2D Protein Gel Image Capture and Analysis

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1 2D Protein Gel Image Capture and Analysis the way you want it S Y N G E N E A DIVISION OF THE SYNOPTICS GROUP

2D protein gel generation, image capture and analysis systems Syngene has a worldwide reputation for producing high quality imaging and analysis systems for proteomics.

2 2D protein gel generation, image capture and analysis systems Syngene has a worldwide reputation for producing high quality imaging and analysis systems for proteomics. Syngene can offer you a selection of products to cover your 2D gel needs: 2D gel electrophoresis tank systems for 1st and 2nd dimensions A scanning system to capture high resolution 2D gel images An advanced 2D gel imaging system for capturing all visible and fluorescent 2D gel images Impressive 2D gel analysis software for the analysis of post-electrophoretically stained gels and for multiplexed gels using pre-electrophoretic dyes Syngene s solutions for protein gel applications Dye requirement Electrophoresis system Image capture systems Image analysis software Post-electrophoretic IEF-SYS Dyversity and Dymension 1, visible dyes - Silver, ProteomeScan 2 and 3 Coomassie Blue Post-electrophoretic IEF-SYS Dyversity Dymension 1, fluorescent dyes 2 and 3 Sypro Ruby, Deep Purple, Pro-Q Diamond, Flamingo Pre-electrophoretic Dyversity Dymension 3 fluorescent dyes with enhanced Cy2, Cy3, Cy5 lighting module

Generating, capturing and analysing 2D protein gels Generation

levels of reproducibility using gel tanks from the Syngene range.

3 Generating, capturing and analysing 2D protein gels Generation Image capture Image analysis Produce quality 2D gels with high levels of reproducibility using gel tanks from the Syngene range. Use Dyversity to capture visible and fluorescent protein gels or ProteomeScan for just visible gels. Dymension is a premium software capable of analysing all 2D gel images quickly and accurately.

4 Over 50,000 scientists world-wide in pharmaceutical and biotech companies, as well as academic and government institutions, have chosen Syngene as their expert imaging partner.

5 Dymension is a very sensitive package. This will benefit the user in terms of lower cost and faster analysis time

D M E N S I O N 2D image analysis software The purpose of a typical 2D gel based proteomics experiment is to look for changes in protein expression as a result of changing a sample condition.

The number of different proteins expressed can be thousands and the differences in protein abundance during expression can cover many orders of magnitude.

6 D M E N S I O N 2D image analysis software The purpose of a typical 2D gel based proteomics experiment is to look for changes in protein expression as a result of changing a sample condition. Protein spots may be lost or gained, up or down regulated or moved due to a post-translational modification. The number of different proteins expressed can be thousands and the differences in protein abundance during expression can cover many orders of magnitude. Clearly software that is easy to use, fast and very accurate is essential. Dymension is revolutionary software that can analyse a typical 2D gel image rapidly. It features novel algorithms for background subtraction, noise filtering, precise warping, rapid matching, spot detection and reduced image editing time. Using its powerful spot detection algorithm, Dymension instantly locates and analyses protein spots. With Dymension, the entire analysis process from background correction to spot matching results and reporting takes minutes, making this the fastest 2D gel analysis package currently available. Dynamically linked image panes, tables and charts Matched spots are blue and non-matched spots are cyan coloured Dymension is available in three versions, and upgrading between the packages is simple: Dymension 1 is a basic level software for the analysis of post-electrophoretically stained gels where the protein spots are compared between samples containing one replicate gel only. Dymension 2 is for the analysis of post-electrophoretically stained gels where the protein spots are compared between samples containing any number of replicate gels. Dymension 3 is for the analysis of post-electrophoretically stained gels where the protein spots are compared between samples containing any number of replicate gels, as well as analysing pre-electrophoretically stained gels, (e.g. Cy dyes).

It offers a range of automatic image correction features and methods for resolving and analysing spots on single

7 D M E N S I O N 1 Dymension 1 is ideal for users looking for software to analyse spots between samples containing one replicate gel only. It offers a range of automatic image correction features and methods for resolving and analysing spots on single gels. The software can be easily upgraded to Dymension 2 or 3 if the proteomic needs of the laboratory change. Interactive process flow panel Warped and non-warped images for assessment of spot differences

The software offers background correction and noise filtering features including a SYPRO Ruby filter.

