List of scientific equipment of the Center for Collective Use "Proteomic Analysis"

1. Complete system for two-dimensional protein electrophoresis(2008, Bio-rad Laboratories, USA).

Accessories for electrophoresis systems:

• The system for isoelectric focusing of proteins in gel PROTEAN IEF Cell is an electrophoresis unit for separating proteins according to their isoelectric parameters in a gel for strips of various lengths and pH ranges.
• Systems for protein isofocusing Protean II xi 2D Electrophoresis Cell and Mini Protean 2D Electrophoresis Cell are electrophoretic units for separating proteins according to their isoelectric parameters in a gel in glass tubes of various lengths and thicknesses.
• MiniProtean 2D electrophoresis systems 3 Electrophoresis Cell и Protean 2 D xi and XL Cell - small and large vertical electrophoresis chambers for separating proteins by mass.
• MiniProtean 2D electrophoresis systems 3 Dodeca Cell and Protean 2 D xi and XL Multi Cell - small and large vertical electrophoresis chambers for separating proteins by mass, allowing to simultaneously work with the number of gels up to 12 things.
• Devices Model 485 Gradient Former и Model 495 Gradient Former to form a gel density gradient in volumes 40 175 Jr. and 100 1500 Jr, respectively with the peristaltic pump Model EP Econo Pump allows you to make polyacrylamide gels of medium and large sizes with a density gradient.
• Chambers for simultaneously pouring several small gels (MiniProtean 3 Multi Casting Chamber) or big (Protean 3 Multi Gel Casting Chamber) size for vertical electrophoresis.
• Chamber for horizontal electrophoresis (SE-2).
• PowerPack power supplies of various capacities to support the system for isoelectrofocusing of proteins in gel and electrophoretic separation of proteins by mass in gels of small and large sizes, destayner, and electroelution.
• Dodeca Stainer Staining and Gel Wash Systems Model 556 Gel Destainer, allowing you to work simultaneously with 12 gels.
• MicroRotofor Cell device for preparative isoelectric focusing of proteins by pi in a solution of small volumes (2,5 Jr).
• VersaDoc Model Image Registration Instrument 4000, allowing image detection in ultraviolet and white light using standard 520LP filters, 530DF70, 610LP. The instrument is equipped with a highly sensitive 3,2 megapixel CCD camera.
• EXQuest Spot Cutter for cutting bands and dots from fluorescent or colorimetric stained single- and 2D gels or blots for further analysis. It is possible to visualize up to 4 gels simultaneously and cut up 600 points per hour.
• Quantity One software can be used to analyze data from 1D and 2D images 1 D Analysis Software PDQuest Advanced 2D Analysis Software.
• Water purification system DIRECT-Q5, Millipore is a high performance dual water system (Type III - pure water and Type I - ultrapure water). Water type 3 needed to power laboratory equipment, rinsing laboratory glassware, preparation of non-critical solutions, supply systems for obtaining water type 1. Application of water type 1: all critical laboratory tasks, instrumental methods of analysis: high performance liquid chromatography with mass spectrometric detector, capillary electrophoresis, preparation of blank samples and standard buffer solutions for spectroscopy, spectrophotometry or other analytical methods, as well as cell and molecular biology, two-dimensional electrophoresis, toxicological studies, etc..

2. maXis Impact High-Performance Quad-To-Flight Combined Mass Spectrometer(2013, Bruker Daltonik GmbH, Germany) – mass spectrometric unit with ultra-high resolution electrospray ionization with liquid chromatography system (TermoScientific Dionex UltiMate 3000 Series) for proteomics research maXis Impact includes Appolo II electrospray ionization source, high precision hyperbolic quadrupole, collision cell for impact dissociation of ions, time-of-flight analyzer with temperature compensation system, electronic systems, syringe pump, software package Compass version 1.4 to control the mass spectrometer and HPLC system, registration and data processing; hybrid nitrogen analyzer NM32LA, proteomics software package Biotools 3.2 SR3, server MASCOT, ProteinScape proteomics software package 3.0, CaptiveSpray ion source, ultra-high pressure binary gradient pump with ternary loading pump and integrated column thermostat, temperature controlled autosampler, Chromeleon CHM-2 software. Allows: detect and identify both known compounds and their metabolites, and unknown compounds in a wide range of masses from 20 to 40 000 Yes (medications, drugs, pesticides, etc.), used to quantify compounds, research of metabolic processes, asked for a biomarker (early diagnosis of diseases), clinical proteomics, top-down proteomics, whole protein analysis, etc..

