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ProteOn XPR36 User Manual

Protein interaction array system
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Protein Interaction Analysis
ProteOn
XPR36
™
Protein Interaction Array System
User Manual

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  • Page 1 Protein Interaction Analysis ProteOn XPR36 ™ Protein Interaction Array System User Manual...
  • Page 3 ™ ™ ProteOn XPR36 Protein Interaction Array System Version 3.1 User Manual...
  • Page 5 Bio-Rad. When running ProteOn Manager™ software in regions of the world where decimals are expressed as commas, an error reading floating point values might occur. Please use U.S. English numeric and date formats, as set in the Control Panel, to avoid this problem.
  • Page 6 Bravman T et al. (2007). Screening, ranking, and epitope mapping of anti- human IL–9 supernatants, Bio-Rad Bulletin 5540. Bravman T et al. (2008). The ProteOn™ XPR36 array system – high throughput kinetic binding analysis of biomolecular interactions, Cellular and Molecular Bioengineering, Vol.
  • Page 7 Bio-Rad Bulletin 5679. AFETY Your safety is important to us. The ProteOn™ XPR36 protein interaction array system contains components that, if handled improperly, are potentially harmful. The protection provided by the equipment can be compromised or the warranty voided if the equipment is used in a manner not specified by Bio-Rad Laboratories.
  • Page 8 OWER UPPLY An uninterruptible power supply is recommended to protect the ProteOn XPR36 from an unstable main power source, harmful spikes, surges or total blackouts. This table contains minimum specifications for an uninterruptible power supply that can be used with the ProteOn instrument.
  • Page 9 ERSONAL AFETY The ProteOn XPR36 instrument weighs 187 lb (85 kg). Follow all personal safety precautions when moving the instrument. If you must lift the instrument, use proper lifting techniques. Have two people lift the instrument, and use the lifting points indicated below:.
  • Page 10 ProteOn XPR36 System | viii...

  • Page 11: Table Of Contents

    Experiment Workflow ..........1 ProteOn Manager Software Features ....... . . 2 Software Overview .
  • Page 12 Experiment Preparation......... . . 64 Dissolving and Aliquoting ProteOn EDAC and Sulfo-NHS ..64 Preparing the Buffers .
  • Page 13 Flushing the System ........67 Preparing the Samples .
  • Page 14 ProteOn XPR36 System | Contents Choosing a Panel Type ......103 Selecting a Protocol Step for Analysis ....103 Grouping Data for Analysis .
  • Page 15 Software-Only Shutdown ........168 Exiting ProteOn Manager Software and the Instrument ... 168...
  • Page 16 Importing/Exporting Secure Files ..... . 182 ProteOn Manager Software Logs......182 Secure Documents .
  • Page 17 Ventilation ..........195 Inside the Instrument.
  • Page 18 Security Edition Hardware Protection Key (HASP Key) ... 233 ProteOn Manager Software Users and Groups ..... . . 234 ProteOn Manager Software User Groups .

  • Page 19: Chapter 1. Introduction

    ProteOn™ XPR36 instrument, the controller (the computer attached to the instrument), a HASP key, and ProteOn Manager™ software. This manual describes how to use the ProteOn XPR36 protein interaction array instrument with ProteOn Manager software. This chapter describes the experiment workflow and provides an overview of ProteOn Manager software.

  • Page 20: Proteon Manager Software Features

    ProteOn XPR36 | Introduction Steps Navigator Tab Navigator Tab Functions 5 Analyze the Analysis Displays only when an experiment is open; analyze datasets Datasets selected processed datasets and view existing analysis data ProteOn Manager Software Features Software feature descriptions and manual pages where they are discussed.

  • Page 21: Software Overview

    98 Security Edition Optional Security Edition aids compliance with U.S. FDA 21 CFR Part 11 regulations page 177 Software Overview ProteOn Manager software opens to the Instrument Control screen, with the Quick Start menu open: Title bar Menu bar Toolbar...

  • Page 22: Instrument Log

    • Navigation panel – includes tabs to choose among application functions, which follow the experiment workflow shown on page 1 NSTRUMENT ProteOn Manager software logs instrument and application events continuously. To open the Instrument Log screen: • Click Log in the navigation panel The instrument log displays the following columns of data: •...