8 D M E N S I O N 2 Dymension 2 is suitable for the analysis of post-electrophoretically stained gels. It has all the features of Dymension 1 but with the added ability to detect and compare protein spots between samples containing multiple gel replicates. The software offers background correction and noise filtering features including a SYPRO Ruby filter. This will detect and automatically remove spots caused by SYPRO Ruby crystals adhering to the gel, thus saving users valuable time. This is suitable for users that need to determine the amount of protein present before and after drug or protein induction treatments. Matched spot plot to assess replicate quality The software automatically detects and assigns statistical confidence to each and every difference in normalised spot volume, thus accurately highlighting proteins of specific interest. Spot assignment following mass spectrometry with molecular weight and pi calibration The results of the analysis are displayed as a dynamically linked table, 3D spot profile, bar chart, scatter and correlation plot, which makes it easy to compare many expression profiles simultaneously and therefore accurately select proteins suitable for further analysis. Independent 2D and 3D renderings in all image panes

D M E N S I O N 3 Dymension 3 is suitable for the analysis of post-electrophoretically stained gels, as well as

It has all the functionality of Dymension 2, so can be used to analyse samples containing multiple gel replicates,

contrasting fluorescent labels for example, Cy2, Cy3 and Cy5.

9 D M E N S I O N 3 Dymension 3 is suitable for the analysis of post-electrophoretically stained gels, as well as pre-electrophoretically stained gels. It has all the functionality of Dymension 2, so can be used to analyse samples containing multiple gel replicates, but with the additional capability to analyse multiplexed fluorescent gel images stained with up to three contrasting fluorescent labels for example, Cy2, Cy3 and Cy5. User selected spots for presentation Correlation plot to assess system variation This software allows users to analyse multiple sets of any type of 2D protein gel, regardless of how it was stained. Accurate spot detection with table and bar chart display

10 D M E N S I O N Dymension Features Benefits Icon driven user interface Accepts data from a TWAIN source Experiment set up wizard Process flow chart Automatic background correction and noise filtering Automatic and precise sample warping Revolutionary spot detection algorithms User definable spot detection parameters Spot editing and filtering functions Automatic spot normalisation View results in a dynamically linked table, 3D spot profile, bar chart, scatter and correlation plot Transfers results to Word or Excel Exports coordinates to automated spot pickers Automatic filtering of Sypro Ruby crystals Optional Gaussian spot fitting Automatic and precise replicate warping Automatic matching of samples containing unlimited number of replicates Internet links to federated databases Dyversity compatible Analysis of multiplexed and non-multiplexed gels Simple software set-up and use Versatile as accepts gel images generated by most commercial scanners Fast, comprehensive analysis Easy guide for user from image loading to obtaining results Saves time with spot editing Faster spot matching Rapid spot detection and splitting Flexible as allows user adjustments Control of spot editing and filtering parameters Improves accuracy of results Easy to compare many expression profiles simultaneously and quickly select proteins of interest Simple production of professional reports Fast and precise interface between Dymension and spot pickers Saves time with spot editing Choice of spot detection models Faster spot matching as the replicate images are properly aligned Improves accuracy by reducing manual editing time Quick presentation of protein sequence and structure Direct analysis of GLP secure images using the Dyversity unique capture system Cost effective as one software will analyse all types of 2D gel stains (e.g. Cy2, Cy3, Cy5)

11 In my experience it is unusual to find reliable and dependable equipment with such great support

Gel staining and image capture With 2D gel electrophoresis, spots can be stained post-electrophoretically using a stain that is visible to the naked eye under white light (Silver or

Alternatively, a dye that is fluorescent when illuminated by light of a specific wavelength (for example Sypro Ruby, Deep Purple, Pro-Q Diamond, Flamingo) can be used.

High dynamic range and excellent resolution are required for an imaging system if spots of different abundance and morphology are to be compared and precisely detected.

