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1.
Biology (Basel) ; 13(4)2024 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-38666884

RESUMO

Obesity is a socially significant disease that is characterized by a disproportionate accumulation of fat. It is also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers and pathological processes linked to obesity is especially vital for young individuals, given their increased potential for lifestyle modifications. By comparing the genetic, proteomic, and metabolomic profiles of individuals categorized as underweight, normal, overweight, and obese, we aimed to determine which omics layer most accurately reflects the phenotypic changes in an organism that result from obesity. We profiled blood plasma samples by employing three omics methodologies. The untargeted GC×GC-MS metabolomics approach identified 313 metabolites. To augment the metabolomic dataset, we integrated a label-free HPLC-MS/MS proteomics method, leading to the identification of 708 proteins. The genomic layer encompassed the genotyping of 647,250 SNPs. Utilizing omics data, we trained sparse Partial Least Squares models to predict body mass index. Molecular features exhibiting frequently non-zero coefficients were selected as potential biomarkers, and we further explored enriched biological pathways. Proteomics was the most effective in single-omics analyses, with a median absolute error (MAE) of 5.44 ± 0.31 kg/m2, incorporating an average of 24 proteins per model. Metabolomics showed slightly lower performance (MAE = 6.06 ± 0.33 kg/m2), followed by genomics (MAE = 6.20 ± 0.34 kg/m2). As expected, multiomic models demonstrated better accuracy, particularly the combination of proteomics and metabolomics (MAE = 4.77 ± 0.33 kg/m2), while including genomics data did not enhance the results. This manuscript is the first multiomics study of obesity in a gender-balanced cohort of young adults profiled by genomic, proteomic, and metabolomic methods. The comprehensive approach provides novel insights into the molecular mechanisms of obesity, opening avenues for more targeted interventions.

2.
Genes (Basel) ; 14(11)2023 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-38003008

RESUMO

Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and immunochemical analysis. For this reason, most scientific studies are limited to assessing the level of mRNA content. At the same time, protein content (and its post-translational status) largely determines the cell's state and behavior. Such a forced extrapolation of conclusions from the transcriptome to the proteome often seems unjustified. The ratios of "transcript-protein" pairs can vary by several orders of magnitude for different genes. As a rule, the correlation coefficient between transcriptome-proteome levels for different tissues does not exceed 0.3-0.5. Several characteristics determine the ratio between the content of mRNA and protein: among them, the rate of movement of the ribosome along the mRNA and the number of free ribosomes in the cell, the availability of tRNA, the secondary structure, and the localization of the transcript. The technical features of the experimental methods also significantly influence the levels of the transcript and protein of the corresponding gene on the outcome of the comparison. Given the above biological features and the performance of experimental and bioinformatic approaches, one may develop various models to predict proteomic profiles based on transcriptomic data. This review is devoted to the ability of RNA sequencing methods for protein abundance prediction.


Assuntos
Proteoma , Proteômica , Proteoma/genética , Proteômica/métodos , Perfilação da Expressão Gênica , Transcriptoma/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
3.
Metabolites ; 13(8)2023 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-37623852

RESUMO

To represent the composition of small molecules circulating in HepG2 cells and the formation of the "core" of characteristic metabolites that often attract researchers' attention, we conducted a meta-analysis of 56 datasets obtained through metabolomic profiling via mass spectrometry and NMR. We highlighted the 288 most commonly studied compounds of diverse chemical nature and analyzed metabolic processes involving these small molecules. Building a complete map of the metabolome of a cell, which encompasses the diversity of possible impacts on it, is a severe challenge for the scientific community, which is faced not only with natural limitations of experimental technologies, but also with the absence of transparent and widely accepted standards for processing and presenting the obtained metabolomic data. Formulating our research design, we aimed to reveal metabolites crucial to the Hepg2 cell line, regardless of all chemical and/or physical impact factors. Unfortunately, the existing paradigm of data policy leads to a streetlight effect. When analyzing and reporting only target metabolites of interest, the community ignores the changes in the metabolomic landscape that hide many molecular secrets.