  • Page 23: Status Bar

    To view specified time periods in the log: 1. Select the From Date in the Filter by Date box and enter the time. The defaults are the date and time when the current ProteOn Manager session began. 2. Select the To Date in the Filter by Date box and enter the time. The defaults are the current date and time.

  • Page 24: Quick Start Menu

    ProteOn XPR36 | Introduction UICK TART To display the Quick Start menu, select View Quick Start on the View menu. Use the Quick Start floating menu to create new protocols, open existing protocols, and analyze data. • New — opens the database browser to create a protocol, experiment, or template •...

  • Page 25: Proteon Manager Software Options

    Sensor Chip Temperature • Autosampler Temperature • Default Buffer Valve Position and Buffer Names To set ProteOn Manager software options: 1. On the Tools menu, select Options. The Options dialog box appears. 2. Edit the settings. 3. Click OK. Database Browser Views To access the database browser: •...

  • Page 26: Start Menu Options

    The same view choices are available in the Instrument Log and Audit Trail screens. Start Menu Options Several utilities are available through the Windows Start menu. Choose Start > All Programs > ProteOn > and the utility you want to use.

  • Page 27: Instrument Shutdown Utility

    To shut down the instrument while ProteOn Manager software continues to run: • Navigate to the Start > All Programs > ProteOn menu and choose Instrument Shutdown Utility A message displays the instrument’s progress as it shuts down. NSTRUMENT...

  • Page 28: Backing Up The Database

    ProteOn XPR36 | Introduction Backing Up the Database It is a best practice to back up the database frequently and keep the backup copies in a safe place. A USB or network hard drive is a good backup solution. Keep in mind that it can take 10–40 min to back up a large database.

  • Page 29: Installing Proteon Manager Software

    1. Insert the ProteOn Manager software 3.1 CD-ROM into a CD drive. 2. Double-click the file CDBrowserStart.exe. The Proteon Manager software splash screen appears. 3. Select Install ProteOn Manager in the upper right corner of the screen. The ProteOn Manager software Installation wizard appears.
  • Page 30 ProteOn XPR36 | Introduction 4. Click Next. The License Agreement screen appears. 5. Read the License Agreement, then click the button to accept it, and then click Next. The next screen shows default destination folders for the program files and the database. The drive with the largest available space is selected for the database.
  • Page 31 Installing ProteOn Manager Software 6. (Optional) To change the selected directory, click Change and select a new destination. If you select the D drive, the database is installed in the root directory. Note: The database can become as large as 40–50 GB. Choose a location that has 100 GB free.

  • Page 32: Upgrading From Earlier Versions (V. 2.1.N, V. 3.0, Or V. 3.0.1) To

    ProteOn XPR36 | Introduction 9. Click Finish when the installation ends. 10. Click the ProteOn Manager icon on the desktop to start the software. ProteOn Manager software opens and displays the main screen. Upgrading From Earlier Versions (v. 2.1.n, v. 3.0, or v. 3.0.1) to v. 3.1 While upgrading ProteOn Manager software, the installation wizard backs up and updates the database.
  • Page 33 Installing ProteOn Manager Software If you upgrade from ProteOn Manager v. 3.0 or from v.3.0.1 and you have previously run the optimizer, your database is already optimized and there is no need to run the optimizer again during upgrade to ProteOn Manager v. 3.1.
  • Page 34 ProteOn XPR36 | Introduction 3. Select Install ProteOn Manager in the upper right corner of the screen. The ProteOn Manager Software Installation wizard appears. 4. Click Next. The License Agreement screen appears. 5. Read the License Agreement, click the button to accept it, and then click Next.
  • Page 35 At the end of the optimization process close the dialog box. 13. Click the ProteOn Manager software icon on the desktop to start the software. ProteOn Manager software opens and displays the main...

  • Page 36: Reinstalling Version 3.1

    ProteOn XPR36 | Introduction Reinstalling Version 3.1 In the event that ProteOn Manager software v. 3.1 has been uninstalled and its data remain unchanged, you can reinstall v. 3.1 and continue to use the database that is already on disk.

