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Article ; Online: Dataset on the effects of environmentally relevant humic acid concentrations on the liver protein profile in Japanese medaka (Oryzias latipes)

Victoria V. Yurchenko / Alexey A. Morozov / Roman A. Fedorov / Ludmila G. Bakina / Victor G. Zgoda / Olga V. Tikhonova

Data in Brief, Vol 40, Iss , Pp 107796- (2022)

2022

Abstract: The data were obtained by a label-free quantification approach from a shotgun proteomics experiment, using STrap sample processing technique for protein digestion and high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) for ... ...

Abstract	The data were obtained by a label-free quantification approach from a shotgun proteomics experiment, using STrap sample processing technique for protein digestion and high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) for peptide analysis. MaxQuant data processing was used to obtain proteomics data. The dataset reflects changes in the liver protein profile of Japanese medaka exposed to 0, 5, 40 and 80 mg/L nominal concentrations of Sigma-Aldrich humic acid for 96 h. Actual concentrations of humic acid were measured using the potassium dichromate photometric method and reported in mg organic carbon/L. These proteomics data are relevant for further insights into fish stress responses to humic substances-related challenge.
Keywords	Humic substances ; Acute exposure ; Japanese rice fish ; Shotgun proteomics ; LFQ ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Proteomic Signature of Extracellular Vesicles for Lung Cancer Recognition

Svetlana E. Novikova / Natalia A. Soloveva / Tatiana E. Farafonova / Olga V. Tikhonova / Pao-Chi Liao / Victor G. Zgoda

Molecules, Vol 26, Iss 6145, p

2021 Volume 6145

Abstract: The proteins of extracellular vesicles (EVs) that originate from tumors reflect the producer cells’ proteomes and can be detected in biological fluids. Thus, EVs provide proteomic signatures that are of great interest for screening and predictive cancer ... ...

Abstract	The proteins of extracellular vesicles (EVs) that originate from tumors reflect the producer cells’ proteomes and can be detected in biological fluids. Thus, EVs provide proteomic signatures that are of great interest for screening and predictive cancer diagnostics. By applying targeted mass spectrometry with stable isotope-labeled peptide standards, we assessed the levels of 28 EV-associated proteins, including the conventional exosome markers CD9, CD63, CD81, CD82, and HSPA8, in vesicles derived from the lung cancer cell lines NCI-H23 and A549. Furthermore, we evaluated the detectability of these proteins and their abundance in plasma samples from 34 lung cancer patients and 23 healthy volunteers. The abundance of TLN1, TUBA4A, HSPA8, ITGB3, TSG101, and PACSIN2 in the plasma of lung cancer patients was measured using targeted mass spectrometry and compared to that in plasma from healthy volunteers. The most diagnostically potent markers were TLN1 (AUC, 0.95), TUBA4A (AUC, 0.91), and HSPA8 (AUC, 0.88). The obtained EV proteomic signature allowed us to distinguish between the lung adenocarcinoma and squamous cell carcinoma histological types. The proteomic cargo of the extracellular vesicles represents a promising source of potential biomarkers.
Keywords	extracellular vesicles ; proteomic signature ; mass spectrometry ; lung cancer ; SRM ; stable isotope-labeled peptide standards ; Organic chemistry ; QD241-441
Subject code	610
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Temperature-induced reorganisation of Schistocephalus solidus (Cestoda) proteome during the transition to the warm-blooded host

Ekaterina V. Borvinskaya / Albina A. Kochneva / Polina B. Drozdova / Olga V. Balan / Victor G. Zgoda

Biology Open, Vol 10, Iss

2021 Volume 11

Abstract: The protein composition of the cestode Schistocephalus solidus was measured in an experiment simulating the trophic transmission of the parasite from a cold-blooded to a warm-blooded host. The first hour of host colonisation was studied in a model ... ...

Abstract	The protein composition of the cestode Schistocephalus solidus was measured in an experiment simulating the trophic transmission of the parasite from a cold-blooded to a warm-blooded host. The first hour of host colonisation was studied in a model experiment, in which sticklebacks Gasterosteus aculeatus infected with S. solidus were heated at 40°C for 1 h. As a result, a decrease in the content of one tegument protein was detected in the plerocercoids of S. solidus. Sexual maturation of the parasites was initiated in an experiment where S. solidus larvae were taken from fish and cultured in vitro at 40°C for 48 h. Temperature-independent changes in the parasite proteome were investigated by incubating plerocercoids at 22°C for 48 h in culture medium. Analysis of the proteome allowed us to distinguish the temperature-induced genes of S. solidus, as well as to specify the molecular markers of the plerocercoid and adult worms. The main conclusion of the study is that the key enzymes of long-term metabolic changes (glycogen consumption, protein production, etc.) in parasites during colonisation of a warm-blooded host are induced by temperature.
Keywords	schistocephalus solidus ; proteome ; parasite ; cestoda ; plerocercoid ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	The Company of Biologists
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Blood Plasma Proteome

