SymBiot I Sample Workstation

Transcription

1 SymBiot I Sample Workstation Getting Started Guide DRAFT August 28, :42 pm Symbfmgs.fm5

2 Copyright 1997, 2001, Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic procedures. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document. ABI PRISM, Applied Biosystems and SymBiot are registered trademarks of Applera Corporation or its subsidiaries in the U.S. and certain other countries. AB (Design), Applera, Biospectrometry, Delayed Extraction, Voyager, and Voyager-DE are trademarks of Applera Corporation or its subsidiaries in the U.S. and certain other countries. IBM is a registered trademark of International Business Machines Corporation. Lexan is a registered trademark of General Electric Company. Microsoft, MS, Windows, and NT are registered trademarks of Microsoft Corporation. Pentium is a registered trademark of Intel Corporation. Teflon is a registered trademark of E. I. Du Pont de Nemours and Co. All other trademarks are the sole property of their respective owners. Printed in the USA, 07/2001 Part Number Rev. A DRAFT August 28, :42 pm Symbfmgs.fm5

3 Table of Contents Table of Contents Chapter 1 Before You Begin 1.1 SymBiot I Workstation Overview Operating the Workstation for the First Time Chapter 2 Preparing the Workstation 2.1 Selecting System Settings Configuring the Syringe Connecting the System Liquid and Flushing the System Chapter 3 Running a Standard Test and Method 3.1 Overview Installing the Trays and Racks Filling the Tube and Wells with Sample and Matrix Adjusting the Provided Rack Configurations Configuring the Pipette Tip Rack Configuring the Matrix/Reagent Racks Configuring the Microtiter Plate Configuring the Voyager Sample Plate Configuring the Offset Voyager Sample Plate Configuring the Sample 0.5mL Reagent 8 Rack Running a Standard Test and Method Verifying Test and Method Performance Stopping, Resuming, and Aborting the Method Chapter 4 Creating and Running a Test and Method 4.1 Moving the Voyager Sample Plate Tray Configuring a Rack with Two Sites Configuring Rack Name and Geometry Configuring the First Site SymBiot I Sample Workstation Getting Started Guide iii

4 Table of Contents Configuring the Second Site Configuring Rack Options Verifying the Configuration Preparing Samples and Matrix Creating a Test Displaying the Test Editor Adding a Group Adding a Test to the Group Adding Pre Reagent and Sample Steps to the Test Adding Commands to the Steps Creating a Method Opening the Method Editor Creating a New Method Selecting Method Options Selecting Automatic Options Selecting Error Options Selecting Wash/DITI Options Running Your Method Verifying Test and Method Performance Chapter 5 Editing a Test 5.1 Using the Test Editor Adding a Control Step to Your Test Adding Commands to the Control Step and Sample Step Running Your Method Verifying Test and Method Performance Index iv Applied Biosystems

5 Before You Begin 1 1 This chapter includes: SymBiot I Sample Workstation Overview Operating the workstation for the first time SymBiot I Sample Workstation Getting Started Guide 1-1

6 Chapter 1 Before You Begin SymBiot I Workstation Overview Workstation overview Figure 1-1 identifies the major components of the SymBiot I Sample Workstation. Reagent tubing Tubing guide System liquid System tubing Syringe (Diluter) Z-Rack Arm Tip ejector sleeve Waste block Waste tubing Waste bin x Rack Tray PB z y Figure 1-1 SymBiot I Sample Workstation 1-2 Applied Biosystems

7 SymBiot I Workstation Overview Operation overview Rack configurations Methods and tests To operate the SymBiot I Sample Workstation, you perform the following tasks: Prepare the workstation by selecting system settings and configuring workstation parameters Connect the system liquid and flush the system Install and configure racks and reagents Create a test Create a method Run the method The flowchart in Figure 1-2 gives a more detailed overview of how to use the SymBiot software to operate the SymBiot I Sample Workstation. The SymBiot software is provided with rack configurations. After adjusting the provided rack configurations, you can use them to run methods and tests. There are three ways to use tests and methods: Standard tests and methods The SymBiot software is provided with Standard methods and tests. You can run a Standard method and test, without having to create your own method and test. Standard tests and methods as templates You can use the Standard methods and tests as templates to create your own methods and tests. Custom tests and methods You can create your own methods and tests. 1 NOTE: The Standard methods and tests are illustrated in the SymBiot User s Guide. SymBiot I Sample Workstation Getting Started Guide 1-3

8 Chapter 1 Before You Begin 1 Edit System Settings: Test definition file (.TTL) COM port Output paths Password Configure Workstation Parameters: Arm Syringe Waste block and waste bin Connect system liquid and flush system Install and configure racks and reagents: Pipette tip racks Racks for sample and destination Reagents Create Sample Rack Files (optional): Define Rack IDs Define Sample IDs Create a test: Select predilution and destination racks Create pipetting scheme Create a method: Select tests Select operation mode Select sample rack Run the method: Select number of samples Select starting position in sample rack Figure 1-2 SymBiot Operation 1-4 Applied Biosystems

9 Operating the Workstation for the First Time 1.2 Operating the Workstation for the First Time 1 In this guide The SymBiot I Sample Workstation Getting Started Guide is designed to help you quickly learn how to use the SymBiot I Sample Workstation. The procedures in this guide show you how to: Prepare the workstation. Run a provided test and method that aspirates and dispenses a sample onto a Voyager sample plate, and then aspirates and dispenses matrix onto the dispensed sample. Reposition the Voyager sample plate and configure it. Create and run a test and method to aspirate and dispense matrix onto the Voyager sample plate, and then aspirate and dispense sample onto the dispensed matrix. Edit the test you created and run the modified method. This guide contains brief procedures. For more detailed procedures and reference information, refer to the SymBiot I Sample Workstation User s Guide. SymBiot I Sample Workstation Getting Started Guide 1-5

10 Chapter 1 Before You Begin 1 What you will learn The following table explains what you will learn in each section of this guide: In Chapter 2, Preparing the Workstation Chapter 3, Running a Standard Test and Method Chapter 4, Creating and Running a Test and Method Chapter 5, Editing a Test You will learn how to Select the system settings Configure the syringe Connect the system liquid and flush the system Install the trays and racks Adjust the provided rack configurations Fill the tubes and wells with liquid Run a Standard test and method Verify the test and method performance Move a tray to a new location and configure it Prepare samples and matrix Create a new test by adding a group, tests to the group, steps to the test, and commands to the steps Create a new method and select options Run the method you create Verify the test and method performance Edit the test you created Run the method containing the edited test Verify the test and method performance This guide is designed to step you through all necessary tasks to run your first experiments. Most sections assume you have completed the tasks in previous sections. 1-6 Applied Biosystems

11 Operating the Workstation for the First Time What you need Assumptions To run the experiments in this guide, you need: The four trays provided with the workstation: Pipette Tip Tray Voyager Sample Plate Tray Microtiter Plate Tray Matrix/Reagent Tray Two 1.5 ml microcentrifuge tubes One Voyager sample plate (two if available) One 96-well microtiter plate Racks containing disposable 10 µl Rainin Pipette tips Water Sample (optional) Matrix (optional) This guide assumes: Your SymBiot I Sample Workstation has been properly assembled and powered up Your SymBiot I Sample Workstation is connected to the computer The provided SymBiot software is installed and started The provided 100 µl syringe is installed You are familiar with the Windows NT operating system 1 NOTE: For detailed installation instructions, see the SymBiot I Sample Workstation User s Guide. SymBiot I Sample Workstation Getting Started Guide 1-7

12 Chapter 1 Before You Begin Applied Biosystems

13 Preparing the Workstation 2 2 In this section, you will: Select the system settings Configure the syringe Connect the system liquid and flush the system SymBiot I Sample Workstation Getting Started Guide 2-1