12 Gel staining and image capture With 2D gel electrophoresis, spots can be stained post-electrophoretically using a stain that is visible to the naked eye under white light (Silver or Coomassie Blue). Alternatively, a dye that is fluorescent when illuminated by light of a specific wavelength (for example Sypro Ruby, Deep Purple, Pro-Q Diamond, Flamingo) can be used. Proteins can also be labelled prior to electrophoresis using Cy dyes. In all cases the 2D gel is captured as a digital file using either a scanner or a CCD camera based system. High dynamic range and excellent resolution are required for an imaging system if spots of different abundance and morphology are to be compared and precisely detected. Protein Dye Mode Advantages Silver White light High sensitivity (0.5-1ng protein) Coomassie Blue White light Quick, easy, inexpensive, good sensitivity (30-50ng protein) Sypro Ruby, Deep Purple, UV or Fluorescence High sensitivity (1-2ng protein), large dynamic range Pro-Q Diamond, Flamingo Cy2, Cy3, Cy5 Fluorescence High sensitivity (1ng for minimal and 0.1ng for saturation dyes)

13 D Y V E R S I T Y High performance 2D gel imaging system The Dyversity high performance imaging system is designed to capture 2D gel images from fluorescent and visible stained gels. At the heart of Dyversity is a choice of 16 bit, cooled, mega-pixel cameras that excel at resolving the high density and large dynamic range of proteins found on a typical 2D gel. The instrument has a unique darkroom enabling excellent access to the chamber for gel manipulation and image preview. This darkroom is fully computer controlled with all lighting and camera settings accessed using the novel GeneSnap image acquisition software provided with the system. Dyversity can capture images across a range of sizes. The system uses lighting modules to illuminate or excite most common 2D gel protein stains; these include Coomassie Blue, Silver, Sypro Ruby, Pro-Q Diamond, Pro-Q Emerald, Deep Purple, Flamingo and Cy dyes. Since it has an array of lighting options, Dyversity can also be used for other sample formats such as DNA and 1D protein gels, membranes, spot-blots, TLC plates, colony plates and microtitre plates. This is achieved by using fluorescence, absorbance and reflectance excitation modes and the appropriate emission filter in the 9-position motorised filter wheel. Dyversity is also suitable for chemiluminescence applications. Dyversity uses a very high resolution camera which enables a single shot of the gel to be captured. There is no need to capture multiple images of the same gel, which would require stitching. This eliminates potential inherent defects as a result of the stitching process. With Dyversity you simply get a high quality image every time resulting in superior accuracy and reliable measurements for all 2D gels. Faster imaging times can be achieved compared to conventional laser scanning and scanning camera systems.

D Y V E R S I T Y Features Ultra high speed image capture Mega pixel resolution using the latest 16 bit

capture images of practically any type of application Multiplexed image capture using Syngene s three

rates Enables a single shot image with no stitching Capture image with low abundance proteins Complete

14 D Y V E R S I T Y Features Ultra high speed image capture Mega pixel resolution using the latest 16 bit cooled CCD technology High sensitivity enabling detection to sub-nanogram levels of protein Dyversity can capture images of practically any type of application Multiplexed image capture using Syngene s three colour lighting module featuring advanced illumination Benefits Rapid image capture improves throughput rates Enables a single shot image with no stitching Capture image with low abundance proteins Complete laboratory workstation Capture images from all typical protein gels including those using Cy dyes with no emission crosstalk

D Y V E R S I T Y Unique to Dyversity is the optional advanced illumination system used to capture images of pre-electrophoretically stained gels.

The illumination module gives excellent spectral separation producing no crosstalk between the dyes. Using this module, pre-electrophoretically stained 2D gels up to 28cm x 21cm can be captured.

15 D Y V E R S I T Y Unique to Dyversity is the optional advanced illumination system used to capture images of pre-electrophoretically stained gels. With its specialised design, the module uses edge illumination to excite proteins stained with Cy2 TM, Cy3 TM or Cy5 TM dyes. The illumination module gives excellent spectral separation producing no crosstalk between the dyes. Using this module, pre-electrophoretically stained 2D gels up to 28cm x 21cm can be captured. A typical Cy dye gel set, (a gel using Cy2, Cy3 and Cy5), can be captured by Dyversity with 90 micron resolution in under 8 minutes. In comparison, a fast laser based system at 100 microns resolution will take around 42 minutes to scan the same gel set. Edge illumination of a typical protein gel using Cy dyes (Cy2, Cy3, Cy5) Cy dye characteristics EXCITATION EMISSION LUMINESCENCE WAVELENGTH Cy2 Cy3 Cy5