Anna A. Kliuchnikova / Svetlana E. Novikova / Ekaterina V. Ilgisonis / Olga I. Kiseleva / Ekaterina V. Poverennaya / Victor G. Zgoda / Sergei A. Moshkovskii / Vladimir V. Poroikov / Andrey V. Lisitsa / Alexander I. Archakov / Elena A. Ponomarenko

International Journal of Molecular Sciences, Vol 24, Iss 1, p

A Meta-Analysis of the Results of Protein Quantification in Human Blood by Targeted Mass Spectrometry

2023 Volume 769

Abstract: 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 ... ...

Abstract	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.
Keywords	proteome ; targeted mass spectrometry analysis ; human proteome project ; knowledge databases ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	610
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Impact of p53 knockdown on protein dataset of HaCaT cells

Daniil D. Romashin / Alexander L. Rusanov / Peter M. Kozhin / Maxim N. Karagyaur / Olga V. Tikhonova / Victor G. Zgoda / Nataliya G. Luzgina

Data in Brief, Vol 42, Iss , Pp 108274- (2022)

2022

Abstract: The HaCaT line of immortalized non-tumor cells is a popular model of keratinocytes used for dermatological studies, in the practice of toxicological tests, and in the study of skin allergic reactions. These cells maintain a stable keratinocyte phenotype, ...

Abstract	The HaCaT line of immortalized non-tumor cells is a popular model of keratinocytes used for dermatological studies, in the practice of toxicological tests, and in the study of skin allergic reactions. These cells maintain a stable keratinocyte phenotype, do not require specific growth factors during cultivation, and respond to keratinocyte differentiation stimuli. HaCaT cells bear two mutant p53 alleles - R282Q and H179Y. At least two mechanisms of GOF (gain-of-function) of mutant p53 are known: it affects functions of p63/p73 by inhibiting their binding to DNA; or it binds to new DNA sites by interacting with other transcription factors (NF-Y, E2F1, NF-KB, VDR, p63). Proteins of the P53 family play an important role in the regulation of proliferation and differentiation processes of human keratinocytes. Proteomic study of HaCaT cells with TP53 gene knockdown provides new data for understanding the limitations of HaCaT cells when using them as an experimental model of normal human keratinocytes.In this article we present datasets obtained through the high-throughput shotgun proteomics analysis of human immortalized HaCaT keratinocytes and p53 knockdown HaCaT keratinocytes. As a protocol for proteomic profiling of cells, we used the approach of obtaining LC-MS/MS measurements followed by their processing with MaxQuant software (version 1.6.3.4). The “RAW” files were deposited to the ProteomeXchange with identifier PXD033538.
Keywords	Keratinocyte ; p53 ; Proteome ; LC-MS/MS ; shRNA ; Knockdown ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	612
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Deep proteomic dataset of human liver samples obtained by two-dimensional sample fractionation coupled with tandem mass spectrometry

Nikita E. Vavilov / Ekaterina V. Ilgisonis / Andrey V. Lisitsa / Elena A. Ponomarenko / Tatiana E. Farafonova / Olga V. Tikhonova / Victor G. Zgoda / Alexander I. Archakov

Data in Brief, Vol 42, Iss , Pp 108055- (2022)

2022

Abstract: 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 ... ...

Abstract	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.
Keywords	Mass-spectrometry ; Proteomics ; Shotgun ; SRM SIS ; Fractionation ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	500
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Impact of p53 Knockout on Protein Data Set of HaCaT Cells in Confluent and Subconfluent Conditions

Alexander L. Rusanov / Daniil D. Romashin / Peter M. Kozhin / Maxim N. Karagyaur / Dmitry S. Loginov / Olga V. Tikhonova / Victor G. Zgoda / Nataliya G. Luzgina

Data, Vol 7, Iss 27, p

2022 Volume 27

Abstract: The immortalized keratinocytes, HaCaT, are a popular model for skin research (toxicity, irritation, allergic reactions, or interaction of cells). They maintain a stable keratinocyte phenotype and respond to keratinocyte differentiation stimuli. However, ... ...

