Bio-rad EXQuest Spot Cutter User Manual

EXQuest™Spot Cutter Instruction ManualCatalog numbers165-7200 EXQuest Spot Cutter 165-7201 EXQuest Spot Cutter With Computer On the Web at http://ww

•Gel Tip Wash Station. The gel tip wash station is located on the left end of the wash station block. Itconsists of a gel tip wash port, a waste basin

Figure 1-8. Supported microplate formats.The microplate rack accommodates plates from a variety of vendors that include Corning, Whatman,Greiner, AxyG

1.2.9 Sensors The spot cutter includes a series of sensors to protect the operator and ensure the proper operation of theinstrument.•Front Door Sensor

1.2.11 Software The EXQuest spot cutter is controlled through Bio-Rad Discovery Series™software PDQuest (7.4.0 orgreater) and Quantity One (4.6 or gre

2.0 SYSTEM INSTALLATIONBefore the EXQuest™spot cutter can be used, the software must be installed and the instrument set up andcalibrated. At the time

CautionThe EXQuest spot cutter must be lifted, by two or more individuals, from its shipping pallet using theremovable lifting handles attached to the

SYSTEM INSTALLATION2-32.3 SYSTEM LEVELING To level the EXQuest spot cutter:1. Place the spot cutter on a lab bench that is sturdy and level.2. Loosen

SYSTEM INSTALLATION2-42.5 MICROPLATE RACK INSTALLATIONThe microplate rack is installed to the left of the gel tray as follows:1. Locate the two micro

Figure 2-5. Installed microplate rack.2.6 CABLE SETUPBefore the spot cutter can be started, the power cord and USB cable must be connected.1. Connect

SYSTEM INSTALLATION2-6Figure 2-6. Spot cutter USB ports and power entry module.2.7 CUTTING HEAD INSTALLATIONThere are two types of cutting heads avai

TABLE OF CONTENTSTABLE OF CONTENTSSAFETYSECTION 1 INTRODUCTION ...

2-7SYSTEM INSTALLATIONTo install or change the gel cutting head1. Open the front door by lifting it all the way up and then lowering it until it latch

SYSTEM INSTALLATION2-85. Insert three clean 1.5 ml capless tubes into the membrane tip wash port slots, located on the washstation’s right side. Fill

SYSTEM INSTALLATION2-97. Read and accept the License Agreement.8. Click Next on the Read Me Screen.9. Enter your Full Name and Organization and then c

3.0 EXQUEST CALIBRATION WIZARDBefore you can use the spot cutter for the first time, you must calibrate it. The calibration wizard helps you toquickly

4. Click Setup spot cutter… to start the "EXQuest Calibration Wizard". The screen that will appeardepends on the current calibration state o

EXQUEST CALIBRATION WIZARD3-3Figure 3-4. “EXQuest Calibration Wizard” screen – calibrated.From this screen you may• Calibrate the camera with the curr

EXQUEST CALIBRATION WIZARD3-4Figure 3-5. Camera focusing dialog.6.Head Height Calibration. The Head Height Calibration dialog is used to set the cutti

EXQUEST CALIBRATION WIZARD3-5Figure 3-6. “Head Height Calibratioin” screen.7.Flat Field Calibration. The flat field calibration step corrects for inho

EXQUEST CALIBRATION WIZARD3-68.Lens Calibration. The lens calibration step corrects for image distortion due to the camera lens. Toperform the lens ca

Figure 3-9. System position calibration.Manual Calibration a. If calibrating the membrane cutting head, install the plastic protective sleeve over th

SECTION 7 LANE VOLUME EXCISION TOOL...7-17.1 Setting Up a Cut Run

Figure 3-10. Plate position calibration: plate selection.b. Use the Left/Right and Front/Back slider to center the cutting tip over well A1, as shown

d. Use the Raise/Lower slider to adjust the tip height. Typically, the gel tip should be placed about0 to 1 mm into the well and the Membrane cutting

Figure 3-13. Wash station position calibration.b. When the tip is centered, check Lower head to adjust wash height to lower the cutting tip intothe we

Figure 3-14. Calibration complete! screen.EXQUEST CALIBRATION WIZARD3-11

4.0 GEL AND BLOT PREPARATIONGel and blot preparation is an important part of setting up a successful cut run. Failure to prepare gels andblots properl

