Proteomics

The Proteomics section comprises of the proteomics itself and protein chemistry investigations. The protein chemistry, being part of structural biology, studies single proteins, their structure, function, structure-functional relationship, location and other individual characteristics. Proteomics itself investigates proteome which can be characterized as the full set of proteins of a particular cell type being developed on a particular stage. In contrast to the protein chemistry, proteomics belongs to the system biology. However, both disciplines share fundamental methods and techniques the core of which is constituted by mass-spectrometry, chromatography, electrophoresis and protein-protein interaction analysis. Corresponding equipment is listed below as well as devices necessary for associated and auxiliary assays and procedures.

Mass-spectrometry is a powerful tool for determination of m/z value of an ionized particle. Available equipment allows screening and semi quantitative analysis to be carried out, as well as simultaneous detection of several proteins/peptides in a complex mixture, amino acid sequencing of proteins/peptides, analysis of posttranslational modifications, MS-imaging of tissues.

Chromatography provides fractionation of complex mixtures, separation of components, isolation of target components, quantitative analysis, estimation of contaminants in protein mixture and oligonucleotide preparation.

Various proteomics tasks can be carried out using techniques and instrumentation of both proteomics and microscopy units. Protein Interaction Array System (see below), designed on the basis of the surface plasmon resonance technique, allows to perform protein-protein interaction analysis, searching and ranking of antibodies, epitope mapping, identification of protein complexes and other molecules. The confocal microscope equipped with the fluorescence (cross-)correlation spectroscopy can be used to study proteins diffusion rate, their interactions and quantities in living cells.

Electron microscopic single particle analysis on bare-grid plunge frozen samples provides information about 3D structure of single proteins and their complexes in the native hydrated state.

Devices for 1D- & 2D-electrophoresis, preparative PAAG-electrophoresis and isoelectrofocusing, blotting,  immunoblotting, homogenization, concentration, filtration, etc. are available for sample preparation and all kinds of routine procedures.

Some special tasks, such as those requiring X-ray diffraction or nuclear magnetic resonance analyse or ones in need of significant complex computations, could be solved in collaboration with other resource research centers of St. Petersburg State University.

Chromatography

• Waters Breeze 2 High Performance Liquid Chromatograph

High performance liquid chromatography (HPLC) is a fundamental technique for wide range of analytical purposes and preparative purification of target substances. Waters Breeze HPLC system is equipped with quaternary pump for two independent gradients, auto sampler, fractions collector, UV and fluorescent detectors. The system combines user-friendly simplicity and reliability; it is compatible with different types of columns and solvents and provides extensive opportunities for identification, isolation, separation of complex mixture components and quantitative analysis. For more information visit www.waters.com.

• Thermo Scientific Dionex UltiMate 3000 NanoFlow Liquid Chromatograph

The Dionex UltiMate 3000 is a smart and powerful instrumentation for UHPLC solutions, very fast and highly resolving. The system provides the opportunity for two independent gradients (with down to 50 nL/min nanoflow and up to 2.5 mL/min analytical flow rates) allowing full realization of 2D-nano-LC-technology. The instrument is equipped with thermostatic auto sampler for microplates and vials, degasser, photometric detector (190-900 nm), fraction collector and controlling software for chromatography process configuration and data visualization. For more information visit www.dionex.com.

• Bruker Proteineer FC II LC-MALDI Fractions Collector

The Proteineer FC II instrument combines two automated functions – collection of nanoflow or capillary Liquid Chromatography separated peptide/protein fractions and deposition of MALDI samples on MTP format anchor targets or well plates. The option of co-elution of post LC column material with matrix is available. Four anchor targets or well plates are offered for parallel material deposition. For more information visit www.bruker.com.

• Agilent 1260 High-Performance Liquid Chromatograch (HPLC) on board of the Agilent 6538 UHD System

HPLC system Agilent 1260 is a comprehensive portfolio of LC solutions with high productivity levels and data quality. It is equipped with both binary pump SL for LC-analysis (for columns with inner diameter 2.1 mm; 3 mm; 4.6 mm) and HPLC-Chip/MS with nanospray source (nanocolumn and nanospray emitter, integrated into a single polymer chip), multiple wavelength detector, micro collection/spotting system, auto sampler and manual injection system. The system is coupled with ESI-mass-spectrometer Agilent 6538 UHD, consequently there are two functional modes: as an independent HPLC-system and as sample-preparing accessory for MS-analysis. For more information visit www.agilent.com.

