High-resolution nanopore peptide sensing, profiling and sequence assembly.
Peptide sequencing just took a leap forward. Researchers at Nanjing University have built a high-resolution nanopore sensor that can directly profile peptides, sequence fragments, and even spot post-translational modifications—all in one shot. Forget the old limitations of proteomics: this method uses a nickel-immobilized Mycobacterium smegmatis porin A (MspA-NTA-Ni) nanopore, pushing the boundaries of what single-molecule peptide analysis can do.
Nat Nanotechnol
by Wang K, An X, Gao X et al.
“High-resolution nanopore peptide sensing, profiling and sequence assembly. Wang K(1)(2), An X(1)(2), Gao X(1)(2), Ouyang Y(1)(2), Wang Z(1)(2), Fan P(1)(2), Li K(1)(2), Xiao Y(1)(2), Jia W(1)(2), Chen J(1)(2), Sun W(1)(2), Zhang P(1), Huang S(3)(4). Author information: (1)State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China. (2)Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, China. (3)State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China. shuo.huang@nju.edu.cn. (4)Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, China. shuo.huang@nju.edu.cn. Nanopores have been explored as a potential platform for protein analysis following the success of nanopore nucleic acid sequencing. However, protein sequencing remains technically challenging and has not yet been established for proteomics use. Here a nickel-immobilized Mycobacterium smegmatis porin A (MspA-NTA-Ni) nanopore is shown to enable the identification of a range of proteomic analytes, including amino acids and peptides up to 39 amino acids in length. Under identical conditions, signals corresponding to 20 proteinogenic amino acids, 4 post-translationally modified amino acids, 32 peptides, 6 modified peptides, 11 bioactive peptides and 2 neoantigen peptides were recorded. Machine-learning-based analysis enabled classification of these analytes with a validation accuracy of up to 97.4% within the studied dataset. The MspA-NTA-Ni nanopore supports both direct peptide identification and peptide profiling following enzymatic hydrolysis. As a proof of concept, a reference peptide was digested using exo- and endopeptidases to generate overlapping peptide fragments. Nanopore measurements combined with machine learning predictions enabled the identification of fragment compositions and partial sequences, allowing reconstruction of the original peptide sequence. This hydrolysis-based approach shows sensitivity to sequence alterations, including mutations, deletions and post-translational modifications, indicating potential utility for targeted peptide characterization. © 2026. The Author(s), under exclusive licence to Springer Nature Limited. Conflict of interest statement: Competing interests: S.H. and K.W. have filed patents describing the nanopore method for peptide sensing and sequencing (PCT Application No. PCT/CN2025/116383), filed with the World Intellectual Property Organization (WIPO). The other authors declare no competing interests.”
Here’s why this matters. Traditional protein sequencing is slow, expensive, and usually misses small changes like mutations or modifications. The team’s nanopore approach nailed the identification of:
All 20 standard amino acids
Four modified amino acids
32 distinct peptides (up to 39 residues)
Multiple bioactive and neoantigen peptides
The real kicker: machine learning algorithms classified these signals with nearly 97.4% accuracy. That’s not just “better.” It’s a different league for peptide analysis.
What’s cool is the sequence assembly trick. The researchers digested a reference peptide with exo- and endopeptidases, then ran the resulting fragments through the nanopore. With data from overlapping fragments, they could reconstruct partial sequences and even pick up sequence tweaks, deletions, and modifications. That level of sensitivity opens new doors for targeted peptide research and customized peptide analytics.
Key takeaway: This hydrolysis-based nanopore method isn’t just a proof of concept. It’s a toolkit for anyone serious about advanced peptide profiling and sequence assembly.
For more on the latest in peptide analytics and sequencing breakthroughs, check out the peptide research index. If you’re sourcing reagents or tools for your own experiments, the vendor directory has you covered. Expect this kind of tech to reshape peptide research workflows.
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