14 Chapter 2 Preparing the Workstation 2.1 Selecting System Settings 2 Paths and files The system settings control how and where the SymBiot I Sample Workstation stores, receives, exports, and displays information. System settings include: Paths and files Instrument and COM ports To run the tests described later in this guide, select the standard tests.ttl Test Definition file in the Paths and Files dialog box: 1. Select Settings from the Edit menu. The Settings dialog box appears (Figure 2-1). Figure 2-1 Settings Dialog Box (Paths and Files Parameters) 2. Select the Paths and Files tab. 3. Type standard tests.ttl in the Test Definitions text box, or click Browse and select standard tests.ttl. 2-2 Applied Biosystems

15 Selecting System Settings Instrument and COM ports To verify which COM port the computer receives information from: 1. Select the Instruments and COM Ports tab (Figure 2-2). 2 Figure 2-2 Instruments and COM Ports Parameters COM Port 2. Make sure the COM Port (COM1 or COM2) to which you connected the SymBiot I Sample Workstation is selected. NOTE: For information on identifying the COM port, see the documentation provided with your computer. 3. Click OK. 4. To verify that you selected the correct COM port, select Configuration from the Edit menu. If the arm initializes by moving through several pre-set Z positions, then stopping over the waste block, you selected the correct COM port. If an Instrument does not respond error message is displayed, repeat step 1 through step 3 and select the other COM port. SymBiot I Sample Workstation Getting Started Guide 2-3

16 Chapter 2 Preparing the Workstation 2.2 Configuring the Syringe 2 Configure the syringe to set the volume of the installed syringe. To configure the syringe: 1. Select Configuration from the Edit menu or click the button. The Edit Configuration dialog box appears. 2. Select the Diluters tab (Figure 2-3). Figure 2-3 Diluters Parameters 3. Click Edit. The Edit Diluter 1 for Arm 1 dialog box appears (Figure 2-4). 2-4 Applied Biosystems

17 Configuring the Syringe Figure 2-4 Edit Diluters Dialog Box 4. Type 100 µl for the syringe volume in the Capacity text box Type 193 for the Maximum pipetting speed and the Maximum wash speed. 6. Click OK to accept the settings. 7. Click OK again to return to the SymBiot window. SymBiot I Sample Workstation Getting Started Guide 2-5

18 Chapter 2 Preparing the Workstation 2.3 Connecting the System Liquid and Flushing the System 2 Connecting the system liquid The system liquid is used to fill the reagent tubing, system tubing and syringe. Deionized water or HPLC-grade water is recommended for the system liquid. To connect the system liquid: 1. Fill a container with filtered deionized water. 2. Submerge the reagent tubing in the liquid. CAUTION Change the system liquid daily to prevent microbial growth. Flushing the system 3. Select Flush Instrument from the Run menu or click the button. The Flush Instrument dialog box appears (Figure 2-5). Figure 2-5 Flush Instrument Dialog Box 2-6 Applied Biosystems

19 Connecting the System Liquid and Flushing the System 4. Type 0 in the Volume in Waste text box. 5. Type 900 µl in the Volume in Cleaner text box. NOTE: To ensure a complete flush, always type a flush volume equal to or greater than two times the volume of the system tubing and reagent tubing. If using the system and reagent tubing provided, a flush volume of 900 µl is sufficient. 6. Select Wash Station #1 from the drop-down list. 7. Click OK. 2 The syringe plunger moves up and down and fills the reagent and system tubing with water. Excess system liquid is dispensed into the waste block. 8. While the system is flushing, observe the barrel of the syringe for air bubbles. If you see any air bubbles, remove the syringe and eliminate the air as described in the SymBiot I Sample Workstation User s Guide. Flush the system again. SymBiot I Sample Workstation Getting Started Guide 2-7

20 Chapter 2 Preparing the Workstation Applied Biosystems

21 Running a Standard Test and Method 3 3 In this chapter, you will: Install the trays and racks Fill the tube and wells with sample and matrix Adjust the provided rack configurations Run a Standard test and method Verify the test and method performance SymBiot I Sample Workstation Getting Started Guide 3-1

22 Chapter 3 Running a Standard Test and Method 3.1 Overview 3 The SymBiot I Sample Workstation is provided with a set of Standard tests and methods. For a list of the Standard tests and methods, see the SymBiot User s Guide. Each method specifies one or more tests. When you run a method, you run the tests specified by that method. In this chapter you will see a demonstration of how the workstation operates by running one of the Standard methods, Method 101 Sample (SP)/Matrix (SP), which specifies one of the Standard tests, Test 101 Sample (SP)/Matrix (SP). The Sample (SP)/Matrix (SP) test and method pipette sample from a microtiter plate onto a Voyager sample plate and then pipette matrix from a microcentrifuge tube onto the dispensed sample. You may use water instead of actual samples and matrix for the demonstration in this chapter. NOTE: This chapter demonstrates the operation of the workstation. For information on configuring racks, creating tests, and creating and running methods, see Chapter 4, Creating and Running a Test and Method. 3-2 Applied Biosystems

23 Installing the Trays and Racks 3.2 Installing the Trays and Racks Trays and racks You will need the following trays on the SymBiot I Sample Workstation. Each tray holds a specific rack, plate, or tube: Pipette Tip Tray Holds three 10 µl pipette tip racks, and a waste bin for used pipette tips NOTE: Use only Rainin 10 µl disposable pipette tips with the SymBiot I Sample Workstation. Other pipette tips are not supported by the workstation and will result in tip drops and poor pipetting performance. To order RT µl tips, contact Rainin Instrument Company, Inc. Voyager Sample Plate Tray Holds five 100-well MALDI plates or five 100-well disposable MALDI plates Microtiter Plate Tray Holds three 96-well or three 384-well microtiter plates 3 Matrix/Reagent Tray Holds eight 1.5 ml and eight 0.5 ml microcentrifuge tubes Chapter SymBiot I Sample Workstation Getting Started Guide 3-3

24 Chapter 3 Running a Standard Test and Method Installing trays and racks To install the trays, racks, and plates in the SymBiot I Sample Workstation: 1. Place the trays on the deck by lining up the locator marks on the trays with the appropriate number on the deck as shown in Figure 3-1. Waste Block Deck A B C D E F G H v v v v Matrix/Reagent Tray Pipette Tip Tray Microtiter Plate Tray Voyager Sample Plate Tray Figure 3-1 Tray and Rack Positions 2. Move the trays forward and backward until the slot in the runner fits over the three pins in the row. 3. Place a 1.5 ml microcentrifuge tube in the rear position of the Matrix/Reagent Tray. 4. Place three full pipette tip racks in the Pipette Tip Tray. 5. Place one 96-well microtiter plate in the rear position of the microtiter plate tray. 6. Place one Voyager sample plate in the rear position of the Voyager Sample Plate Tray. 3-4 Applied Biosystems

25 Filling the Tube and Wells with Sample and Matrix 3.3 Filling the Tube and Wells with Sample and Matrix You can use actual sample and matrix or water for the demonstration of the Standard test and method: 1. Add 1.0 ml of matrix or water to the 1.5 ml tube in the Matrix/Reagent Tray. 2. Add 0.3 ml of sample or water to each of the 12 wells (A1 A12) in the first row of the microtiter plate. NOTE: We recommend using water instead of matrix and sample for the procedures detailed in this guide. 3 Chapter SymBiot I Sample Workstation Getting Started Guide 3-5

26 Chapter 3 Running a Standard Test and Method 3.4 Adjusting the Provided Rack Configurations Overview The SymBiot I Sample Workstation is provided with seven pre-set rack configurations. In this section, you will adjust the provided configurations so the X, Y, and Z values are correct for your workstation. Adjust the seven provided rack configurations in the order they are listed in the following table: Provided Rack Configuration Uses the Following Tray on the SymBiot Deck At Position 3 Tip10 Pipette Tip Tray Row 7 1.5mL Matrix/Reagent Row 1 Matrix/Reagent Tray Row 1 0.5mL Matrix/Reagent Row 1 Matrix/Reagent Tray Row 1 Sample 0.5mL Reagent 8 Matrix/Reagent Tray Row 1 Microtiter Plate on Row 13 Microtiter Plate Tray Row 13 MALDI 10x10 on Row 16 Voyager Sample Plate Tray Row 16 MALDI 10x10 on Row 16 Offset Voyager Sample Plate Tray Row 16 After adjusting the provided rack configurations, you will update the provided reagent configurations, which are based on two of the provided rack configurations. 3-6 Applied Biosystems