4.
Curr Issues Mol Biol ; 45(4): 3406-3418, 2023 Apr 13.
Artigo em Inglês | MEDLINE | ID: mdl-37185747

RESUMO

Database records contain useful information, which is readily available, but, unfortunately, limited compared to the source (publications). Our study reviewed the text fragments supporting the association between the biological macromolecules and diseases from Open Targets to map them on the biological level of study (DNA/RNA, proteins, metabolites). We screened records using a dictionary containing terms related to the selected levels of study, reviewed 600 hits manually and used machine learning to classify 31,260 text fragments. Our results indicate that association studies between diseases and macromolecules conducted on the level of DNA and RNA prevail, followed by the studies on the level of proteins and metabolites. We conclude that there is a clear need to translate the knowledge from the DNA/RNA level to the evidence on the level of proteins and metabolites. Since genes and their transcripts rarely act in the cell by themselves, more direct evidence may be of greater value for basic and applied research.

5.
Int J Mol Sci ; 24(3)2023 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-36768195

RESUMO

The beginning of the twenty-first century witnessed novel breakthrough research directions in the life sciences, such as genomics, transcriptomics, translatomics, proteomics, metabolomics, and bioinformatics. A newly developed single-molecule approach addresses the physical and chemical properties and the functional activity of single (individual) biomacromolecules and viral particles. Within the alternative approach, the combination of "single-molecule approaches" is opposed to "omics approaches". This new approach is fundamentally unique in terms of its research object (a single biomacromolecule). Most studies are currently performed using postgenomic technologies that allow the properties of several hundreds of millions or even billions of biomacromolecules to be analyzed. This paper discusses the relevance and theoretical, methodological, and practical issues related to the development potential of a single-molecule approach using methods based on molecular detectors.


Assuntos
Genômica , Vírus , Genômica/métodos , Proteômica/métodos , Biologia Computacional , Metabolômica/métodos
6.
Int J Mol Sci ; 24(1)2023 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-36614211

RESUMO

A meta-analysis of the results of targeted quantitative screening of human blood plasma was performed to generate a reference standard kit that can be used for health analytics. The panel included 53 of the 296 proteins that form a "stable" part of the proteome of a healthy individual; these proteins were found in at least 70% of samples and were characterized by an interindividual coefficient of variation <40%. The concentration range of the selected proteins was 10−10−10−3 M and enrichment analysis revealed their association with rare familial diseases. The concentration of ceruloplasmin was reduced by approximately three orders of magnitude in patients with neurological disorders compared to healthy volunteers, and those of gelsolin isoform 1 and complement factor H were abruptly reduced in patients with lung adenocarcinoma. Absolute quantitative data of the individual proteome of a healthy and diseased individual can be used as the basis for personalized medicine and health monitoring. Storage over time allows us to identify individual biomarkers in the molecular landscape and prevent pathological conditions.


Assuntos
Proteínas Sanguíneas , Plasma , Proteoma , Humanos , Proteínas Sanguíneas/metabolismo , Ceruloplasmina/metabolismo , Espectrometria de Massas/métodos , Plasma/metabolismo , Proteômica
7.
Int J Mol Sci ; 25(1)2023 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-38203578

RESUMO

This work demonstrates the use of a modified mica to concentrate proteins, which is required for proteomic profiling of blood plasma by mass spectrometry (MS). The surface of mica substrates, which are routinely used in atomic force microscopy (AFM), was modified with a photocrosslinker to allow "irreversible" binding of proteins via covalent bond formation. This modified substrate was called the AFM chip. This study aimed to determine the role of the surface and crosslinker in the efficient concentration of various types of proteins in plasma over a wide concentration range. The substrate surface was modified with a 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) photocrosslinker, activated by UV irradiation. AFM chips were incubated with plasma samples from a healthy volunteer at various dilution ratios (102X, 104X, and 106X). Control experiments were performed without UV irradiation to evaluate the contribution of physical protein adsorption to the concentration efficiency. AFM imaging confirmed the presence of protein layers on the chip surface after incubation with the samples. MS analysis of different samples indicated that the proteomic profile of the AFM-visualized layers contained common and unique proteins. In the working series of experiments, 228 proteins were identified on the chip surface for all samples, and 21 proteins were not identified in the control series. In the control series, a total of 220 proteins were identified on the chip surface, seven of which were not found in the working series. In plasma samples at various dilution ratios, a total of 146 proteins were identified without the concentration step, while 17 proteins were not detected in the series using AFM chips. The introduction of a concentration step using AFM chips allowed us to identify more proteins than in plasma samples without this step. We found that AFM chips with a modified surface facilitate the efficient concentration of proteins owing to the adsorption factor and the formation of covalent bonds between the proteins and the chip surface. The results of our study can be applied in the development of highly sensitive analytical systems for determining the complete composition of the plasma proteome.