3. V3 Western Workflow System for Blotting and Visualizing Mini Gels (2014, Bio Rad Laboratories, USA) is a simple five-step system for optimizing all steps of Western blotting: from protein separation to quantitative analysis, including using paintless technology. Allows for highly sensitive gel- and blot chemiluminescence, 2-D protein gel electrophoresis, including DIGE and other multicolor differential electrophoretic methods; 1-D electrophoresis of proteins and nucleic acids; western-, northern- and Southern blot; quantum dot visualization; multiplex gel- and blot visualization. Available detection methods: fluorescence, chemiluminescence, gel documentation, colorimetry (densitometry).

4. Optical analysis module based on confocal scanning Typhoon FLA 9500 Imager scanner (2014, GE Healthcare, Switzerland) — high-precision laser scanner for autoradiographic, fluorescent and chemiluminescent analysis of gels, blots for a wide range of tasks, including, related to molecular biological analysis. Allows detection and analysis of biomolecule samples, labeled with isotopes and fluorescent dyes, in microarray format, microplate, 1-D and 2-D gels, DIKES, chemifluorescent signal, with computer control and the possibility of further processing of the received data.

5. Module for high-performance multi-parameter analysis of biosamples lnCell Analyzer 2200 System (2014, GE Healthcare, Great Britain) — an automated system for high-speed multi-parametric screening of live cell cultures in real time to perform such work as: study of cell viability and proliferation; study of cytotoxicity of chemicals and other agents on cell cultures, including assessment of apoptosis and cell death; real-time cell detection: cell adhesion and migration analysis; statistical analysis of the localization and distribution of fluorescently labeled proteins on living cells and on fixed preparations.

6. Software and hardware complex for laser microdissection of biological objects with the possibility of contamination-free extraction of parts for subsequent biochemical analysis or reclamation based on AXIO OBSERVER Palm MicroBeam (2013, Carl Zeiss, Germany) – laser dissector, allowing to cut with high precision fragments from a fixed, frozen tissue, including various structures, individual cells and even subcellular structures (organelles, chromosomes, etc.). All these structures are determined by traditional microscopic methods.: bright field, dark field, polarized light illumination, phase contrast and fluorescence. Besides, this method is also used for living cells, for example, for the isolation of clones and cells of a certain type with subsequent cultivation, as well as to study the interaction of cells in culture.

7. Set of equipment for high performance liquid chromatography based on liquid chromatograph LC-30 NEXERA (2014, Shimadzu, Japan) — provides the possibility of gradient chromatography and spectrophotometric (UV/Vis), fluorescent and electrochemical detection. These types of chromatography are widely used in the quantitative analysis of the content of various components in biological samples., in particular, when studying the biological effects of chemical compounds and conducting pharmacokinetic evaluations of new potential drugs.

8. MiSeq Illumina Genetic Sequencer(2019, Illumina Inc., USA) - desktop integrated tool for NGS, including blocks for sample preparation in one instrument (cluster formation), sequencing and data processing and management interface. Sequencing principle based on Solexa technologies, including enrichment by bridge-PCR on a flow chip, sequencing by the synthesis method (SBS) using fluorescently labeled nucleotides and detection of fluorescence light from DNA clusters. Used in basic scientific research (genomic analysis of human and animal diseases, stem cell research, epigenomic and metagenomic studies, ancient DNA research, etc.), in clinical and forensic medicine, epidemiology. Main Applications: amplicon library resequencing; checking the results of cloning and genetic modification; multiplex high-throughput sequencing of small genomes (for example, microorganisms); targeted high-throughput genome sequencing for the analysis of genetically associated diseases; search for mutations; HLA typing; small RNA sequencing; epigenetic studies, methylation profile analysis; targeted resequencing and de novo sequencing, etc.. d. Characteristics: launch duration, hours - 4-55; maximum performance, GB - 15; number of reads per run, million - 1-25; maximum reading length - 2 × 300 bp.