27 Adjusting the Provided Rack Configurations Configuring the Pipette Tip Rack To adjust the configuration of the pipette tip rack: 1. Make sure a plastic pipette tip is not mounted on the stainless steel cone of the SymBiot arm. If a plastic pipette tip is mounted on the stainless steel cone of the SymBiot arm, remove the tip, exit and restart the SymBiot software. CAUTION Be sure to complete step 1 before proceeding. If a pipette tip is on the SymBiot arm when the workstation initializes, the Z-values you set for the pipette tip rack will be inaccurate. 2. Select Configuration from the Edit menu or click the button on the toolbar to initialize the SymBiot arm. The Edit Configuration dialog box appears. 3. Select the Racks tab (Figure 3-2). 3 Figure 3-2 Racks Parameters Chapter SymBiot I Sample Workstation Getting Started Guide 3-7

28 Chapter 3 Running a Standard Test and Method 4. Select Tip10 and then click Edit. The Edit Rack Tip10 dialog box appears. 3 Figure 3-3 Edit Rack Tip10 Dialog Box 5. Select 1 in the Current Site text box. 6. Click the button to the right of X (well #1) and Y (well #1). The pipette tip assembly moves to the stored X and Y location for well #1 (rear-left). 7. Press and hold the Control key while pressing the Page Down key to lower the pipette tip assembly until it is close to, but not touching the pipette tip. 8. Press and hold the Control key while pressing the,,, and keys (on the keyboard) to center the pipette tip assembly perfectly over the pipette tip. NOTE: Press the,,, and keys without holding the Control key for finer X and Y adjustment. 3-8 Applied Biosystems

29 Adjusting the Provided Rack Configurations 9. Press the Page Down key to slowly lower the arm into the pipette tip until the tip ejector sleeve (white Teflon ) becomes offset and the Z-Rack stops moving. Lower the arm 40 more steps. NOTE: You can track the number of steps the arm is moving by observing the values in the Current Position dialog box. 10. Click Adjust. The Tip10 rack configuration provided with the SymBiot software is adjusted so the position locations are correct for your workstation. 11. Click the button to the right of Z-Travel to raise the pipette tip assembly. 12. Make sure the arm picked up a pipette tip. If it did not, repeat step 9, and lower the arm 20 more steps. CAUTION If a Step Loss error is displayed, exit and restart the SymBiot software Remove the pipette tip from the arm. NOTE: Assure the pipette tip was firmly mounted. If the tip is loose, repeat step 9 through step 13, lowering the arm 20 more steps. 14. Click the button to the right of X (well #96) and Y (well #96). The pipette tip assembly moves to the stored X and Y location for well #96 (front-right). 15. Press and hold the Control key while pressing the Page Down key to lower the pipette tip assembly until it is close to, but not touching the pipette tip. Chapter SymBiot I Sample Workstation Getting Started Guide 3-9

30 Chapter 3 Running a Standard Test and Method 16. Assure the arm is centered over the pipette tip. If necessary, center the arm by pressing the,,, and keys. 17. If you adjusted the arm in step 16, store the new values by clicking the button to the right of X (well #96) and Y (well #96). 18. Select 2 in the Current Site text box and repeat step 6 through step Select 3 in the Current Site text box and repeat step 6 through step Click OK to accept the edited configuration Configuring the Matrix/Reagent Racks 3 Configuring 1.5 ml rack The Matrix/Reagent Tray holds 16 microcentrifuge tubes, eight 1.5 ml and eight 0.5 ml. The eight 1.5 ml tubes are configured as one rack, and the eight 0.5 ml tubes are configured as a second rack. To adjust the configuration of the 1.5 ml microcentrifuge tube rack: 1. Place a plastic pipette tip over the stainless steel cone of the pipette tip assembly. 2. Exit and restart the SymBiot software. CAUTION Be sure to complete step 1 and step 2 before proceeding. If no pipette tip is on the SymBiot arm when the workstation initializes, the Z-values you set will be inaccurate. 3. Select Configuration from the Edit menu or click the Config button on the toolbar to initialize the SymBiot arm. The Edit Configuration dialog box appears Applied Biosystems

31 Adjusting the Provided Rack Configurations 4. Select the Racks tab (see Figure 3-2 on page 3-7). 5. Select 1.5 ml in Matrix/Reagent row 1 and click Edit to display the Edit Rack 1.5 ml in Matrix/Reagent row 1 dialog box. 6. Click the button to the right of X (well #1) and Y (well #1). The pipette tip moves to the stored X and Y location for well #1 (rear). 7. If necessary, use the,,, and keys to center the tip over the tube. 8. Press and hold the Control key while pressing the Page Down key to lower the pipette tip halfway into the tube or lower, depending on the volume of liquid in the tube. Press the Page Down key without holding the Control key for finer vertical adjustment. NOTE: This height will be the Z-Max height or the height of the pipette tip when aspirating liquid Click Adjust. The 1.5 ml in Matrix/Reagent row 1 rack configuration provided with the SymBiot software is adjusted so the position locations are correct for your workstation. 10. Click the button to the right of X (well #8) and Y (well #8). The pipette tip assembly moves to the stored X and Y location for well #8 (front). 11. Assure the arm is centered over the position. If necessary, center the arm by pressing the,,, and keys. 12. If you adjusted the arm in step 11, store the new values by clicking the button to the right of X (well #8) and Y (well #8). 13. Click OK to accept the edited configuration. Chapter SymBiot I Sample Workstation Getting Started Guide 3-11

32 Chapter 3 Running a Standard Test and Method Configuring 0.5 ml rack To adjust the configuration of the 0.5 ml microcentrifuge tube rack: 1. Select 0.5 ml in Matrix/Reagent row 1 and click Edit to display the Edit Rack 0.5 ml in Matrix/Reagent row 1 dialog box. 2. Click the button to the right of X (well #1) and Y (well #1). The pipette tip moves to the stored X and Y location for well #1. 3. If necessary, use the,,, and keys to center the tip over the tube Press and hold the Control key while pressing the Page Down key to lower the pipette tip halfway into the tube or lower, depending on the volume of liquid in the tube. Press the Page Down key without holding the Control key for finer vertical adjustment. NOTE: This height will be the Z-Max height or the height of the pipette tip when aspirating liquid. 5. Click Adjust. The 0.5 ml in Matrix/Reagent row 1 rack configuration provided with the SymBiot software is adjusted so the position locations are correct for your workstation. 6. Click the button to the right of X (well #8) and Y (well #8). The pipette tip assembly moves to the stored X and Y location for well #8 (front). 7. Assure the arm is centered over the position. If necessary, center the arm by pressing the,,, and keys. 8. If you adjusted the arm in step 7, store the new values by clicking the button to the right of X (well #8) and Y(well#8). 9. Click OK to accept the edited rack configurations Applied Biosystems

33 Adjusting the Provided Rack Configurations Updating the provided reagent configurations After adjusting the configuration of the 1.5 ml microcentrifuge tube rack and the 0.5 ml microcentrifuge tube rack, update the provided reagent configurations within these two racks. To update the provided reagent configurations: 1. Select Configuration from the Edit menu or click the Config button on the toolbar. The Edit Configuration dialog box appears. 2. Select the Reagents tab (Figure 3-4). 3 Figure 3-4 Reagents Tab 3. Select 0.5 ml Reagent 1 and click Edit to display the Edit Reagent 0.5 ml Reagent 1 dialog box. 4. Click OK to update the reagent configuration with the adjusted rack configuration. 5. Repeat step 3 and step 4 for the 15 remaining reagent configurations. 6. Click OK to close the Edit Configuration dialog box. Chapter SymBiot I Sample Workstation Getting Started Guide 3-13