Assuntos
Proteínas Sanguíneas , Proteômica , Humanos , Silicatos de Alumínio , Espectrometria de Massas
8.
Front Mol Biosci ; 9: 944639, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36545510

RESUMO

It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM > 0 and TPM > 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for various types of biological material was carried out, and the HepG2 cell line transcriptome was compared with the transcriptome of liver tissue cells. In addition, the contribution of variability in the coverage of expressed genes in human transcriptomes to the creation of a draft human transcriptome was evaluated. For human liver tissues, ONT makes an extremely insignificant contribution to the overall coverage of the transcriptome. Thus, to ensure maximum coverage of the liver tissue transcriptome, it is sufficient to apply only one technology: Illumina RNA-Seq (FPKM > 0).

9.
Cells ; 11(22)2022 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-36428976

RESUMO

Both biological and technical variations can discredit the reliability of obtained data in omics studies. In this technical note, we investigated the effect of prolonged cultivation of the HepG2 hepatoma cell line on its metabolomic profile. Using the GC × GC-MS approach, we determined the degree of metabolic variability across HepG2 cells cultured in uniform conditions for 0, 5, 10, 15, and 20 days. Post-processing of obtained data revealed substantial changes in relative abundances of 110 metabolites among HepG2 samples under investigation. Our findings have implications for interpreting metabolomic results obtained from immortal cells, especially in longitudinal studies. There are still plenty of unanswered questions regarding metabolomics variability and many potential areas for future targeted and panoramic research. However, we suggest that the metabolome of cell lines is unstable and may undergo significant transformation over time, even if the culture conditions remain the same. Considering metabolomics variability on a relatively long-term basis, careful experimentation with particular attention to control samples is required to ensure reproducibility and relevance of the research results when testing both fundamentally and practically significant hypotheses.


Assuntos
Metaboloma , Metabolômica , Humanos , Reprodutibilidade dos Testes , Células Hep G2 , Metabolômica/métodos , Cromatografia Gasosa-Espectrometria de Massas/métodos
10.
Molecules ; 27(8)2022 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-35458675

RESUMO

We sought to identify the characteristic metabolite profile of blood plasma samples obtained from patients with preeclampsia. Direct high-resolution mass spectrometry was used to analyze samples from 79 pregnant women, 34 of whom had preeclampsia. We performed a comparative analysis of the metabolite profiles and found that they differed between pregnant women with and without preeclampsia. Lipids and sugars were identified as components of the metabolite profile that are likely to be associated with the development of preeclampsia. While PE was established only in the third trimester, a set of metabolites specific for the third trimester, including 2-(acetylamino)-1,5-anhydro-2-deoxy-4-O-b-D-galactopyranosyl-D-arabino-Hex-1-enitol, N-Acetyl-D-glucosaminyldiphosphodolichol, Cer(d18:0/20:0), and allolithocholic acid, was already traced in the first trimester. These components are also likely involved in lipid metabolism disorders and the development of oxidative stress.


Assuntos
Pré-Eclâmpsia , Biomarcadores , Feminino , Humanos , Metabolômica/métodos , Pré-Eclâmpsia/diagnóstico , Gravidez , Primeiro Trimestre da Gravidez , Estudos Retrospectivos
11.
Data Brief ; 42: 108055, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35345844

RESUMO

The data was acquired from 3 normal human liver tissues by LC-MS methods. The tissue liver samples from male subjects post mortem were obtained from ILSBio LLC (https://bioivt.com/). Liver tissue was frozen in liquid nitrogen, transported and shipped on dry ice. The proteins were extracted and purified followed up by trypsin hydrolysis. The peptide mixture was aliquoted and analyzed by different LC-MS approaches: one-dimensional shotgun LC-MS, two-dimensional LC-MS, two-dimensional SRM SIS (Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards). The Shotgun assay resulted in a qualitative in-depth human liver proteome, and a semi-quantitative iBAQ (intensity-based absolute quantification) value was calculated to show the relative protein content of the sample. Absolute quantitative concentrations of proteins encoded by human chromosome 18 using SRM SIS were obtained.

