scholarly journals Protein identification by nanopore peptide profiling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Florian Leonardus Rudolfus Lucas ◽  
Roderick Corstiaan Abraham Versloot ◽  
Liubov Yakovlieva ◽  
Marthe T. C. Walvoort ◽  
Giovanni Maglia

AbstractNanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification.

Author(s):  
Peter M. Goodwin ◽  
W. Patrick Ambrose ◽  
Hong Cai ◽  
W. Kevin Grace ◽  
Erica J. Larson ◽  
...  

2015 ◽  
Vol 61 (11) ◽  
pp. 1372-1380 ◽  
Author(s):  
Carlos Cabrera ◽  
Lei Chang ◽  
Mars Stone ◽  
Michael Busch ◽  
David H Wilson

Abstract BACKGROUND Nucleic acid testing (NAT) has become the standard for high sensitivity in detecting low levels of virus. However, adoption of NAT can be cost prohibitive in low-resource settings where access to extreme sensitivity could be clinically advantageous for early detection of infection. We report development and preliminary validation of a simple, low-cost, fully automated digital p24 antigen immunoassay with the sensitivity of quantitative NAT viral load (NAT-VL) methods for detection of acute HIV infection. METHODS We developed an investigational 69-min immunoassay for p24 capsid protein for use on a novel digital analyzer on the basis of single-molecule-array technology. We evaluated the assay for sensitivity by dilution of standardized preparations of p24, cultured HIV, and preseroconversion samples. We characterized analytical performance and concordance with 2 NAT-VL methods and 2 contemporary p24 Ag/Ab combination immunoassays with dilutions of viral isolates and samples from the earliest stages of HIV infection. RESULTS Analytical sensitivity was 0.0025 ng/L p24, equivalent to 60 HIV RNA copies/mL. The limit of quantification was 0.0076 ng/L, and imprecision across 10 runs was <10% for samples as low as 0.09 ng/L. Clinical specificity was 95.1%. Sensitivity concordance vs NAT-VL on dilutions of preseroconversion samples and Group M viral isolates was 100%. CONCLUSIONS The digital immunoassay exhibited >4000-fold greater sensitivity than contemporary immunoassays for p24 and sensitivity equivalent to that of NAT methods for early detection of HIV. The data indicate that NAT-level sensitivity for acute HIV infection is possible with a simple, low-cost digital immunoassay.


2017 ◽  
Author(s):  
G. Sampath

This work demonstrates a minimal single-molecule proteolysis-free approach that requires very small samples, is non-destructive, and can be translated with currently available technology into a portable device for possible use in the field or in an academic setting, or in a pre-screening step preceding conventional mass spectrometry.<br>


2021 ◽  
Author(s):  
Carlos de Lannoy ◽  
Giovanni Maglia ◽  
Dick de Ridder

The identification of proteins at the single-molecule level would open exciting new venues in biological research and disease diagnostics. Previously we proposed a nanopore-based method for protein identification called chop-n-drop fingerprinting, in which the fragmentation pattern induced and measured by a proteasome-nanopore construct is used to identify single proteins. However whether such fragmentation patterns are sufficiently characteristic of proteins to identify them in complex samples remained unclear. In the simulation study presented here, we show that 97.9% of human proteome constituents are uniquely identified under close to ideal measuring circumstances, using a simple alignment-based classification method. We show that our method is robust against experimental error, as 78.8% can still be identified if the resolution is twice as low as currently attainable and 10% of proteasome restriction sites and protein fragments are randomly ignored. Based on these results and our experimental proof-of-concept, we argue that chop-n-drop fingerprinting has the potential to make cost-effective single-molecule protein identification feasible in the near future.


2017 ◽  
Author(s):  
G. Sampath

This work demonstrates a minimal single-molecule proteolysis-free approach that requires very small samples, is non-destructive, and can be translated with currently available technology into a portable device for possible use in the field or in an academic setting, or in a pre-screening step preceding conventional mass spectrometry.<br>


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