Abstract	The immortalized keratinocytes, HaCaT, are a popular model for skin research (toxicity, irritation, allergic reactions, or interaction of cells). They maintain a stable keratinocyte phenotype and respond to keratinocyte differentiation stimuli. However, programs of stratification and expression of differentiation markers in HaCaT keratinocytes are aberrant. In HaCaT cells, there are two mutant p53 alleles (i.e., R282Q and H179Y) that contain gain-of-function (GOF) mutations resulting from spontaneous immortalization (mutp53). At the same time, mutp53 acts as a transcription factor and also affects the interaction of p63 protein with its transcription targets. Proteins of the p53 family are crucial for regulation of proliferation and differentiation processes in human keratinocytes, although the involvement of mutp53 in these processes is not fully clear. We present data sets obtained as a result of high-performance proteomic analysis of immortalized HaCaT keratinocytes with p53 knockout in two different states, subconfluent and confluent, which are characterized by different intensites of cell differentiation processes. To obtain the proteomic profiles of the cells, we applied LC-MS/MS measurements processed with MaxQuant software (version 1.6.3.4).
Keywords	keratinocyte ; p53 ; proteome ; LC-MS/MS ; knockout ; confluent ; Bibliography. Library science. Information resources ; Z
Subject code	572
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dataset of target mass spectromic proteome profiling for human chromosome 18

Ekaterina V. Ilgisonis / Arthur T. Kopylov / Victor G. Zgoda

Data in Brief, Vol 8, Iss , Pp 1365-

2016 Volume 1369

Abstract: Proteome profiling is a type of quantitative analysis that reveals level of protein expression in the sample. Proteome profiling by using selected reaction monitoring is an approach for the Chromosome-centric Human Proteome Project (C-HPP). Here we ... ...

Abstract	Proteome profiling is a type of quantitative analysis that reveals level of protein expression in the sample. Proteome profiling by using selected reaction monitoring is an approach for the Chromosome-centric Human Proteome Project (C-HPP). Here we describe dataset generated in the course of the pilot phase of Russian part of C-HPP, which was focused on human Chr 18 proteins. Proteome profiling was performed using stable isotope-labeled standards (SRM/SIS) for plasma, liver tissue and HepG2 cells. Dataset includes both positive and negative results of protein detection.These data were partly discussed in recent publications, “Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells” [1] and “Chromosome 18 transcriptoproteome of liver tissue and HepG2 Cells and targeted proteome mapping in depleted plasma: Update 2013” [2], supporting the accompanying publication “State of the Chromosome 18-centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells” [3], and are deposited at the ProteomeXchange via the PASSEL repository with the dataset identifier PASSEL: PASS00697 for liver and HepG2 cell line.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	610
Language	English
Publishing date	2016-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Proteome Profiling of PMJ2-R and Primary Peritoneal Macrophages

Alexander L. Rusanov / Peter M. Kozhin / Olga V. Tikhonova / Victor G. Zgoda / Dmitry S. Loginov / Adéla Chlastáková / Martin Selinger / Jan Sterba / Libor Grubhoffer / Nataliya G. Luzgina

International Journal of Molecular Sciences, Vol 22, Iss 6323, p

2021 Volume 6323

Abstract: In vitro models are often used for studying macrophage functions, including the process of phagocytosis. The application of primary macrophages has limitations associated with the individual characteristics of animals, which can lead to insufficient ... ...

Abstract	In vitro models are often used for studying macrophage functions, including the process of phagocytosis. The application of primary macrophages has limitations associated with the individual characteristics of animals, which can lead to insufficient standardization and higher variability of the obtained results. Immortalized cell lines do not have these disadvantages, but their responses to various signals can differ from those of the living organism. In the present study, a comparative proteomic analysis of immortalized PMJ2-R cell line and primary peritoneal macrophages isolated from C57BL/6 mice was performed. A total of 4005 proteins were identified, of which 797 were quantified. Obtained results indicate significant differences in the abundances of many proteins, including essential proteins associated with the process of phagocytosis, such as Elmo1, Gsn, Hspa8, Itgb1, Ncf2, Rac2, Rack1, Sirpa, Sod1, C3, and Msr1. These findings indicate that outcomes of studies utilizing PMJ2-R cells as a model of peritoneal macrophages should be carefully validated. All MS data are deposited in ProteomeXchange with the identifier PXD022133.
Keywords	PMJ2-R ; peritoneal macrophages ; phagocytosis ; proteome ; LC-MS/MS ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: MS Identification of Blood Plasma Proteins Concentrated on a Photocrosslinker-Modified Surface

Arina I. Gordeeva / Anastasia A. Valueva / Elizaveta E. Rybakova / Maria O. Ershova / Ivan D. Shumov / Andrey F. Kozlov / Vadim S. Ziborov / Anna S. Kozlova / Victor G. Zgoda / Yuri D. Ivanov / Ekaterina V. Ilgisonis / Olga I. Kiseleva / Elena A. Ponomarenko / Andrey V. Lisitsa / Alexander I. Archakov / Tatyana O. Pleshakova

International Journal of Molecular Sciences, Vol 25, Iss 1, p

2023 Volume 409

Abstract: 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 ...

Abstract	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 (10 2 X, 10 4 X, and 10 6 X). 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 ...
Keywords	protein immobilization ; atomic force microscopy ; crosslinker ; mass spectrometry ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	500
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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