12.
J Pers Med ; 12(3)2022 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-35330478

RESUMO

Within the Human Proteome Project initiative framework for creating functional annotations of uPE1 proteins, the neXt-CP50 Challenge was launched in 2018. In analogy with the missing-protein challenge, each command deciphers the functional features of the proteins in the chromosome-centric mode. However, the neXt-CP50 Challenge is more complicated than the missing-protein challenge: the approaches and methods for solving the problem are clear, but neither the concept of protein function nor specific experimental and/or bioinformatics protocols have been standardized to address it. We proposed using a retrospective analysis of the key HPP repository, the neXtProt database, to identify the most frequently used experimental and bioinformatic methods for analyzing protein functions, and the dynamics of accumulation of functional annotations. It has been shown that the dynamics of the increase in the number of proteins with known functions are greater than the progress made in the experimental confirmation of the existence of questionable proteins in the framework of the missing-protein challenge. At the same time, the functional annotation is based on the guilty-by-association postulate, according to which, based on large-scale experiments on API-MS and Y2H, proteins with unknown functions are most likely mapped through "handshakes" to biochemical processes.

13.
Scientometrics ; 127(4): 1953-1967, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35221395

RESUMO

The paper describes a scheme for the comparative analysis of the sets of Pubmed publications. The proposed analysis is based on the comparison of the frequencies of occurrence of keywords-MeSH terms. The purpose of the analysis is to identify MeSH terms that characterize research areas specific to each group of articles, as well as to identify trends-topics on which the number of published works has changed significantly in recent years. The proposed approach was tested by comparing a set of medical publications and a group of articles in the field of personalized medicine. We analyzed about 700 thousand abstracts published in the period 2009-2021 and indexed them with MeSH terms. Topics with increasing research interest have been identified both in the field of medicine in general and specific to personalized medicine. Retrospective analysis of the keywords frequency of occurrence changes has shown the shift of the scientific priorities in this area over the past 10 years. The revealed patterns can be used to predict the relevance and significance of the scientific work direction in the horizon of 3-5 years. The proposed analysis can be scaled in the future for a larger number of groups of publications, as well as adjusted by introducing filters at the stage of sampling (scientific centers, journals, availability of full texts, etc.) or selecting a list of keywords (frequency threshold, use of qualifiers, category of generalizations). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11192-022-04292-y.

14.
J Pers Med ; 11(2)2021 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-33494491

RESUMO

Obesity is a frightening chronic disease, which has tripled since 1975. It is not expected to slow down staying one of the leading cases of preventable death and resulting in an increased clinical and economic burden. Poor lifestyle choices and excessive intake of "cheap calories" are major contributors to obesity, triggering type 2 diabetes, cardiovascular diseases, and other comorbidities. Understanding the molecular mechanisms responsible for development of obesity is essential as it might result in the introducing of anti-obesity targets and early-stage obesity biomarkers, allowing the distinction between metabolic syndromes. The complex nature of this disease, coupled with the phenomenon of metabolically healthy obesity, inspired us to perform data-centric, hypothesis-generating pilot research, aimed to find correlations between parameters of classic clinical blood tests and proteomic profiles of 104 lean and obese subjects. As the result, we assembled patterns of proteins, which presence or absence allows predicting the weight of the patient fairly well. We believe that such proteomic patterns with high prediction power should facilitate the translation of potential candidates into biomarkers of clinical use for early-stage stratification of obesity therapy.

15.
J Proteome Res ; 19(12): 4901-4906, 2020 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-33202127

RESUMO

One of the main goals of the Chromosome-Centric Human Proteome Project (C-HPP) is detection of "missing proteins" (PE2-PE4). Using the UPS2 (Universal proteomics standard 2) set as a model to simulate the range of protein concentrations in the cell, we have previously shown that 2D fractionation enables the detection of more than 95% of UPS2 proteins in a complex biological mixture. In this study, we propose a novel experimental workflow for protein detection during the analysis of biological samples. This approach is extremely important in the context of the C-HPP and the neXt-MP50 Challenge, which can be solved by increasing the sensitivity and the coverage of the proteome encoded by a particular human chromosome. In this study, we used 2D fractionation for in-depth analysis of the proteins encoded by human chromosome 18 (Chr 18) in the HepG2 cell line. Use of 2D fractionation increased the sensitivity of the SRM SIS method by 1.3-fold (68 and 88 proteins were identified by 1D fractionation and 2D fractionation, respectively) and the shotgun MS/MS method by 2.5-fold (21 and 53 proteins encoded by Chr 18 were detected by 1D fractionation and 2D fractionation, respectively). The results of all experiments indicate that 111 proteins encoded by human Chr 18 have been identified; this list includes 42% of the Chr 18 protein-coding genes and 67% of the Chr 18 transcriptome species (Illumina RNaseq) in the HepG2 cell line obtained using a single sample. Corresponding mRNAs were not registered for 13 of the detected proteins. The combination of 2D fractionation technology with SRM SIS and shotgun mass spectrometric analysis did not achieve full coverage, i.e., identification of at least one protein product for each of the 265 protein-coding genes of the selected chromosome. To further increase the sensitivity of the method, we plan to use 5-10 crude synthetic peptides for each protein to identify the proteins and select one of the peptides based on the obtained mass spectra for the synthesis of an isotopically labeled standard for subsequent quantitative analysis. Data are available via ProteomeXchange with the identifier PXD019263.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Cromossomos Humanos , Humanos , Proteoma/genética , Transcriptoma
16.
J Proteome Res ; 18(12): 4206-4214, 2019 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-31599598

