–1340 (2023).
Yu, L. et al. Unidirectional single-file transport of full-length proteins through a nanopore. Nat. Biotechnol. 41, 1130–1139 (2023).
Sauciuc, A., Morozzo della Rocca, B., Tadema, M. J., Chinappi, M. & Maglia, G. Translocation of linearized full-length proteins through an engineered nanopore under opposing electrophoretic force. Nat. Biotechnol. 42, 1275–1281 (2024).
Faller, M., Niederweis, M. & Schulz, G. E. The structure of a mycobacterial outer-membrane channel. Science 303, 1189–1192 (2004).
Cao, J. et al. Giant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore. Nat. Commun. 10, 5668 (2019).
Wang, Y. et al. Nanopore sequencing accurately identifies the mutagenic DNA lesion O6-carboxymethyl guanine and reveals its behavior in replication. Angew. Chem. Int. Ed. 58, 8432–8436 (2019).
Liu, Y. et al. Nanopore identification of alditol epimers and their application in rapid analysis of alditol-containing drinks and healthcare products. J. Am. Chem. Soc. 144, 13717–13728 (2022).
Wang, Y. et al. Identification of nucleoside monophosphates and their epigenetic modifications using an engineered nanopore. Nat. Nanotechnol. 17, 976–983 (2022).
Zhang, S. et al. A nanopore-based saccharide sensor. Angew. Chem. Int. Ed. 61, e202203769 (2022).
Wang, K. et al. Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore. Nat. Methods 21, 92–101 (2024).
de la Torre, D. & Chin, J. W. Reprogramming the genetic code. Nat. Rev. Genet. 22, 169–184 (2021).
Maras, B. et al. Aminopeptidase from Streptomyces griseus. Eur. J. Biochem. 236, 843–846 (1996).
David, M., Dursi, L. J., Yao, D., Boutros, P. C. & Simpson, J. T. Nanocall: an open source basecaller for Oxford Nanopore sequencing data. Bioinformatics 33, 49–55 (2017).
Kovaka, S. et al. Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment. Nat. Methods 22, 681–691 (2025).
Compeau, P. E. C., Pevzner, P. A. & Tesler, G. How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol. 29, 987–991 (2011).
Bloom, S. et al. Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials. Nat. Chem. 10, 205–211 (2018).
Beckett, D., Kovaleva, E. & Schatz, P. J. A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation. Protein Sci. 8, 921–929 (1999).
Fundoiano-Hershcovitz, Y. et al. Identification of the catalytic residues in the double-zinc aminopeptidase from Streptomyces griseus. FEBS Lett. 571, 192–196 (2004).
Zhang, H. et al. Chiral discrimination of all proteinogenic amino acid enantiomers by nanopore sensing. Angew. Chem. Int. Ed. 64, e202515531 (2025).