Biomolecule Interactions

• Bio-Rad ProteOn XPR36 Protein Interaction Array System

The ProteOn XPR36 device is a protein interaction array system specially designed for comprehensive study of various characteristics of protein interactions, including affinity, specificity, concentration, interaction kinetics, temperature dependant parameters, etc. The device provides the possibility to simultaneously analyze up to 36 different interactions of various biomolecules and compounds in a single run, such as proteins/peptides, nucleic acids, lipids and cell membrane associated molecules, low molecular weight compounds, viruses and bacteria, and even whole cells. For more information visit www.bio-rad.com.

• Scanning confocal microscope with multi-photon excitation Leica TCS SP5 MP

The Leica TCS SP5 MP comprises confocal microscope and multiphoton system and is designed for deep imaging. The microscope is equipped with 6 lasers covering almost all confocal and multiphoton applications. For more information visit www.leica-microsystems.com.

• Fluorescence Lifetime Correlation Spectroscopy System Leica TCS SMD FLCS

Leica TCS SMD FLCS is the complementary device for the confocal microscope providing FLIM (Fluorescence Lifetime Imaging) measurements in the combination with the FCS (Fluorescence Correlation Spectroscopy). The device allows single molecule detection (SMD), fluorescence attenuation with FLIM, fluorescence anisotropy measuring, fluorescence correlation and cross-correlation spectroscopy measuring, etc. For more information visit www.leica-microsystems.com.

Structural Biology of Proteins

• Jeol JEM-1400 Transmission Electron Microscope (with an acceleration voltage of 40-120 кВ)

For specifications visit www.jeol.com.

• Jeol JEM-2100HC Transmission Electron Microscope (with an accelaration voltage of 80-200 кВ)

For specifications visit www.jeol.com.

• Automatic Plunge Freezing with Bare Grid Technique Leica EM GP

Leica EM GP is an automated system for fast plunge freezing of water-containing samples, suspensions and colloidal solutions in the secondary cryogenic medium, such as liquid ethane, on grids designed to work with electron microscopy tasks. For more information visit www.leica-microsystems.com.

Protein allocation in cells and tissues

• Liquid robotics system Tecan GenePaint Evo 150/4

The GenePaint Evo 150/4 is the robotic workstation designed to handle repetitive liquid transfer tasks. The workstation comprises the flexible robotic 4-channel liquid handling tool of variable volume and independent processing. It can be used in different fields of biological investigations and allows to perform immunostaining and in situ hybridization reactions (including fluorescence in situ hybridization), nucleic acid extractions, enzyme-linked immunosorbent assays, serial dilutions, MALDI spottings, etc. For specifications visit www.tecan.com.

• Matrix Deposition Device for MALDI Imaging in Histology Bruker ImagePrep

ImagePrep is a fully automated tissue sample preparation station providing spatial distribution of protein biomarkers on histological tissue samples for MALDI imaging. For specifications visit www.bruker.com.

• Leica Vibratome VT-1200S

Leica VT1200 S is a fully automated vibrating blade microtome predominantly designed for cutting fresh non-fixed soft tissues, and for cutting series sections of fixed specimen as well. For specifications visit www.leicabiosystems.com.

• Leica LMD7000 Laser Microdissection System

Leica LMD laser microdissection system provides laser-based microscopic dissection of regions of interests of biological samples with the precision of single cell from all types of tissues and cell cultures, and subsequent contamination-free collection of the homogeneous ultra-pure sample. For specifications visit www.leica-microsystems.com.

Software support

• BioRad PDQuest 2-D Analysis Software

PDQuest 2-D Analysis Software is designed to perform 2-D gel electrophoretic data analysis. The software includes automated spot detection and auto-matching algorithms allowing to accurately match gels; sophisticated quantitation; visualization and statistical analysis tools; sample classification; spot cutting configurations for high accuracy. For more information visit www.bio-rad.com.