RESUMO

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.


Assuntos
Proteínas/análise , Proteoma , Proteômica/métodos , Técnicas Biossensoriais , Eletroforese em Gel Bidimensional , Genoma Humano , Humanos , Microscopia de Força Atômica/métodos , Nanotecnologia/métodos , Processamento de Proteína Pós-Traducional , Proteínas/isolamento & purificação , Federação Russa , Sensibilidade e Especificidade , Espectrometria de Massas por Ionização por Electrospray , Espectrometria de Massas em Tandem , Fluxo de Trabalho
17.
J Proteome Res ; 18(1): 120-129, 2019 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-30480452

RESUMO

This work continues the series of the quantitative measurements of the proteins encoded by different chromosomes in the blood plasma of a healthy person. Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards (SRM SIS) and a gene-centric approach, which is the basis for the implementation of the international Chromosome-centric Human Proteome Project (C-HPP), were applied for the quantitative measurement of proteins in human blood plasma. Analyses were carried out in the frame of C-HPP for each protein-coding gene of the four human chromosomes: 18, 13, Y, and mitochondrial. Concentrations of proteins encoded by 667 genes were measured in 54 blood plasma samples of the volunteers, whose health conditions were consistent with requirements for astronauts. The gene list included 276, 329, 47, and 15 genes of chromosomes 18, 13, Y, and the mitochondrial chromosome, respectively. This paper does not make claims about the detection of missing proteins. Only 205 proteins (30.7%) were detected in the samples. Of them, 84, 106, 10, and 5 belonged to chromosomes 18, 13, and Y and the mitochondrial chromosome, respectively. Each detected protein was found in at least one of the samples analyzed. The SRM SIS raw data are available in the ProteomeXchange repository (PXD004374, PASS01192).


Assuntos
Cromossomos Humanos/química , Plasma/química , Proteoma , Cromossomos Humanos/genética , Cromossomos Humanos Par 13/química , Cromossomos Humanos Par 18/química , Cromossomos Humanos Y/química , Bases de Dados de Proteínas , Voluntários Saudáveis , Humanos , Mitocôndrias/ultraestrutura , Proteoma/genética
18.
J Proteome Res ; 17(11): 3889-3903, 2018 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-30298734

RESUMO

Adenosine-to-inosine RNA editing is one of the most common types of RNA editing, a posttranscriptional modification made by special enzymes. We present a proteomic study on this phenomenon for Drosophila melanogaster. Three proteome data sets were used in the study: two taken from public repository and the third one obtained here. A customized protein sequence database was generated using results of genome-wide adenosine-to-inosine RNA studies and applied for identifying the edited proteins. The total number of 68 edited peptides belonging to 59 proteins was identified in all data sets. Eight of them being shared between the whole insect, head, and brain proteomes. Seven edited sites belonging to synaptic vesicle and membrane trafficking proteins were selected for validation by orthogonal analysis by Multiple Reaction Monitoring. Five editing events in cpx, Syx1A, Cadps, CG4587, and EndoA were validated in fruit fly brain tissue at the proteome level using isotopically labeled standards. Ratios of unedited-to-edited proteoforms varied from 35:1 ( Syx1A) to 1:2 ( EndoA). Lys-137 to Glu editing of endophilin A may have functional consequences for its interaction to membrane. The work demonstrates the feasibility to identify the RNA editing event at the proteome level using shotgun proteomics and customized edited protein database.