4.3 BLOT PREPARATION1. Store PVDF and nitrocellulose blots in a container that keeps them protected and hydrated untilneeded for spot cutting.2. Remov

5.0 MANUAL EXCISION TOOLThe Manual Excision Tool is a general-purpose excision tool included in both the PDQuest™and QuantityOne®software. It has the

Figure 5-2. Manual excision tool.7. Close the spot cutter front door and click Acquire Image to take an image of the gel tray contents.Do not open the

12. Optional. Check Hydrate in the "Hydration Options" panel to automatically hydrate the gel during thecut run. Specify how often it is to

17. Click Begin/Resume to open the "Plates for Cut Run" dialog (see Section 8.9) and then enter theplate name and barcode/plate ID in their

SAFETY INFORMATIONRead the manual before operating the EXQuest Spot Cutter. For technical assistance, contact your local Bio-Rad representative or, in

Figure 5-5. Import excision coordinate list.3. If the first line of your file is header information, check Skip first line of file.4. Enter the column

MANUAL EXCISION TOOL5-6Figure 5-6. Confirm cuts pop-up.2. Read the instructions on the "Image Microtiter Plate" screen.Figure 5-7. “Image Mi

5.3.2 Identifying Re-cuts from a Gel Image1. When the cut run is finished, return to the "Manual Excision Tool" screen and click Confirm Cu

6.0 ANALYSIS SET EXCISION TOOLThe Analysis Set Excision Tool is designed to use the advanced capabilities of the PDQuest™software increating cut reque

ANALYSIS SET EXCISION TOOL6-24. Click Next to continue. The wizard screen that appears will depend on whether a cut request list hasalready been creat

From the "Analysis Set with Unfinished Cuts" screen (Figure 6-4):– Select Resume cut run and finish these cuts and then click Next, to finis

Figure 6-6. “Select Gels to Cut” ScreenFrom the "Select Gels to Cut" screen, select one or more gels to cut. Multiple gels may beselected by

a. From the "Automatically Select Gels to Cut" screen, set the Tolerance. The tolerance value isused to determine the spot quantity range th

•PVDF: This option is available only when the spot cutter is in membrane cutting mode, and isused to specify that either a PVDF or Nitrocellulose memb

Figure 6-9. Analysis Set Excision Control Tool•Analysis set name: This text field displays the name of the selected analysis set.•Analysis set spot co

1.0 INTRODUCTION1.1 OVERVIEWThe EXQuest™spot cutter is a precision instrument that accurately locates and excises protein spots andbands from one and

Figure 6-10. Place Gel/Blot on Spot Cutter dialog box: Single Gel PlacementFigure 6-11. Place Gel/Blot on Spot Cutter dialog box: Multiple Gel Placeme

14. Align the spots on the cutter image (right side of Figure 6-12) with spots in the analysis set image(left side of Figure 6-12).Figure 6-12. Align

Figure 6-14. Align Analysis and Cutter Images: Step 2 – Perform Alignment Panel•Automatic Alignment. Automatic alignment uses a Gaussian fitting algor

Figure 6-16. Align Analysis and Cutter Images: Jump and ConfirmThe following image options are available in this window:•Display cropped image. Check

Figure 6-17. Align Analysis and Cutter Images: Cut Overlaps15. Click Proceed to hydrate the gel or blot (if hydration is turned on) and open the "

17. When the run is finished, you will be prompted to place the next gel on the spot cutter, if you arecutting multiple gels. Place the gel on the gel

ANALYSIS SET EXCISION TOOL6-143. Check Analysis Set Excision Tool advanced user mode in the "Spot cutter" panel and then clickOK.4. Make sur

Figure 6-23. Step 2 – Select Gels: Select from ListAuto-selecta. Choose Auto-select to let PDQuest automatically select the best gel(s) to cut based o

12. Optional. Click the Review tab and review the cut selections. The Review tab displays the gel spotsby Standard Spot Number (SSP) along with their

•Plastic-backed Gels. Select this option to use a protocol optimized for cutting plastic-backedgels. When this option is used, gel plugs are cut and t

1.2 SYSTEM DESCRIPTIONThe EXQuest spot cutter is a fully integrated system controlled through PDQuest™and Quantity One®software. It consists of an enc