34 Chapter 3 Running a Standard Test and Method Configuring the Microtiter Plate To adjust the configuration of the microtiter plate: 1. In the Racks tab of the Edit Configuration dialog box, select Microtiter Plate on row 13 and click Edit to display the Edit Rack Microtiter Plate on row 13 dialog box. 2. Select 1 in the Current Site text box. 3. Click the button to the right of X (well #1) and Y (well #1). The pipette tip moves to the stored X and Y location for well #1 (rear-left) If necessary, use the,,, and keys to center the tip over the well. NOTE: Centering the tip accurately is important if your microtiter plate has conical wells. 5. Use the Page Up and Page Down keys to lower the pipette tip halfway into the well or lower, depending on the volume of liquid in the well. NOTE: This height will be the Z-Max height or the height of the pipette tip when aspirating liquid. 6. Click Adjust. The Microtiter Plate on row 13 rack configuration provided with the SymBiot software is adjusted so the position locations are correct for your workstation. 7. Click the button to the right of X (well #96) and Y (well #96). The pipette tip assembly moves to the stored X and Y location for well #96 (front-right) Applied Biosystems

35 Adjusting the Provided Rack Configurations 8. Assure the arm is centered over the position. If necessary, center the arm by pressing the,,, and keys. 9. If you adjusted the arm in step 8, store the new values by clicking the button to the right of X (well #96) and Y (well #96). 10. Select 2 in the Current Site text box and repeat step 3 through step Select 3 in the Current Site text box and repeat step 3 through step Click OK to accept the edited configuration. 3 Chapter SymBiot I Sample Workstation Getting Started Guide 3-15

36 Chapter 3 Running a Standard Test and Method Configuring the Voyager Sample Plate To adjust the configuration of the Voyager sample plate: 1. In the Racks parameters of the Edit Configuration dialog box, select MALDI 10 X 10 on row 16 and click Edit to display the Edit Rack MALDI 10 X 10 on row 16 dialog box. 2. Select 1 in the Current Site text box. 3. Click the button to the right of X (well #1) and Y(well#1). The pipette tip moves to the stored X and Y location for well #1 (rear-left) Press and hold the Control key while pressing the Page Down key to lower the pipette tip until it is approximately 1 mm above the sample plate. 5. Press and hold the Control key while pressing the,,, and keys to center the pipette tip perfectly over well 1 (rear-left) on the Voyager sample plate. NOTE: Press the,,, keys without holding the Control key for finer X and Y adjustment. 6. Press and hold the Control key while pressing the Page Down key to position the pipette tip just above the sample plate, but not touching it (approximately 1 mm). Press the Page Down key without holding the Control key for finer vertical adjustment. NOTE: This height will be the Z-Max height or the height of the pipette tip when aspirating liquid. 7. Click Adjust. The MALDI 10 X 10 on row 16 rack configuration provided with the SymBiot software is adjusted so the position locations are correct for your workstation Applied Biosystems

37 Adjusting the Provided Rack Configurations 8. Click the button to the right of X (well #100) and Y (well #100). The pipette tip assembly moves to the stored X and Y location for well #100 (front-right). 9. Assure the arm is centered over the position. If necessary, center the arm by pressing the,,, and keys. 10. If you adjusted the arm in step 9, store the new values by clicking the button to the right of X (well #100) and Y (well #100). 11. Select 2 in the Current Site text box and repeat step 3 through step Select 3 in the Current Site text box and repeat step 3 through step Select 4 in the Current Site text box and repeat step 3 through step Select 5 in the Current Site text box and repeat step 3 through step Click OK to accept the edited configuration. Chapter SymBiot I Sample Workstation Getting Started Guide 3-17

38 Chapter 3 Running a Standard Test and Method Configuring the Offset Voyager Sample Plate 3 The Offset Voyager sample plates are in the same location on the SymBiot deck as the Voyager sample plates. However, the configured positions are offset 7 to 10 steps to the right of (X axis) and 7 to 10 steps behind (Y axis) the actual wells on the plate. Using both the Voyager sample plate configuration and the Offset Voyager sample plate configuration allows you to double the number of wells on one plate. To adjust the configuration of the offset Voyager sample plate: 1. In the Racks parameters of the Edit Configuration dialog box, select MALDI 10 X 10 on row 16 Offset and click Edit to display the Edit Rack MALDI 10 X 10 on row 16 Offset dialog box. 2. Select 1 in the Current Site text box. 3. Click the button to the right of X (well #1) and Y (well #1). The pipette tip moves to the stored X and Y location for well #1 (rear-left). 4. Press and hold the Control key while pressing the Page Down key to lower the pipette tip until it is approximately 1 mm above the sample plate. 5. Press and hold the Control key while pressing the,,, and keys to center the pipette tip perfectly over well 1 (rear-left) on the Voyager sample plate. Use the key to move the tip 7 to 10 steps to the right. Use the key to move the tip 7 to 10 steps to the rear. NOTE: Press the,,, keys without holding the Control key for finer X and Y adjustment Applied Biosystems

39 Adjusting the Provided Rack Configurations 6. Press and hold the Control key while pressing the Page Down key to position the pipette tip just above the sample plate, but not touching it (approximately 1 mm). Press the Page Down key without holding the Control key for finer vertical adjustment. NOTE: This height will be the Z-Max height or the height of the pipette tip when aspirating liquid. 7. Click Adjust. The MALDI 10 X 10 on row 16 Offset rack configuration provided with the SymBiot software is adjusted so the position locations are correct for your workstation. 8. Click the button to the right of X (well #100) and Y (well #100). The pipette tip assembly moves to the stored X and Y location for well #100 (front-right). 9. Assure the arm is offset 7 to 10 steps to the right and 7 to 10 steps behind well #100. If necessary, adjust the arm by pressing the,,, and keys If you adjusted the arm in step 9, store the new values by clicking the button to the right of X (well #100) and Y (well #100). 11. Select 2 in the Current Site text box and repeat step 3 through step Select 3 in the Current Site text box and repeat step 3 through step Select 4 in the Current Site text box and repeat step 3 through step Select 5 in the Current Site text box and repeat step 3 through step Click OK to accept the edited configuration. Chapter SymBiot I Sample Workstation Getting Started Guide 3-19

40 Chapter 3 Running a Standard Test and Method Configuring the Sample 0.5mL Reagent 8 Rack 3 The Sample 0.5mL Reagent 8 rack is a single site rack with 100 positions (10 x 10). The 100 positions are configured within 0.5 ml tube #8 of the Matrix/Reagent Tray on row 1. This rack configuration allows you to repeatedly (up to 100 times) aspirate from a single tube and dispense into multiple positions on a destination rack. For an example of tests that use the Sample 0.5mL Reagent 8 rack configuration, see tests 132, 133, 134, and 135 in the SymBiot User s Guide. To adjust the configuration of the Sample 0.5mL Reagent 8 rack: 1. In the Racks tab of the Edit Configuration dialog box, select Sample 0.5mL Reagent 8 and click Edit to display the Edit Rack Sample 0.5mL Reagent 8 dialog box. 2. Select 1 in the Current Site text box. 3. Click the button to the right of X (well #1) and Y (well #1). The pipette tip moves to the stored X and Y location for well #1 (rear-left). 4. If necessary, use the,,, and keys to move the tip to the rear-left edge of the tube. 5. Use the Page Up and Page Down keys to lower the pipette tip halfway into the tube or lower, depending on the volume of liquid in the tube. NOTE: This height will be the Z-Max height or the height of the pipette tip when aspirating liquid Applied Biosystems