Assuntos
Adenosina/metabolismo , Drosophila melanogaster/genética , Inosina/metabolismo , Proteínas de Insetos/genética , Proteogenômica/métodos , Edição de RNA , Aciltransferases/química , Aciltransferases/genética , Aciltransferases/metabolismo , Adenosina Desaminase/genética , Adenosina Desaminase/metabolismo , Sequência de Aminoácidos , Animais , Sequência de Bases , Encéfalo/metabolismo , Bases de Dados de Proteínas , Conjuntos de Dados como Assunto , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/química , Drosophila melanogaster/metabolismo , Proteínas de Insetos/classificação , Proteínas de Insetos/metabolismo , Modelos Moleculares , Anotação de Sequência Molecular , Proteoma/genética , Proteoma/metabolismo , Proteínas Qa-SNARE/genética , Proteínas Qa-SNARE/metabolismo , Vesículas Sinápticas/química , Vesículas Sinápticas/metabolismo
19.
J Proteome Res ; 17(12): 4258-4266, 2018 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-30354151

RESUMO

Currently, great interest is paid to the identification of "missing" proteins that have not been detected in any biological material at the protein level (PE1). In this paper, using the Universal Proteomic Standard sets 1 and 2 (UPS1 and UPS2, respectively) as an example, we characterized mass spectrometric approaches from the point of view of sensitivity (Sn), specificity (Sp), and accuracy (Ac). The aim of the paper was to show the utility of a mass spectra approach for protein detection. This sets consists of 48 high-purity human proteins without single aminoacid polymorphism (SAP) or post translational modification (PTM). The UPS1 set consists of the same 48 proteins at 5 pmols each, and in UPS2, proteins were grouped into 5 groups in accordance with their molar concentration, ranging from 10-11 to 10-6 M. Single peptides from the 92% and 96% of all sets of proteins could be detected in a pure solution of UPS2 and UPS1, respectively, by selected reaction monitoring with stable isotope-labeled standards (SRM-SIS). We also found that, in the presence of a biological matrix such as Escherichia coli extract or human blood plasma (HBP), SRM-SIS makes it possible to detect from 63% to 79% of proteins in the UPS2 set (sensitivity) with the highest specificity (∼100%) and an accuracy of 80% by increasing the sensitivity of shotgun and selected reaction monitoring combined with a stable-isotope-labeled peptide standard (SRM-SIS technology) by fractionating samples using reverse-phase liquid chromatography under alkaline conditions (2D-LC_alk). It is shown that this technique of sample fractionation allows the SRM-SIS to detect 98% of the single peptides from the proteins present in the pure solution of UPS2 (47 out of 48 proteins). When the extracts of E. coli or Pichia pastoris are added as biological matrixes to the UPS2, 46, and 45 out of 48 proteins (∼95%) can be detected, respectively, using the SRM-SIS combined with 2D-LC_alk. The combination of the 2D-LC_alk SRM-SIS and shotgun technologies allows us to increase the sensitivity up to 100% in the case of the proteins of the UPS2 set. The usage of that technology can be a solution for identifying the so-called "missing" proteins and, eventually, creating the deep proteome of a particular chromosome of tissue or organs. Experimental data have been deposited in the PeptideAtlas SRM Experiment Library with the dataset identifier PASS01192 and the PRIDE repository with the dataset identifier PXD007643.


Assuntos
Cromatografia Líquida/métodos , Espectrometria de Massas/normas , Proteogenômica/métodos , Proteoma/análise , Cromatografia de Fase Reversa/métodos , Cromossomos Humanos/genética , Humanos , Proteínas/análise , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
20.
J Proteome Res ; 16(12): 4311-4318, 2017 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-28956606

RESUMO

In this work targeted (selected reaction monitoring, SRM, PASSEL: PASS00697) and panoramic (shotgun LC-MS/MS, PRIDE: PXD00244) mass-spectrometric methods as well as transcriptomic analysis of the same samples using RNA-Seq and PCR methods (SRA experiment IDs: SRX341198, SRX267708, SRX395473, SRX390071) were applied for quantification of chromosome 18 encoded transcripts and proteins in human liver and HepG2 cells. The obtained data was used for the estimation of quantitative mRNA-protein ratios for the 275 genes of the selected chromosome in the selected tissues. The impact of methodological limitations of existing analytical proteomic methods on gene-specific mRNA-protein ratios and possible ways of overcoming these limitations for detection of missing proteins are also discussed.


Assuntos
Cromossomos Humanos Par 18/genética , Proteínas/análise , RNA Mensageiro/análise , Células Hep G2 , Humanos , Fígado/metabolismo , Proteínas/genética , Proteômica/métodos , Transcriptoma
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