D Y V E R S I T Y Dropdown menus for selection of excitation source and emission filters Image capture panel Brightness and contrast optimisation System specification Darkroom Cameras Lens Sample

16 D Y V E R S I T Y Dropdown menus for selection of excitation source and emission filters Image capture panel Brightness and contrast optimisation System specification Darkroom Cameras Lens Sample tray Filter mechanism Application options: Sypro Ruby Deep Purple Pro-Q Diamond Flamingo Coomassie Silver Cy dyes Pro-Q Emerald Illumination options Choose from the list in the table Software Computer option Printer option Power input G:BOX extended configuration Light tight with enclosed camera and lens DYVERSITY 6 CCD camera 6m pixels (3072 x 2048) 16 bit 0-65,535 black/white level Deep and low cooling F1.4 manual lens Motor driven adjustable sample tray 9 position motor driven filter wheel DYVERSITY 4 CCD camera 4m pixels (2048 x 2048) 16 bit 0-65,535 black/white level Deep cooling Edge illumination Cy2 with Cy3 filter or use UV Transilluminator with UV filter Edge illumination Cy3 with Cy3 filter or use UV Transilluminator with UV filter Edge illumination Cy3 with Cy3 filter or use UV Transilluminator with UV filter Edge illumination Cy2 with Cy3 filter or use UV Transilluminator with Short Pass filter Use visible light with ND filter Use visible light with ND filter Edge illumination Cy2, Cy3, Cy5 with Cy2, Cy3, Cy5 filters UV Transilluminator with short pass filter UV Transilluminator 20cm x 20cm UV Transilluminator 25cm x 30cm Visible light NovaGlo Epi white light Epi UV Edge Cy dye lighting module large (illumination table up to 28cm x 21cm sample size) Edge Cy dye lighting module standard (illumination table up to 15cm x 16cm sample size) GeneSnap image acquisition only Check latest specifications before ordering Digital thermal black and white 256 black/white levels Print speed under 4 seconds V

P R O T E O M E S C A N Scanner imaging system The ProteomeScan scanner is designed for those users imaging 2D gels that have been stained with visible dyes such as Silver and Coomassie Blue.

It is supplied with icon driven software and can generate, in seconds, high quality 2D gel images that can be automatically transferred into Dymension analysis software.

17 P R O T E O M E S C A N Scanner imaging system The ProteomeScan scanner is designed for those users imaging 2D gels that have been stained with visible dyes such as Silver and Coomassie Blue. The scanner has been optimised for use with wet gels as it is sealed and has a special filter fitted. It is supplied with icon driven software and can generate, in seconds, high quality 2D gel images that can be automatically transferred into Dymension analysis software. With ProteomeScan, users can switch between transmittance and reflectance modes and can select image quality. The system can generate images of up to 12,800 x 12,800 dpi resolution to ensure detection of the smallest protein spots. The product is available in two versions; the A4 Pro or the A3 Pro for imaging gels up to 21cm x 29cm and to 31cm x 43cm, respectively. Features User-friendly icon driven software User controlled resolution, compression and scan speed Transmittance and reflectance mode Variable colour scanning Fully sealed unit Direct image transfer into Dymension software Benefits Saves time with system set up and use Versatile - choice of high quality or rapid image generation Flexible imaging applications Accurate detection of all visible coloured proteomic dyes Safe as protected against leaks of hazardous liquids from gels Fast workflow

P R O T E O M E S C A N Captured image and image manipulation Image capture settings System specification ProteomeScan A4

reflectance Transmittance and reflectance Maximum gel size 216mm x 297mm 310mm x 437mm Optical resolution 1600 x 3200 dpi

16 bit grey levels, 24 bit colour Scan optical density range 3.6 OD 3.8 OD Scan speed 9.2ms/line (colour) 5.