• MASCOT Search Engine

MASCOT software is a huge protein search portal. Possessing protein database, it provides identification, characterisation and quantitation of proteins using mass spectrometry data. For more information visit www.matrixscience.com.

• DNAStar Lasergene 10 Software

Lasergene software is the complex of several applications aimed at the comprehensive analysis of genome, such as DNA, RNA and protein sequence analysis. Using the Lasergene software researchers can construct contigs and scaffolds, form physical maps, analyze mutations and different variations, etc. For more information visit www.dnastar.com.

Electrophoresis and Documentation

• Typhoon FLA 9500 Laser Scanner

Typhoon FLA 9500 is a high resolution laser scanner (pixel is up to 10 µm), providing imaging of multifluorescent-, chemifluorescent-, radioisotope-labeled, and colorimetric samples including polyacrylamide and agarose gels, blot membranes, tissue sections on glass slides, and arrays. The system is well adapted for 2-D DIGE gels analysis: the instrument is equipped with three lasers (473±5nm, 532±5nm and 635±5nm); simultaneous imaging of two DIGE gels is possible; process of recognizing and comparison of tracks/spots could be automated. For more information visit www.gelifesciences.com.

• BioRad GS-800 Calibrated Densitometer

BioRad GS-800 is an automatically calibrated quite simple and effective device for imaging of colorimetric (mainly), chemiluminescent and fluorescent samples (1D- and 2D-gels, slides, blots etc.). Two modes of imaging (transmissive and reflective) are available providing both transparent and opaque samples imaging.In the last case most accurate analysis of superficial molecules on membranes (after different types of blots) is allowed. For more information visit www.bio-rad.com.

• BioRad ChemiDoc MP Imaging System

The ChemiDoc MP is an effective and easy to use instrument for gel/blot documentation. It is equipped with CCD high sensitive detector for high-resolution imaging and Image Lab software for automated image capture and its electronic analysis. The system supports multiple detection methods (chemiluminescence, fluorescence, colorimetry). The instrument possesses trans-UV and epi-white excitation sources the combination of which is available, thus providing opportunities not only for imaging, but for manipulations with visualized gel/membrane as well. You can find more information at www.bio-rad.com.

• BioRad Prep Cell Preparative Electrophoresis System

BioRad Prep Cell uses cylindrical gel for continuous-elution preparative electrophoresis. Fractions, migrating through the gel as ring-shaped bands, are collected from the elution chamber at the bottom of the gel via elution tube by peristaltic pump. Band's substances are drawn to the fractions collector in an elution buffer. Any buffer system (denaturizing or not), gel material (acrylamide of agarose) and percentage can be used for efficient separation and/or purification of proteins, nucleic acids or other biomolecules. For more information visit www. bio-rad.com.

• BioRad Rotofor Isoelectrofocusing System

Biorad Rotofor system is designed for carrying out preparative version of peptide/protein electrophoresis on the basis of isoelectrofocusing, i.e. fractionation of peptide/protein mixtures on their isoelectric points. Focusing occurs in free solution without any denaturation/modification/linkage of components, thus preserving functional activity of target proteins. Focusing chamber is separated into 20 sections, each working as a source for fraction collection by vacuum pump after finishing of the focusing process. It allows obtaining target protein in minimal solution volume with up to 1000-fold enrichment. Big amounts of total protein (from milligrams to grams) could be fractionated by Biorad Rotofor. For more information visit www.bio-rad.com.

• BioRad Trans-Blot Turbo Transfer System

Trans-Blot Turbo Transfer System is a very fast and efficient tool for protein transferring from electrophoretic gel onto cellulose or PVDF membrane. The system has two functioning modes – the turbo run mode (down to 3 min for proteins of 5-150 kDa) and convenient semi-dry protocol. Transfer can be carried out from four mini-gels simultaneously. Simple and convenient interface allows optimizing the preloaded protocols. More information is available at www.bio-rad.com.

• Agilent 2100 Bioanalyzer

Agilent 2100 is a capillar electrophoresis system designed on the basis of the microfluidics platform SDS-PAGE. It allows to perform sizing, quantification and quality control of DNA, RNA, proteins and cells. The device automates processes of gel application on microchips, molecule separation in the direct current field, detection and analysis of the obtained results. For more information visit www.agilent.com.