9. Sequencer according to Senger SeqStudio (2019, Thermo Fisher Scientific, USA) — tocapillary analyzer SeqStudio for Sanger sequencing and fragment analysis. Characteristics: the number of capillaries in the block - 4; capillary length, cm - 28; format - 96-well plates or 8-well strips; internal storage for storage 14000 reaction results; standard read lengths from 40bp - 800bp; performance up to 192 samples per day; number of detected targets — 6; two types of cartridges: 125 injections (500 samples) and 250 injections (1000 samples); universal polymer (POP-1) for sequencing and fragment analysis; does not require spectral calibration when using Applied Biosystems kits; SeqStudio Data Collection Management Firmware.
Peculiarities: universal - a single format of consumables (universal cartridge) and for sequencing, and fragment analysis; a wide range of tasks - the entire range of applications of capillary electrophoresis; computer and software built into the device; primary data analysis is carried out in real time.
Software: Sequencing Analysis Software - Analysis, editing and interpretation of primary sequencing results; SeqScape Software - Mutation Detection and Analysis, SNP study and validation, pathogen typing, allele identification and sequence confirmation based on library data, resequencing; Variant Reporter - Mutation Detection and Analysis, SNP discovery and evaluation and sequence confirmation; GeneMapper Software - for all major fragment analysis applications (genotyping, allele discrimination, analysis of single nucleotide polymorphisms); Minor Variant Finder(minor mutation detection (SNP); MicroSEQ ID - Microorganism Sequencing and Identification.

10. Thermal cycler for nucleic acid amplification CFX96 Touch (2014, Bio-rad Laboratories, USA) — a high-speed PCR instrument with the ability to register reaction products in real time. Tasks to be solved: real time PCR (to 5 dyes in one tube); PCR with endpoint analysis; PCR without analysis of results; melt curve analysis, including HRM; FRET analysis; selection of the optimal temperature for PCR. The device is compatible with ready-made test systems from various manufacturers, and the possibility of using different dyes makes it easy to adapt the device for numerous applications; CFX Manager software allows gene expression analysis and quantification of the genetic material of multiple infectious agents in dozens of samples; Precision Melt Analysis software enables genotyping of samples based on high-resolution analysis of nucleic acid melt curves. The device has a registration certificate of the Ministry of Health of the Russian Federation.

11. Analyzer automatic for real-time PCR analysis LightCycler® 96 Instrument (2014, Roche Diagnostics GmbH, Switzerland) - high performance device, allowing for various types of real-time PCR analysis, including qualitative and quantitative determination of nucleic acids, genotyping, gene expression analysis, HRM analysis. Innovative optical system, as well as the design of the LightCycler thermoblock 96, guarantee the accuracy of the experiment, temperature homogeneity and reproducibility of results.

12. QuantStudio real-time PCR system 5 (2019, Thermo Fisher Scientific, USA, 2 PCS.) — DNA amplifier, designed for polymerase chain reaction (PCR) with detection of amplification results in real time. PCR in "real time" (or quantitative PCR, kPCR, qPCR) allows amplification of a specific DNA fragment and detection of the accumulation of PCR products directly during amplification. In qPCR, the amount of DNA is measured after each cycle using fluorescent dyes., which increase the fluorescent signal in direct proportion to the amount of PCR products obtained (amplicons). qPCR is used in a wide range of applications: gene expression analysis, SNP genotyping, gene copy analysis, pathogen detection, analysis of protein complexes based on thermal denaturation, miRNA profiling, etc.. The use of qPCR makes it possible to detect a 2-fold difference in DNA copies.
Key features of QuantStudio 5: thermoblock format — 96×0.1 / ×0.2 ml; the volume of the reaction mixture is 10-30 / 10-100µl or 5-20µl; excitation source - white LED (LED); optical detector — 6 independent filters; excitation / detection wavelength - 450-680nm / 500-730nm;• multiplex - up to 6 targets; temperature gradient: 6 зон VeriFlex; d Temperature homogeneity over the block — ± 0,4 °C; temperature maintenance accuracy — ± 0,25 °C; maximum heating rate / block cooling — 9 °C/s / 6,5 °C/s; average heating rate / block cooling — 3,66 °C/s; temperature range — 4–99.9 °C.