41 Adjusting the Provided Rack Configurations 6. Click Adjust. The Sample 0.5mL Reagent 8 rack configuration provided with the SymBiot software is adjusted so the position locations are correct for your workstation. 7. Click OK to accept the edited configuration. 3 Chapter SymBiot I Sample Workstation Getting Started Guide 3-21

42 Chapter 3 Running a Standard Test and Method 3.5 Running a Standard Test and Method To run the #101 Sample (SP)/Matrix (SP) test and method: 1. Select Start from the Run menu or click the button. The Select Method dialog box appears (see Figure 3-5). 3 Figure 3-5 Select Method Dialog Box 2. Select Method 101 Sample (SP)/Matrix (SP) and click OK. The Enter Number of Samples dialog box appears (Figure 3-6). Figure 3-6 Enter Number of Samples Dialog Box 3-22 Applied Biosystems

43 Running a Standard Test and Method 3. Type 12 for the number of samples. 4. Leave the First Position in Sample Rack at Click OK. The instrument layout appears (Figure 3-7) reflecting the racks and reagents selected in test and method 101 Sample (SP)/Matrix (SP). 1.5 ml Reagent 1 Tip10 (Pipette tip rack) Microtiter plate Voyager sample plate Deck area Layout dialog box Zoom view 3 Reserve area Status area Figure 3-7 Instrument Layout (Gather View) 6. Verify that the instrument layout matches the actual racks you installed on the SymBiot deck. 7. Click the Start button in the Layout dialog box to run the method on the first 12 samples in the microtiter plate. 8. Verify the test and method performance as described in Section 3.6, Verifying Test and Method Performance. Chapter SymBiot I Sample Workstation Getting Started Guide 3-23

44 Chapter 3 Running a Standard Test and Method 3.6 Verifying Test and Method Performance Observing After starting method #101 Sample (SP)/Matrix (SP), make sure the workstation performs the following steps: Sample step 1. Picks up a pipette tip. 2. Aspirates 1 µl liquid from position A1 in the microtiter plate. 3. Dispenses 1 µl liquid onto well 1 (rear-left) of the Voyager sample plate. 4. Disposes the tip. 5. Repeats step 1 through step 4 for all 12 sample positions. 3 Post Reagent step 6. Aspirates 1 µl liquid from the 1.5 ml microcentrifuge tube. 7. Dispenses 1 µl liquid onto one of the 12 positions on the Voyager sample plate. 8. Disposes the tip. 9. Repeats step 6 through step 8 for the first 12 positions on the Voyager sample plate Applied Biosystems

45 Verifying Test and Method Performance Troubleshooting If the arm did not aspirate or dispense liquid, check the following: 1. Make sure the syringe is installed properly. 2. Make sure the tubing is inserted completely in the syringe valves. 3. Make sure the compression fittings on the syringe valves are tightened. 4. Make sure the ferrules and lock rings on the tip assembly are secure. 5. Make sure the stainless steel cone is tight enough so that the tubing does not slide. 6. Make sure the tip assembly is tight enough to prevent leaks. 7. Flush the system For detailed information, refer to the SymBiot I Sample Workstation User s Guide. 3 Chapter SymBiot I Sample Workstation Getting Started Guide 3-25

46 Chapter 3 Running a Standard Test and Method 3.7 Stopping, Resuming, and Aborting the Method Stopping Resuming or aborting If you want to stop the SAMPLE/MATRIX method, click the button. After stopping the method, you can: Resume running the method by clicking the button OR Abort the method by clicking the button 3 CAUTION If you abort a method, the pipette tip counter does not count the tips used during the partial method run. The counter is set at the same site and position as at the start of the method. Either add pipette tips to the rack or reset the counter as described in the SymBiot I Sample Workstation User s Guide Applied Biosystems

47 Creating and Running a Test and Method 4 4 In this chapter, you will: Move the Voyager Sample Plate Tray to a new location Configure the Voyager Sample Plate Tray as a rack with two sites Prepare samples and matrix Create a new test Create a new method Run the method you create Verify test and method performance SymBiot I Sample Workstation Getting Started Guide 4-1

48 Chapter 4 Creating and Running a Test and Method 4.1 Moving the Voyager Sample Plate Tray To move the Voyager Sample Plate Tray: 1. Move the Voyager Sample Plate Tray from row 16 to row 20 (Figure 4-1). Deck A B C D E F G H Site 1 Site 2 v v v v v 20 4 Voyager Sample Plate Tray Figure 4-1 Moving the Voyager Sample Plate Tray 2. If available, place a second Voyager sample plate on site two. NOTE: If you do not have a second Voyager sample plate, you can use one plate and move it when you configure the second site. 4-2 Applied Biosystems

49 Configuring a Rack with Two Sites 4.2 Configuring a Rack with Two Sites In this section you will learn how to configure a rack with two sites to teach the workstation the physical location of the positions (wells) on two Voyager sample plates. NOTE: Although the following test and method require only one Voyager sample plate (one site), you will configure a rack with two sites to learn the Copy and Adjust features. To configure a rack with two sites: Configure the rack name and geometry Configure the first site Configure the second site Configure rack options 4 SymBiot I Sample Workstation Getting Started Guide 4-3

50 Chapter 4 Creating and Running a Test and Method Configuring Rack Name and Geometry To configure rack name and geometry: 1. Place a plastic pipette tip snugly over the stainless steel cone of the SymBiot arm. 2. Exit and restart the SymBiot software to initialize the SymBiot arm. CAUTION Be sure to complete step 1 and step 2 before proceeding. If no pipette tip is on the SymBiot arm when the workstation initializes, the Z-values you set will be inaccurate. 3. Select Configuration from the Edit menu or click the button. The Edit Configuration dialog box appears. 4. Select the Racks tab (Figure 4-2). 4 Figure 4-2 Racks Parameters 5. Click New to display the Enter Name dialog box. 4-4 Applied Biosystems

51 Configuring a Rack with Two Sites Rack name 6. Type MY MALDI TRAY for the rack name and click OK. The Edit Rack and Current Position dialog boxes appear (Figure 4-3). Figure 4-3 Edit Rack and Current Position Dialog Boxes Rack type 7. Select Rectangular for the rack type. Placement 8. Select for the placement. Positions 9. In the Rack section, select 10 for Wells (X) and 10 for Wells (Y). 4 Sites 10. In the Rack section, select 2 from the Number of Sites text box. SymBiot I Sample Workstation Getting Started Guide 4-5

52 Chapter 4 Creating and Running a Test and Method Configuring the First Site 4 Configure the first site by defining the rear-left and front-right positions of the first site: 1. Select 1 in the Current Site text box. 2. Press and hold the Control key while pressing the,,, and keys to move the pipette tip over the rear Voyager sample plate. 3. Press and hold the Control key while pressing the Page Down key to lower the pipette tip so it is just above the sample plate, but not touching it (approximately 1 mm). Press the Page Down key without holding the Control key for finer vertical adjustment. 4. Click the load button to the right of Z-Dispense and Z-Max. 5. Press and hold the Control key while pressing the,,, and keys to center the pipette tip over well 1 (rear-left) on the Voyager sample plate. Press the,,, and keys without holding the Control key for finer X and Y adjustment. 6. Click the load button to the right of X (well #1) and Y(well#1). 7. Press the Page Up key to raise the pipette tip about 10 steps. Click the load button to the right of Z-Start. 8. Press the Page Up key to raise the pipette tip about 10 more steps. Click the load button to the right of Z-Travel. 9. Press and hold the Control key while pressing the,,, and keys to center the pipette tip over well 100 (front-right) on the Voyager sample plate. NOTE: For easier X and Y adjustment, lower the pipette tip to the Z-Dispense height by clicking the button to the right of Z-Dispense. 10. Click the load button to the right of X (well 100) and Y (well 100). 4-6 Applied Biosystems