• BioRad EXQuest Spot Cutter

The EXQuest spot cutter is a robotic instrument facilitating allocation and excision of protein bands or spots from stained in different ways 1-D and 2-D gels or blots. System is easily operated through Quantity One 1-D analysis or PDQuest 2-D analysis software, controlling imaging and cutting processes. Cut out slices are automatically loaded into microplates or tubes for further analysis. More information is available at www.bio-rad.com.

• Electrophoresis Accessories

The full set of electrophoresis accessories, including power suppliers, gel hand-casting systems, electrophoretic & transfer cells and vacuum-blotting devices, are available.

The BioRad PowerPac Universal Power Supply System is compatible with different types of horizontal and vertical electrophoretic chambers. Interface allows easy configuring run conditions in terms of voltage or current; programming of multistep methods is also possible.

The BioRad Mini-PROTEAN Tetra 4-gel cells are designed for vertical 1D-electrophoresis in different buffers, for second dimension run 2D-electrophoresis and for gel to membrane transfer. Four gels or 2 transfers could be run at the same time.

The Millipore Snap i.d. Protein Detection System provides very fast and convenient technnique for western blotting, effective speeding up steps of blocking, washing, and primary & secondary AB-staining. Full staining procedure duration is shortened down to 30 min. The system is fully compatible with conventional blocking buffers and AB-visualization modes.

• Beckman Coulter Optima L-100XP Preparative Ultracentrifuge

BC Optima L-100XP preparative ultracentrifuge is designed for both special and routine tasks of the separation, isolation and sedimentation of different compounds, cells and subcellular fractions applied in various research works in genomics, metabolomics and proteomics. The ultracentrifuge is equipped with three rotors (Type 100 Ti, SW 32 Ti and Type 25 Rotor) for different volume tubes. For more information visit www.beckmancoulter.com.

• Beckman Coulter Avanti J-30I Centrifuge

BC Avanti J-30I is the maximum g-force high-performance fully automatic floor centrifuge. It provides fast separation forces of 100000 x g at speeds up to 30000 rpm for volumes up to 4 liters or 10 microplates per run. The centrifuge allows separation of homogeneous tissues components, isolation of cell membranes on a density gradient, separation and fractioning of cellular organelles, DNA isolation on microplates, protein sedimentation, purification of the culture medium by cell debris sedimentation. For specifications visit www.beckmancoulter.com.

• Beckman Coulter Optima MAX-XP Ultracentrifuge

The Optima MAX-XP is easy-to-use compact tabletop ultracentrifuge providing fast efficient routine and special tasks of separation and sedimentation of different compounds, cells and subcellular fractions. It allows to perform separation of chromosomal, mitochondrial and plasmid DNA, differential separation of subcellular particles, differential flotation lipoprotein centrifugation, multicomponent sample sedimentation, separation of viruses and microsomes, etc. For specifications visit www.beckmancoulter.com.

• Labconco CentriVap Centrifugal Vacuum Concentrator

CentriVap concentrator is a benchtop vacuum concentrator designed to rapidly concentrate biological substances in both water and alcohol solutions in a wide variety of temperatures using the combination of centrifugal force, vacuum and heat techniques. For more information visit www.labconco.com.

• Agilent Cary Eclipse Fluorescence Spectrophotometer

The Cary Eclipse Spectrophotometer, equipped with xenon flash lamp, is a comprehensive instrument for any kind of luminescent spectrometric analysis – fluorescence, chemiluminescence, bioluminiscence. Besides wide range sensitive photomultiplier tube detectors (200-900 nm), list of its advantages includes auto excitation & emission polarizers (for anisotropy measurements), thermostatic changeable cell holders (including one for multi-well plates) and possibility of up to 80 points per second rate measurements for fast kinetic processes analysis. User-friendly software (in an Analysis package) provides fundamental instrument-controlling and analytical functions (alignment, scanning, concentration determination, simple and advanced reads etc.). For further acquaintance visit www.agilent.com.

• Matrix Deposition Device for MALDI Imaging in Histology Bruker ImagePrep

ImagePrep is a fully automated tissue sample preparation station providing spatial distribution of protein biomarkers on histological tissue samples for MALDI imaging. For specifications visit www.bruker.com.