Single-molecule protein identification by sub-nanopore sensors

Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore t...

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Published inPLoS computational biology Vol. 13; no. 5; p. e1005356
Main Authors Kolmogorov, Mikhail, Kennedy, Eamonn, Dong, Zhuxin, Timp, Gregory, Pevzner, Pavel A.
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 01.05.2017
Public Library of Science (PLoS)
Subjects
Algorithms
Artificial intelligence
Bacteria
Biology and Life Sciences
Colleges & universities
Computer engineering
Computer science
Databases, Protein
Deoxyribonucleic acid
DNA
DNA sequencing
Electric currents
Electrical engineering
Fragmentation
Gene sequencing
Identification
Ions
Mass spectrometry
Mass spectroscopy
Matching
Methods
Nanopores
Nanostructure
Nanotechnology - methods
Observations
Physical Sciences
Porosity
Protein-protein interactions
Proteins
Proteins - chemistry
Proteins - classification
Proteomics
Research and Analysis Methods
Scientific imaging
Sensitivity
Sensors
Silicon nitride
Software
Technology
Translocation
La Jolla California
California
Indiana
United States > US
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Abstract Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisitely sensitive to single intact molecules, but it has only been successfully applied to DNA sequencing, so far. Here, we explore the potential of sub-nanopores for single-molecule protein identification (SMPI) and describe an algorithm for identification of the electrical current blockade signal (nanospectrum) resulting from the translocation of a denaturated, linearly charged protein through a sub-nanopore. The analysis of identification p-values suggests that the current technology is already sufficient for matching nanospectra against small protein databases, e.g., protein identification in bacterial proteomes.
AbstractList Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisitely sensitive to single intact molecules, but it has only been successfully applied to DNA sequencing, so far. Here, we explore the potential of sub-nanopores for single-molecule protein identification (SMPI) and describe an algorithm for identification of the electrical current blockade signal (nanospectrum) resulting from the translocation of a denaturated, linearly charged protein through a sub-nanopore. The analysis of identification p-values suggests that the current technology is already sufficient for matching nanospectra against small protein databases, e.g., protein identification in bacterial proteomes.
Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisitely sensitive to single intact molecules, but it has only been successfully applied to DNA sequencing, so far. Here, we explore the potential of sub-nanopores for single-molecule protein identification (SMPI) and describe an algorithm for identification of the electrical current blockade signal (nanospectrum) resulting from the translocation of a denaturated, linearly charged protein through a sub-nanopore. The analysis of identification p-values suggests that the current technology is already sufficient for matching nanospectra against small protein databases, e.g., protein identification in bacterial proteomes. Protein identification is the key step in many proteomics studies. Currently, the most popular technique for intact protein analysis is top-down mass spectrometry which recently enabled high-throughput identification of many proteins and their proteoforms. However, this approach requires large amounts of materials and is currently limited to short proteins, typically less than 30 kDa. On the other hand, nanopore sensors promise single molecule sensitivity in protein analysis, but an approach for the identification of a single protein from its blockade current (nanospectrum) has remained elusive, since the signal from the sensors relates to the amino acid sequence of the protein in a poorly understood way. In this work we describe the first algorithm for protein identification based on nanospectra associated with translocation of proteins through pores with sub-nanometer diameters. While identification accuracy currently does not allow reliable processing of complex protein samples yet, we believe, that the rapidly improving experimental protocols along with the new computational algorithms will transform into a viable protein identification approach in the near future.
Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisitely sensitive to single intact molecules, but it has only been successfully applied to DNA sequencing, so far. Here, we explore the potential of sub-nanopores for single-molecule protein identification (SMPI) and describe an algorithm for identification of the electrical current blockade signal (nanospectrum) resulting from the translocation of a denaturated, linearly charged protein through a sub-nanopore. The analysis of identification p-values suggests that the current technology is already sufficient for matching nanospectra against small protein databases, e.g., protein identification in bacterial proteomes.Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisitely sensitive to single intact molecules, but it has only been successfully applied to DNA sequencing, so far. Here, we explore the potential of sub-nanopores for single-molecule protein identification (SMPI) and describe an algorithm for identification of the electrical current blockade signal (nanospectrum) resulting from the translocation of a denaturated, linearly charged protein through a sub-nanopore. The analysis of identification p-values suggests that the current technology is already sufficient for matching nanospectra against small protein databases, e.g., protein identification in bacterial proteomes.
Audience Academic
Author Pevzner, Pavel A.
Kolmogorov, Mikhail
Timp, Gregory
Kennedy, Eamonn
Dong, Zhuxin
AuthorAffiliation 2 Electrical Engineering and Biological Science, University of Notre Dame, Notre Dame, Indiana, United States of America
1 Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America
University of North Carolina at Chapel Hill, UNITED STATES
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ContentType Journal Article
Copyright COPYRIGHT 2017 Public Library of Science
2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA (2017) Single-molecule protein identification by sub-nanopore sensors. PLoS Comput Biol 13(5): e1005356. https://doi.org/10.1371/journal.pcbi.1005356
2017 Kolmogorov et al 2017 Kolmogorov et al
2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA (2017) Single-molecule protein identification by sub-nanopore sensors. PLoS Comput Biol 13(5): e1005356. https://doi.org/10.1371/journal.pcbi.1005356
Copyright_xml – notice: COPYRIGHT 2017 Public Library of Science
– notice: 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA (2017) Single-molecule protein identification by sub-nanopore sensors. PLoS Comput Biol 13(5): e1005356. https://doi.org/10.1371/journal.pcbi.1005356
– notice: 2017 Kolmogorov et al 2017 Kolmogorov et al
– notice: 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA (2017) Single-molecule protein identification by sub-nanopore sensors. PLoS Comput Biol 13(5): e1005356. https://doi.org/10.1371/journal.pcbi.1005356
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PAP is a co-founder, has an equity interest and receives income from Digital Proteomics, LLC. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. All other authors have declared that no competing interests exist.
Conceptualization: MK PAP.Data curation: MK EK ZD.Formal analysis: MK EK ZD GT PAP.Funding acquisition: PAP.Investigation: MK EK GT PAP.Methodology: MK PAP.Project administration: PAP.Resources: EK ZD GT.Software: MK.Supervision: GT PAP.Validation: MK EK GT PAP.Visualization: MK EK.Writing – original draft: MK PAP.Writing – review & editing: MK EK GT PAP.
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Snippet Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass...
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StartPage e1005356
SubjectTerms Algorithms
Artificial intelligence
Bacteria
Biology and Life Sciences
Colleges & universities
Computer engineering
Computer science
Databases, Protein
Deoxyribonucleic acid
DNA
DNA sequencing
Electric currents
Electrical engineering
Fragmentation
Gene sequencing
Identification
Ions
Mass spectrometry
Mass spectroscopy
Matching
Methods
Nanopores
Nanostructure
Nanotechnology - methods
Observations
Physical Sciences
Porosity
Protein-protein interactions
Proteins
Proteins - chemistry
Proteins - classification
Proteomics
Research and Analysis Methods
Scientific imaging
Sensitivity
Sensors
Silicon nitride
Software
Technology
Translocation
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Title Single-molecule protein identification by sub-nanopore sensors
URI https://www.ncbi.nlm.nih.gov/pubmed/28486472
https://www.proquest.com/docview/1910463045
https://www.proquest.com/docview/1899793213
https://pubmed.ncbi.nlm.nih.gov/PMC5423552
https://doaj.org/article/c9c3deff1b50448ca7dd887c4a9b0076
http://dx.doi.org/10.1371/journal.pcbi.1005356
Volume 13
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