7.0 LANE/VOLUME EXCISION TOOLThe Lane/Volume Excision Tool is designed to provide a simple and efficient method for cutting lanes andbands from 1D gel

Tips for cutting membranes– Fill microplate wells with DI water to within 1 to 2 mm of the top. In order to release the cutmembrane into a microplate

Figure 7-3. Lane/Volume Excision Tool image with lanes3. Click Stretch Frame and then click and drag the frame anchors to fit the frame over the gel.4

6. Adjust Horizontal slider to control the horizontal cut spacing. Use the zoom tool to see the effect ofchanging the Horizontal control.Figure 7-5. T

Figure 7-7. Lane/Volume Excision Tool: Display Excisions4. Review the "Run Info" panel (see Section 8.8) for the number of cuts selected, th

EXCISION TOOL CONTROLS8-18.0 EXCISION TOOL CONTROLSThis section describes the excision tool controls that are common between the Manual Excision Tool,

EXCISION TOOL CONTROLS8-28.3 TRANSFORM DIALOG BOXThe "Transform" dialog box is used to adjust the image brightness and contrast. It contain

EXCISION TOOL CONTROLS8-3Image Panel•Max: This text box displays the intensity of the image's most intense pixel. Image units aredetermined by th

EXCISION TOOL CONTROLS8-4•Material: Use this drop-down menu to select the gel type that will be cut, e.g., "Free gel", "Plastic-backed

EXCISION TOOL CONTROLS8-5•Define hydration area. To define the cutting deck area to hydrate, click this button and then click anddrag a box around the

INTRODUCTION1-3Figure 1-3. Light enclosure.1.2.2 Imaging SystemThe gel and blot imaging system consists of a CCD camera (1600 x 1200 pixels, 12 bit AD

EXCISION TOOL CONTROLS8-68.9 PLATES FOR CUT RUNFigure 8-9. “Plates for Cut Run” dialog boxThe "Plates for Cut Run" dialog is used to identi

EXCISION TOOL CONTROLS8-78.10 LOAD PLATE ON CUTTER DIALOGFigure 8-10. “Load Plate on Cutter” dialog boxThis dialog helps the operator correctly place

ACCESSORIES9-19.0 ACCESSORIES, SUPPLIES, REPLACEMENT PARTSCatalogNumber Description 165-7208 EXQuest Cutting Sheets (S), pkg of 15165-7205 EXQuest Ca

10.0 MAINTENANCE10.1 ROUTINE MAINTENANCE• The gel tray should be cleaned after use with a damp nonabrasive cloth. Mild detergents may beused. Do not u

MAINTENANCE10-2Figure 10-2. UV EPI Lamp Partially Removed3. Place the lamp assembly upside down on a flat surface and then rotate each fluorescent tub

MAINTENANCE10-3Figure 10-4. Spot cutter fuse

TROUBLESHOOTING11-111.0 TROUBLESHOOTINGSymptom Cause SolutionComputer does not USB cable not Ensure that both the USB cable and power cord communi

TROUBLESHOOTING11-2Symptom Cause SolutionHydration and clamping Excess water on the gel tray causes backed gels toslide when the gel plug is being scr

TROUBLESHOOTING11-3If all the settings seem to be correct, contact Bio-Rad for further troubleshooting. For technical assistancewith the system includ

12.0 WARRANTYEXQUEST™SPOT CUTTER WARRANTY INFORMATIONThis warranty statement may vary outside of the continental United States. Please contact your l

INTRODUCTION1-4Figure 1-4. Gel tray with clamps.1.2.4 Cutting HeadsThe EXQuest spot cutter supports both gel and membrane (blot) cutting heads. The ge

SYSTEM RECORDSSerial NumberDate of PurchasePurchase OrderNumberNotesService RecordDate Description of Problem Name SignatureWARRANTY12-2

Life ScienceGroup00-000 0000 Sig 1204Bulletin 0000 US/EG Rev ABio-Rad Laboratories, Inc.Web site www.bio-rad.com USA (800) 4BIORAD Austr

INTRODUCTION1-5•Membrane Cutting Head. The membrane cutting head is an optional accessory that is used forcutting PVDF and nitrocellulose membranes. A