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Calling the Amino Acid Sequence of a Protein/Peptide from the Nanospectrum Produced by a Sub-nanometer Diameter Pore
Open accessPreprint — published as 10.1038/s41598-022-22305-x · Paper page
Abstract
The blockade current that develops when a protein translocates across a thin membrane through a sub-nanometer diameter pore (i.e., a nanospectrum) informs with extreme sensitivity on the sequence of amino acids that constitute the protein. Whereas mass spectrometry (MS) is still the dominant technology for protein identification, it suffers limitations. In proteome-wide studies, MS fails to sequence proteins de novo , but merely classifies a protein and it is not very sensitive requiring about a femtomole to do that. Compared with MS, a sub-nanometer diameter pore (i.e. a sub-nanopore) directly reads the amino acids constituting a single protein molecule, but efficient computational tools are still required for processing and interpreting the blockade current. Here, we delineate computational methods for processing sub-nanopore nanospectra and predicting electrical blockade currents from protein sequences, which are essential for protein identification.
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Metadata
- Authors
- Liu, X., Dong, Z., & Timp, G.
- Affiliations
- Tulane University (US)
- University of Notre Dame (US)
- Corresponding author
- Liu, Xiaowen
- Timp, Gregory
- Venue
- Scientific Reports
- Publisher
- openRxiv
- Published
- 2021-10-18
- Volume
- 12
- Issue
- 1
- Pages
- 17853-17853
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC9596471
- OpenAlex
- W4307201121
- Cited by
- 7
- References
- 1
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 1 · 2022: 3
- FWCI
- 0.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Scientific Reports (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Open Philanthropy Project
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- nanopore sequencing, protein translocation, amino acid sequence determination, protein identification, single-molecule protein sequencing
- MeSH terms
- Amino Acid Sequence, Amino Acids, Peptides, Proteome, Nanopores
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