53 Configuring a Rack with Two Sites Configuring the Second Site Configure the second site by defining the rear-left and front-right positions of the second site: 1. Raise the pipette tip to the Z-Travel height by clicking the button to the right of Z-Travel. 2. Place the second Voyager sample plate on the rack or move the Voyager sample plate to the second site (see Figure 4-1 on page 4-2). 3. Select 2 in the Current Site text box. 4. Press and hold the Control key while pressing the,,, and keys to move the pipette tip over the second Voyager sample plate. 5. Press and hold the Control key while pressing the Page Down key to lower the pipette tip so it is just above the sample plate, but not touching it (approximately 1 mm). Press the Page Down key without holding the Control key for finer vertical adjustment. 6. Press and hold the Control key while pressing the,,, and keys to center the pipette tip over well 1 (rear-left) in the second site. Press the,,, and keys without holding the Control key for finer X and Y adjustment. 7. Click the Copy button in the Current Position dialog box. The X and Y coordinates for Well #1 and Well #100 of site 1 appear in the dialog box Click Adjust. The X and Y coordinates adjust to reflect the location of site 2. SymBiot I Sample Workstation Getting Started Guide 4-7

54 Chapter 4 Creating and Running a Test and Method Configuring Rack Options Configure rack options to set the area of the positions on the Voyager sample plate: 1. Select the Options tab in the Edit Configuration dialog box (Figure 4-4). 4 Figure 4-4 Options Parameters Area 2. Type 5.0 mm 2 for the area of the wells in the Voyager sample plate. NOTE: The SymBiot software uses the area value to create a graphical display of the configured rack when you run a method. 3. Click OK to add the rack to the configuration. Click OK again to save the configuration. 4-8 Applied Biosystems

55 Configuring a Rack with Two Sites Verifying the Configuration You can verify the configuration for each site by clicking the buttons, which display the stored values for the position and move the arm to the stored position. To verify the configuration of MY MALDI TRAY: 1. Make sure a plastic pipette tip is on the stainless steel cone of the SymBiot arm. If there is no tip, attach a tip, then exit and restart the SymBiot software to initialize the SymBiot arm. CAUTION Be sure to complete step 1 before proceeding. If no pipette tip is on the SymBiot arm when the workstation initializes, the Z-values you observe will be inaccurate. 2. Select Configuration from the Edit menu or click the button. The Edit Configuration dialog box appears. 3. Select the Racks tab. 4. Select MY MALDI TRAY and click Edit. The Edit Rack and Current Position dialog boxes appear. 5. Select 1 from the Current Site text box Click to the right of X (well #1) and Y (well #1), then click to the right of Z-Max. Verify that the pipette tip moves to the center of well 1 (rear-left). 7. Click to the right of Z-Travel. SymBiot I Sample Workstation Getting Started Guide 4-9

56 Chapter 4 Creating and Running a Test and Method 8. Click to the right of X (well #100) and Y (well #100), then click to the right of Z-Max. Verify that the pipette tip moves to the center of well 100 (front-right). 9. Select 2 from the Current Site text box. 10. Repeat step 6 through step Click OK twice to return to The SymBiot window. If the arm does not move as configured, perform procedures in Section 4.2, Configuring a Rack with Two Sites, again Applied Biosystems

57 Preparing Samples and Matrix 4.3 Preparing Samples and Matrix You can use actual sample and matrix or water for the test and method you will create. To prepare samples and matrix: 1. Make sure that 0.3 ml of sample or water is in each of the first 12 wells (A1 A12) in the first row of the microtiter plate. 2. Make sure that 1.0 ml matrix or water is in the 1.5 ml microcentrifuge tube in the Matrix/Reagent Tray. NOTE: We recommend using water instead of matrix and sample for the procedures detailed in this guide. 4 SymBiot I Sample Workstation Getting Started Guide 4-11

58 Chapter 4 Creating and Running a Test and Method 4.4 Creating a Test Overview In this section, you will create a test that pipettes matrix onto a Voyager Sample Plate, and then pipettes sample on top of the matrix. To create the test: Display the Test Editor Add a group Add a test to the group Add Pre Reagent and Sample steps to the test Add commands to the steps Applied Biosystems

59 Creating a Test Displaying the Test Editor Display the Test Editor (Figure 4-5), by selecting Test Definitions from the Edit menu or clicking the button. 4 Figure 4-5 Test Editor The STANDARD TESTS.TTL test definition file you selected in the system settings appears in the window. This test definition file contains: System Liquid Classes (3) System DITI Modes (1) Standard tests (40) SymBiot I Sample Workstation Getting Started Guide 4-13

60 Chapter 4 Creating and Running a Test and Method Adding a Group A group allows you to define a common output format and optimizing mode for a group of tests. To add a group to the Test Definition file: 1. Select Group 1 in the Test Editor. 2. Select New Element from the Edit menu or press the Insert key. The Select New Element dialog box appears (Figure 4-6). Figure 4-6 Select New Element Dialog Box 3. Select Group and click OK. The Insert New Group dialog box appears (Figure 4-7) Applied Biosystems

61 Creating a Test Figure 4-7 Insert New Group Dialog Box 4. Type 12 for the number. 5. Type MY TESTS for the Name. 6. Click OK to add the group to the Test Editor. GROUP 12 MY TESTS appears at the bottom of the test definition file. 4 SymBiot I Sample Workstation Getting Started Guide 4-15

62 Chapter 4 Creating and Running a Test and Method Adding a Test to the Group Add a test to the group to define the destination rack. To add a test to the group: 1. In the Test Editor, select GROUP 12 MY TESTS. 2. Select New Element from the Edit menu or press the Insert key. The Select New Element dialog box appears (see Figure 4-6 on page 4-14). 3. Select Test and click OK. The Insert New Test dialog box appears (Figure 4-8). 4 Figure 4-8 Insert New Test Dialog Box 4. Type 3 for the Number. 5. Type MY NEW TEST for the Name. 6. Select MY MALDI TRAY from the Destination Rack drop-down list box. 7. Click OK to add the test to the group. TEST 3 MY NEW TEST appears at the bottom of the test definition file Applied Biosystems

63 Creating a Test Adding Pre Reagent and Sample Steps to the Test Adding a Pre Reagent step There are five types of steps: Pre Reagent, Control, Sample, End Control, and Post Reagent. Steps determine the sequence in which commands are executed in a test. Steps also determine which positions in the destination rack will receive reagent, control, and sample. You will add a Pre Reagent step to pipette matrix and a Sample step to pipette sample. To add steps to MY NEW TEST: 1. In the Test Editor, select MY NEW TEST. 2. Select New Element from the Edit menu or press the Insert key. The Insert New Step dialog box appears (Figure 4-9). 4 Figure 4-9 Insert New Step Dialog Box 3. Select Pre Reagent and click OK. A Pre Reagent step is added to MY NEW TEST. SymBiot I Sample Workstation Getting Started Guide 4-17

64 Chapter 4 Creating and Running a Test and Method Adding a Sample step 4. Select MY NEW TEST. 5. Select New Element from the Edit menu or press the Insert key. The Insert New Step dialog box appears (Figure 4-9). 6. Select Sample and click OK. A Sample step is added to MY NEW TEST Applied Biosystems

65 Creating a Test Adding Commands to the Steps Creating a command sequence Commands instruct the workstation to aspirate, dispense, and mix sample. When you add commands, you create a sequence. A sequence starts with a Draw or Mix command and ends with a Mix or Drop command that changes the pipette tip (Change DITIS selected). NOTE: The first command in a test must be Draw or Mix. In this section, you will add Draw commands to aspirate matrix and sample, and Drop commands to dispense the matrix and sample. Adding a Draw command to the Pre Reagent step A Draw command defines how liquid is aspirated. You can add a Draw command to all steps. To add a Draw command to the Pre Reagent step: 1. Select the Pre Reagent step in MY NEW TEST. 2. Select New Element from the Edit menu or press the Insert key. The Choose New Command dialog box appears (Figure 4-10). 4 Figure 4-10 Choose New Command Dialog Box 3. Select Draw and click OK. The Insert New Draw dialog box appears (Figure 4-11). SymBiot I Sample Workstation Getting Started Guide 4-19