13. Real time PCR cycler CFX96 (2020, Bio-rad Laboratories, USA) — a high-speed PCR instrument with the ability to register reaction products in real time. Tasks to be solved: real time PCR (to 6 dyes in one tube); PCR with endpoint analysis; PCR without analysis of results; melt curve analysis; selection of the optimal temperature for PCR. The device is compatible with ready-made test systems from various manufacturers, and the possibility of using different dyes makes it easy to adapt the device for numerous applications; CFX Manager software allows gene expression analysis and quantification of the genetic material of multiple infectious agents in dozens of samples; Precision Melt Analysis software enables genotyping of samples based on high-resolution analysis of nucleic acid melt curves. Characteristic: number and format of tubes low-profile strips and plates on 96 holes; volume of the reaction mixture 1-50 mcl; maximum temperature change rate 5 ˚C/sec, temperature maintenance accuracy +/-0.2˚С; gradient heating (1-24 ºС); the number of simultaneously detected targets in the sample is 5; number of channels - 6; memory over 1 000 typical programs on board, not limited to USB-flash; temperature control calculated, on the block - the cover is heated up to 105°С, mechanized; reaction error reports, system errors; excitation 6 LEDs (450-684 nm); detection 6 photodiodes (515-730 nm); fluorescence excitation/detection range 450-730 nm; dynamic range 10 orders of magnitude. The device has a registration certificate of the Ministry of Health of the Russian Federation.

14. QX200 AutoDG Droplet Digital PCR System for Quantitative Nucleic Acid Amplification(2016, Bio-rad Laboratories, USA) — digital drop PCR system with automatic sample preparation and analysis of results in the QuantaSoft program. Digital drip PCR is the third generation of PCR technology. Unlike real-time PCR, well-known quantitative relative method, digital PCR is absolute, less sensitive to inhibitors, measurement method. The ddPCR system determines the absolute number of nucleic acid molecules, encapsulated in discrete drops of water-oil emulsion by volumetric method. The concentration of target DNA is determined in the original sample as the number of copies per microliter with sensitivity up to 1 molecules. The method has a high reproducibility of results in a wide range of concentrations. This equipment is necessary for high-precision analysis of gene expression (accuracy ±10%;); detection of changes in the number of somatic copies of a gene (determination of CNV with ratio accuracy 1.2x), what is the hallmark of many types of cancer; high-precision detection of rare mutations (detection sensitivity 0,001% mutants), allowing for more sensitive and less invasive diagnostics; detecting the presence of tumor cells at a very low titer; study of clonal heterogeneity in cell populations by the level of expression of target genes; study of gene expression variability at the level of single cells; performing miRNA analysis with higher accuracy and sensitivity compared to RT-PCR; high-precision study of the epigenome, in particular, the nature of target gene methylation and chromatin modification at the level of single cells; pathogen detections, determination and monitoring of viral load; use in the field of Next generation sequencing (library preparation and quantification for high throughput sequencing). 

15. ULT Freezer Upright Freezer (2019, Thermo Fisher Scientific, USA) - Upright Freezer for storing biological samples down to -86°C. Used for long-term storage of nucleic acid samples, fabrics, cells, blood plasma, vaccine. Characteristics: 288 l, 2 external, 4 internal doors, 4 shelves, temperature range from -50 ° C to -86 ° C., CE conformity certificate.