Visualization and identification of hepatitis c viral particles by atomic force microscopy combined with ms/ms analysis

Kaysheva, Anna L.; Ivanov, Yu. D.; Згода, В. Г.; Frantsuzov, P. A.; Pleshakova, Tatyana O.; Krokhin, N. V.; Ziborov, Vadim S.; Archakov, Alexander I.

doi:10.18097/pbmc20105601026

Cited by 14 publications

(4 citation statements)

References 31 publications

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“…Proteolysis of the fished-out proteins was carried out directly on the HOPG surface under standard conditions at a constant temperature of 42°C and 100% humidity [21]. The proteolytic solutions contained 100 mM bicarbonate buffer (pH 7.4), a 1% solution of glycerol and porcine trypsin in a proportion of 1 : 50 to the target protein.…”

Section: Ms Identification Of the Proteins Fished Out Onto The Hopg Smentioning

confidence: 99%

Highly sensitive protein detection by combination of atomic force microscopy fishing with charge generation and mass spectrometry analysis

et al. 2014

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An approach combining atomic force microscopy (AFM) fishing and mass spectrometry (MS) analysis to detect proteins at ultra‐low concentrations is proposed. Fishing out protein molecules onto a highly oriented pyrolytic graphite surface coated with polytetrafluoroethylene film was carried out with and without application of an external electric field. After that they were visualized by AFM and identified by MS. It was found that injection of solution leads to charge generation in the solution, and an electric potential within the measuring cell is induced. It was demonstrated that without an external electric field in the rapid injection input of diluted protein solution the fishing is efficient, as opposed to slow fluid input. The high sensitivity of this method was demonstrated by detection of human serum albumin and human cytochrome b5 in 10−17–10−18 m water solutions. It was shown that an external negative voltage applied to highly oriented pyrolytic graphite hinders the protein fishing. The efficiency of fishing with an external positive voltage was similar to that obtained without applying any voltage.

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Section: Ms Identification Of the Proteins Fished Out Onto The Hopg Smentioning

confidence: 99%

Highly sensitive protein detection by combination of atomic force microscopy fishing with charge generation and mass spectrometry analysis

et al. 2014

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“…onto the HOPG Surface Trypsinolysis of proteins fished by means of electric AFM fishing was performed directly on the HOPG surface at constant temperature 42°C and a humidity of about 100%, using the standard scheme [16]. The solution for trypsinolysis contained 100 mM bicar bonate buffer, pH 7.4, 10% acetonitrile, 1% glycerol, porcine trypsin (the ratio trypsin : target proteins of 1 : 50).…”

Section: Ms Identification Of Proteins Fishedmentioning

confidence: 99%

AFM-based protein fishing in the pulsed electric field

Ivanov

Pleshakova

Malsagova

et al. 2015

Biochem. Moscow Suppl. Ser. B

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A combination of (atomic force microscopy) based fishing (AFM fishing) and mass spectrometry allows to capture protein molecules from solutions, concentrate and visualize them on an atomically flat sur face of the AFM chip and identify by subsequent mass spectrometric analysis. In order to increase the AFM fishing efficiency we have applied pulsed voltage with the rise time of the front of about 1 ns to the AFM chip. The AFM chip was made using a conductive material, highly oriented pyrolytic graphite (HOPG). The increased efficiency of AFM fishing has been demonstrated using detection of cytochrome b 5 protein. Selec tion of the stimulating pulse with a rise time of 1 ns, corresponding to the GHz frequency range, by the effect of intrinsic emission from water observed in this frequency range during water injection into the cell.

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“…The ability to detect proteins present in biological fluid using a combination of AFM and MS methods has already been shown . For example, using this technique, viral hepatitis C marker proteins are registered and identified in the blood serum of patients . Chips with immobilized antibodies or aptamers as affinity reagents are used for biospecific AFM/MS analysis .…”

Section: Introductionmentioning

confidence: 99%

Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

Archakov

Aseev

Быков³

et al. 2019

J. Proteome Res.

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This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the “dark part” of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.

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Visualization and identification of hepatitis c viral particles by atomic force microscopy combined with ms/ms analysis

Cited by 14 publications

References 31 publications

Highly sensitive protein detection by combination of atomic force microscopy fishing with charge generation and mass spectrometry analysis

Highly sensitive protein detection by combination of atomic force microscopy fishing with charge generation and mass spectrometry analysis

AFM-based protein fishing in the pulsed electric field

Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

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