66 Chapter 4 Creating and Running a Test and Method Figure 4-11 Insert New Draw Dialog Box 4. Type 1 µl for the Volume. 5. Select Aqueous from the Liquid Class drop-down list. 6. Select Multi Pipetting mode. 4 NOTE: When the test runs, Multi Pipetting mode instructs the workstation to aspirate once from a single position and dispense into multiple positions in the destination rack. 7. Select Reagent for the Location. 8. Select 1.5 ml Reagent 1 from the reagent list box. 9. Click OK to add the Draw command to the Pre Reagent step Applied Biosystems

67 Creating a Test Adding a Drop command to the Pre Reagent step A Drop command defines how liquid is dispensed. You can add a Drop command to all steps, but only immediately after a Draw command. To add a Drop command to the Pre Reagent step: 1. Select the Draw command in the Pre Reagent step in MY NEW TEST. 2. Select New Element from the Edit menu or press the Insert key. The Insert New Drop dialog box appears (Figure 4-12). 4 Figure 4-12 Insert New Drop Dialog Box 3. Type 1 µl for the Volume. 4. Select Aqueous from the Liquid Class drop-down list box. 5. Select Destination Rack for the location. 6. Type 1 for Position X and 1 for Position Y. SymBiot I Sample Workstation Getting Started Guide 4-21

68 Chapter 4 Creating and Running a Test and Method 7. Select the Change DITIS check box to end the command sequence. 8. Select 10 µl DITI from the drop-down list box. 9. Click OK to add the Drop command to the Pre Reagent step. Adding a Draw command to the Sample step To add a Draw command to the Sample step: 1. Select the Sample step in MY NEW TEST. 2. Select New Element from the Edit menu or press the Insert key. The Choose New Command dialog box appears (see Figure 4-10 on page 4-19). 3. Select Draw and click OK. The Edit Draw dialog box appears (Figure 4-11). 4. Type 1 µl for the Volume. 5. Select Aqueous from the Liquid Class drop-down list box. 6. Select Single Pipetting mode. 4 NOTE: Single Pipetting mode instructs the workstation to aspirate from a single position on the sample rack and dispense into a single position in the destination rack. 7. Select Sample for the Location. 8. Click OK to add the Draw command to the Sample step Applied Biosystems

69 Creating a Test Adding a Drop command to the Sample step To add a Drop command to the Sample step: 1. Select the Draw command in the Sample step in MY NEW TEST. 2. Select New Element from the Edit menu or press the Insert key. The Choose New Command dialog box appears (see Figure 4-10 on page 4-19). 3. Select Drop and click OK. The Insert New Drop dialog box appears (see Figure 4-12 on page 4-21). 4. Type 1 µl for the Volume. 5. Select Aqueous from the Liquid Class drop-down list box. 6. Select Destination Rack for the location. 7. Type 1 for Position X and 1 for Position Y. 8. Select the Change DITIS check box to end the command sequence. When you run MY METHOD, the workstation will change the pipette tip between dispensing and aspirating different samples. 9. Select 10 µl DITI from the drop-down list box. 10. Click OK to add the Drop command to the Sample step. The new test should look like Figure SymBiot I Sample Workstation Getting Started Guide 4-23

70 Chapter 4 Creating and Running a Test and Method 4 Figure 4-13 MY NEW TEST 11. Select Save from the File menu. 12. Select Exit from the File menu to return to the SymBiot window Applied Biosystems

71 Creating a Method 4.5 Creating a Method Overview In this section, you will: Open the Method Editor Create a new method Select Method, Automatic, Error, and Wash/DITI options In this section, you will create your own method. The method will specify a test and the location and number of samples to run the test on Opening the Method Editor To display the Method Editor (Figure 4-14), select Methods from the Edit menu or click the button. 4 Figure 4-14 Method Editor The Method Editor contains 42 methods provided with the SymBiot software. Two methods to use when installing a syringe (#001 and #002) Forty Standard methods to use as examples or templates (#101 through #140) SymBiot I Sample Workstation Getting Started Guide 4-25

72 Chapter 4 Creating and Running a Test and Method Creating a New Method To create a new method: 1. Click the New button in the Edit Methods dialog box. The Edit Method No Name dialog box appears (Figure 4-15). 2. Select the following options as described in the following sections: Method Automatic Error Wash/DITI NOTE: In the following sections, you will select the most commonly used Automatic, Error, and Wash/DITI options. For more information on these options, see the SymBiot I Sample Workstation User s Guide Selecting Method Options 4 Select method options to define the following for your method: Method name Operation mode Sample rack Tests To select method options: 1. Select the Method tab in the Edit Method No Name dialog box (Figure 4-15) Applied Biosystems

73 Creating a Method Figure 4-15 Method Parameters Method name 2. Type MY METHOD for the Name. Operation mode 3. Select Sample Rack - Batch & No Scan from the Sample Source and Operation Mode drop-down list box. Sample rack 4. Select Microtiter Plate on row 13 from the Type of Sample Rack drop-down list box. 4 Tests 5. Select MY NEW TEST from the Tests list box. NOTE: If MY NEW TEST does not appear in the list box, verify that you selected STANDARD TESTS.TTL as the test definition file in the system settings. For more information, see Paths and files on page 2-2. SymBiot I Sample Workstation Getting Started Guide 4-27

74 Chapter 4 Creating and Running a Test and Method Selecting Automatic Options Select Automatic options to automate different functions during your method run. To select Automatic options: 1. Select the Automatic tab in the Edit Method No Name dialog box (Figure 4-16). 4 Figure 4-16 Automatic Parameters 2. Select Generate Layout of Robot Automatically. When you start your method, the layout of the instrument based on the configured racks is displayed. The reserved racks you select in the test and method appear at the bottom of the display for you to add to the layout. If you enable this option, the workstation automatically adds the reserved racks to the display Applied Biosystems

75 Creating a Method Selecting Error Options Select Error options to control how the workstation handles errors during method runs. To select Error options: 1. Select the Error tab in the Edit Method Name dialog box (Figure 4-17). Figure 4-17 Error Parameters 4 2. Select If DITI is not fetched, try 3 times then proceed at next DITI position. When you enable this option, if the tip assembly does not pick up the tip, the workstation tries three additional times to pick up a disposable tip (DITI) in the same position, then moves to the next tip position. NOTE: If you do not enable this option, an error message is displayed if the arm does not pick up a tip. SymBiot I Sample Workstation Getting Started Guide 4-29

76 Chapter 4 Creating and Running a Test and Method Selecting Wash/DITI Options To select Wash/DITI options: 1. Select the Wash/DITI tab in the Edit Method No Name dialog box (Figure 4-17). 4 Figure 4-18 Wash/DITI Tab 2. Select Wash/Change DITI Between the Same Liquids. When you run MY METHOD, the workstation will change the disposable tip (DITI) between dispensing and aspirating, even if it will be pipetting the same liquid as it will in the Pre Reagent step. NOTE: This feature can prevent cross contamination of samples when dispensing matrix into positions containing different samples. 3. Click OK to add MY METHOD to the Method Editor. 4. Click OK again to return to the SymBiot window Applied Biosystems

77 Running Your Method 4.6 Running Your Method To run MY METHOD: 1. Select Start from the Run menu or click the button. The Select Method dialog box appears (Figure 4-19). Figure 4-19 Select Method Dialog Box 2. Select MY METHOD and click OK. The Enter Number of Samples dialog box appears (Figure 4-20). 4 Figure 4-20 Enter Number of Samples Dialog Box 3. Type 12 for the number of samples. SymBiot I Sample Workstation Getting Started Guide 4-31