18 P R O T E O M E S C A N Captured image and image manipulation Image capture settings System specification ProteomeScan A4 Pro ProteomeScan A3 Pro System High quality 2D image scanner High quality 2D image scanner Modes Transmittance and reflectance Transmittance and reflectance Maximum gel size 216mm x 297mm 310mm x 437mm Optical resolution 1600 x 3200 dpi 2400 x 4800 dpi Interpolated resolution x dpi x dpi Resolution 16 bit grey levels, 48 bit colour 16 bit grey levels, 24 bit colour Scan optical density range 3.6 OD 3.8 OD Scan speed 9.2ms/line (colour) 5.3ms/line greyscale 2400 dpi 16ms/line colour 2400 dpi Interface Fast SCSI, USB IEEE 1394 firewire, high speed USB2 Power input V V

19 We chose Syngene because of their innovative products

2 D G E L T A N K IEF-SYS high resolution 2D gel electrophoresis system The IEF-SYS is a robust, acrylic horizontal gel tank designed for running both immobilised ph gradient (IPG) strips and

20 2 D G E L T A N K IEF-SYS high resolution 2D gel electrophoresis system The IEF-SYS is a robust, acrylic horizontal gel tank designed for running both immobilised ph gradient (IPG) strips and pre-cast acrylamide gels on two separate frames supplied with the system. This enables both dimensions of the 2D gel electrophoresis process to be achieved within the same tank. IPG strips, which are widely acknowledged as the best method of resolving proteins by their isoelectric point, are laid on the hollow frame of the IEF-SYS system [capillary gels can also be run]. The position of positive and negative electrodes on the hollow frame can be adjusted depending on the length of the IPG strips and to ensure optimum contact with their edges, making it easy to control the voltage gradient across the strip. A ceramic cooling block filled with Hexid, the best super cooling fluid currently available, is placed under the hollow frame, allowing users to run high voltage through the IPG strips. Precisely focused protein spots with every sample. Following first dimension electrophoresis, the IPG strip is positioned against a pre-cast acrylamide horizontal gel placed on the glass bottomed electrode frame of the IEF-SYS system to run the second dimension molecular weight separation. Perfect 2D gel separation results can be obtained using just one tank before the gel is stained to show the protein spots. Features Top frame options with variable electrode spacing systems Two sets of electrodes supplied Large cooled ceramic top plate Buffer drainage ports Benefits Hollow frame for IEF, where the strips are placed directly onto the ceramic plate, and glass bottomed frame for pre-cast horizontal gels Detachable and tank mounted electrodes for ease of use Provides uniform cooling of the gel platform The built-in shut-off valve is opened when the drainage tube is connected to empty the buffer chamber

2 D G E L T A N K System specification for IEF-SYS Gel tank Frames Ceramic cooling block Electrodes Depth Buffer volume Horizontal acrylic tank with built-in buffer drainage ports

wick gels Detachable set for running IPG strips or acrylamide gels 430mm (tanks and cooling connectors) 340mm (tank only) 275ml Power input 100-240V Dimensions 460mm x 115mm The

21 2 D G E L T A N K System specification for IEF-SYS Gel tank Frames Ceramic cooling block Electrodes Depth Buffer volume Horizontal acrylic tank with built-in buffer drainage ports Hollow frame for IPG strips Glass bottomed frame for precast acrylamide gels 27cm x 27cm sealed block with integral cooling coil and auto shut-off valves Tank mounted set for running wick gels Detachable set for running IPG strips or acrylamide gels 430mm (tanks and cooling connectors) 340mm (tank only) 275ml Power input V Dimensions 460mm x 115mm The IEF-SYS has a safely lid with integral power leads and shrouded power connectors with long life platinum electrodes and gold plated terminals to resist corrosion and is fully CE compliant.

22 Syngene s service is exceptional - whenever we call with a question we get immediate response

23 Syngene Europe and International Headquarters: Beacon House Nuffield Road Cambridge CB4 1TF UK Tel: +44 (0) Fax: +44 (0) Syngene USA Headquarters: 5108 Pegasus Court Suite M Frederick MD USA Tel: / Fax: ussales@syngene.com Website: A.0044.B All trademarks acknowledged

Gel imaging at a touch S Y N G E N E A DIVISION OF THE SYNOPTICS GROUP

Gel imaging at a touch S Y N G E N E A DIVISION OF THE SYNOPTICS GROUP Use the large colour touch screen to navigate your way through the functions of. The icon driven menu is both intuitive and easily