78 Chapter 4 Creating and Running a Test and Method 4. Leave the First position In Sample Rack set to Click OK. The instrument layout appears (Figure 4-21) reflecting the racks and reagents you selected in MY NEW TEST and MY METHOD. 1.5 ml Reagent 1 Tip10 (Pipette tip rack) Microtiter plate Voyager sample plate Deck area Layout dialog box 4 Reserve area Zoom view Status area Figure 4-21 Instrument Layout (Scatter View) 6. Verify that you arranged the trays, plates, and reagents on the rack as shown in the instrument layout. 7. Click the Start button in the Layout dialog box to run the method on the first 12 samples in the microtiter plate. 8. Verify the test and method performance as described in Section 4.7, Verifying Test and Method Performance Applied Biosystems

79 Verifying Test and Method Performance 4.7 Verifying Test and Method Performance Observing After starting MY METHOD, make sure the workstation performs the following steps: Pre Reagent step 1. Picks up a pipette tip. 2. Aspirates liquid from the 1.5 ml tube. 3. Dispenses 1 µl liquid onto several of the 12 positions on the Voyager sample plate. 4. Disposes the tip. 5. Repeats step 1 through step 4 for the remaining positions on the Voyager sample plate. Sample step 6. Picks up a pipette tip. 7. Aspirates 1 µl liquid from position A1 in the microtiter plate. 8. Dispenses 1 µl liquid onto well 1 (rear-left) of the Voyager sample plate. 9. Disposes the tip. Troubleshooting Stopping the method Resuming or aborting 10. Repeats step 6 through step 9 for all 12 sample positions. If the arm did not aspirate or dispense liquid, see Troubleshooting on page If you want to stop the method, click the toolbar. button on the After stopping the method, you can: Resume running the method by clicking the button OR Abort the method by clicking the button 4 SymBiot I Sample Workstation Getting Started Guide 4-33

80 Chapter 4 Creating and Running a Test and Method Applied Biosystems

81 Editing a Test 5 5 In this chapter, you will: Use the Test Editor to edit your test Add a Control step to your test Add Multiply, Draw, Drop, and Mix commands Run the method containing the edited test Verify the test and method performance Overview In this chapter you will modify MY NEW TEST so that it instructs the workstation to: Pipette controls (external standards) in every third position of the Voyager sample plate Mix samples in the microtiter plate before transferring to the Voyager sample plate SymBiot I Sample Workstation Getting Started Guide 5-1

82 Chapter 5 Editing a Test 5.1 Using the Test Editor Display the Test Editor (Figure 5-1), by selecting Test Definitions from the Edit menu or clicking the button. Figure 5-1 Test Editor Applied Biosystems

83 Adding a Control Step to Your Test 5.2 Adding a ControlSteptoYourTest To edit the test you created in the previous chapter: 1. Select MY NEW TEST from the Test Editor window. 2. Select New Element from the Edit menu or press the Insert key. The Insert New Step dialog box appears (Figure 5-2). Figure 5-2 Insert New Step Dialog Box 3. Select Control (Before Samples). 4. Select Delete Unused Controls. When you run the test, the workstation does not pipette Controls in positions following the last sample position in the destination rack (MALDI plate). 5. Click OK. A Control step is added to MY NEW TEST. 5 SymBiot I Sample Workstation Getting Started Guide 5-3

84 Chapter 5 Editing a Test 5.3 Adding Commands to the Control Step and Sample Step Overview Adding a Multiply command In this section you will add: Multiply, Draw, and Drop commands to the Control step A Mix command to the Sample step To add a Multiply command to the Control step: 1. Select the Control step line in MY NEW TEST. 2. Select New Element from the Edit menu or press the Insert key. The Choose New Command dialog box appears. 3. Select Multiply and click OK. The Insert New Multiply dialog box appears (Figure 5-3). Figure 5-3 Insert New Multiply Dialog Box 4. Type 1 for the start position. 5. Type 3 for the distance Click OK to add the Multiply command to the Control step. When you add a Multiply command to a Control step using the settings shown in Figure 5-3, the SymBiot software designates the first position in the rack as a Control, and every third position thereafter as a Control. The command sequence following the Multiply command is performed for each position designated as a Control. 5-4 Applied Biosystems

85 Adding Commands to the Control Step and Sample Step Adding a Draw command To add a Draw command to the Control step: 1. Select the Multiply command. 2. Select New Element from the Edit menu or press the Insert key. The Insert New Draw dialog box appears (Figure 5-4). Figure 5-4 Insert New Draw Dialog Box 3. Type 1 µl for the Volume. 4. Select Aqueous for the Liquid Class. 5. Select Single Pipetting mode. 6. Select Reagent for the location. 7. Select 1.5 ml Reagent 2 from the reagent list box. 8. Click OK to add the Draw command to the step. 5 SymBiot I Sample Workstation Getting Started Guide 5-5

86 Chapter 5 Editing a Test Adding a Drop command To add a Drop command to the Control step: 1. Select the Draw command you added in the previous section. 2. Select New Element from the Edit menu or press the Insert key. The Insert New Drop dialog box appears (Figure 5-5). Figure 5-5 Insert New Drop Dialog Box 3. Type 1 µl in the Volume text box. 4. Select Aqueous for the Liquid Class. 5. Select Destination Rack for the location Type 1 for Position X and 1 for Position Y. 7. Select the Change DITIS check box to end the command sequence. 8. Select 10 µl DITI from the drop-down list box. 9. Click OK to add the Drop command to the Control step. 5-6 Applied Biosystems

87 Adding Commands to the Control Step and Sample Step Adding a Mix command A Mix command mixes by aspirating and dispensing a specific volume of liquid a specific number of times. You can add a Mix command to all steps, but only immediately after a Drop command or at the start of a sequence. Add a Mix command to the Sample step to mix the sample before transferring it to the destination rack. To add a Mix command to the Sample step: 1. Select the Sample command. 2. Select New Element from the Edit menu or press the Insert key. The Choose New Command dialog box appears. Figure 5-6 Choose New Command Dialog Box 5 SymBiot I Sample Workstation Getting Started Guide 5-7

88 Chapter 5 Editing a Test 3. Select Mix and click OK. The Insert New Mix dialog box appears (Figure 5-7). Figure 5-7 Insert New Mix Dialog Box 4. Type 5 µl for the volume. 5. Type 5 for the cycle number in the Mix Cycles text box to specify the number of times the mix sequence (aspirate/dispense) should occur. 6. Select Aqueous for the Liquid Class. 7. Select Sample for the location for the workstation to mix sample Applied Biosystems

89 Adding Commands to the Control Step and Sample Step 8. Click OK to add the Mix command to the Sample step. The modified test should look like Figure 5-8. Figure 5-8 MY NEW TEST Modified 9. Select Save from the File menu to save the changes you made to MY NEW TEST. 10. Select Exit from the File menu. 5 SymBiot I Sample Workstation Getting Started Guide 5-9

90 Chapter 5 Editing a Test 5.4 Running Your Method In this section, you will add a tube containing control to the Matrix/Reagent Tray and run the method that specifies the edited test. To run the method you edited: 1. Place a 1.5 ml tube containing 1.0 ml matrix or water in the second position of the Matrix/Reagent tray. 2. Select Start from the Run menu or click the button. The Select Method dialog box appears (Figure 5-9). Figure 5-9 Select Method Dialog Box 3. Select MY METHOD and click OK. The Enter Number of Samples dialog box appears (Figure 5-10) Applied Biosystems

91 Running Your Method Figure 5-10 Enter Number of Samples Dialog Box 4. Type 12 for the number of samples. 5. Leave the First position In Sample Rack set to Click OK. The instrument layout appears (Figure 5-11) reflecting the racks and reagents you selected in MY NEW TEST and MY METHOD. 1.5 ml Reagent 1 Tip10 (Pipette tip rack) Microtiter plate Voyager sample plate 1.5 ml Reagent 2 Deck area Layout dialog box Reserve area Zoom view Status area 5 Figure 5-11 Instrument Layout (Scatter View) SymBiot I Sample Workstation Getting Started Guide 5-11