  • Page 37: Importing Example Chip Conditioning Protocols

    Once you have installed ProteOn Manager software, you can import example chip conditioning protocols. These protocols are located on the disk drive where you installed ProteOn Manager, at Bio-Rad > ProteOn Manager > Chip Conditioning and Example Protocols. Importing Files from Another Computer Experiments and protocols can be transferred from the instrument controller to a stand-alone computer or drive for convenience and backup.

  • Page 38: Saving/Exporting Data

    3. Click Import. Saving/Exporting Data ProteOn Manager software automatically saves your data to a database. The data can be exported into a variety of file formats. See Saving and Exporting Data on page 141 for details. Importing Data from Previous Versions Data from previous versions (2.1, 3.0, 3.0.1) can be imported into the new...

  • Page 39: Starting And Exiting Proteon Manager Software

    Note: You must first start the instrument and then wait 2 min before starting ProteOn Manager software. To start ProteOn Manager software: • Select ProteOn Manager from the Windows Start menu or double- click the ProteOn Manager desktop icon ProteOn Manager software opens and displays the Instrument Control screen. XITING First, follow the guidelines in Shutdown Procedures on page 166.

  • Page 40: Proteon Xpr36 Instrument

    ProteOn XPR36 | Introduction ProteOn XPR36 Instrument Starting the Instrument To start the instrument: • Locate the on/off switch on the lower left side of the instrument and switch the power on System Shutdown There are three shutdown methods, each with its own uses and maintenance requirements.

  • Page 41: Status Bar Instrument State Messages

    Either the instrument has not yet been turned on or it has not finished initial startup operations. Note: You must turn on the ProteOn XPR36 instrument before starting ProteOn Manager software. If the software is started when the instrument is not connected or is powered down, the state remains Inactive.

  • Page 42: Power Up State

    ProteOn XPR36 | Introduction OWER TATE When communication is established and the instrument is ready to receive commands, it goes into Power Up state. From this time on, the computer monitors the current values of instrument parameters. Temperature control begins as soon as the powering-up process is complete in order to stabilize the instrument.

  • Page 43: Stop State To Ready State

    ProteOn XPR36 Instrument To interrupt the protocol: • Click Cancel, Stop, or Abort If a critical error is discovered, the instrument interrupts the protocol. At the end of the experiment, the state changes to Ready. TATE TO EADY TATE To change the state from Running to Stop: •...

  • Page 44: Maintenance State

    The instrument state changes to Shutting Down while performing the shutdown operations. If ProteOn Manager software remains open, the instrument returns to the Inactive state. The instrument cannot be reconnected in this state.

  • Page 45: Flushing State

    The system can be primed only on the Maintenance screen in ProteOn Manager software. See Priming the System on page 66.

  • Page 46: Selecting Buffer Bottles

    UFFER OTTLES The two ProteOn XPR36 instrument buffer bottles can hold either identical or different fluids. At any given time, the fluidics system is connected to a single source. The fluids for both syringe pumps flow from a single buffer bottle.
  • Page 47 ProteOn XPR36 Instrument Flushing the System with ProteOn Manager Software You can select buffer bottles with ProteOn Manager software by using the left (Buffer A) and right (Buffer B) buttons on the Instrument Control screen. The Buffer buttons switch the buffer valves between the right and left buffer bottle positions.
  • Page 48 ProteOn XPR36 | Introduction Selecting Buffer Positions with the Instrument Buttons State or Action Description Diagram Running state with The system is running a protocol using Buffer A Buffer A. The green LED indicates that the left bottle is the active source in this case.

  • Page 49: Chapter 2. Protocol Design

    Creating and Saving Protocols Protocols contain the instrument configuration settings, sample information, and the workflow for an experiment. Using ProteOn Manager software, you can create protocols at the time an experiment is run or create them ahead of time to store on the controller (the computer attached to the instrument) or on a separate workstation running ProteOn Manager software.
  • Page 50 ProteOn XPR36 System | Protocol Design To create a protocol from a template: 1. Select New in the File menu or on the Quick Start menu to open the database browser. 2. Select a template. The Template and Protocol checkboxes are selected by default.
  • Page 51 Creating and Saving Protocols 4. In the Steps screen, select a step and change its value in the Step Details area of the screen. Note: To change the configuration for all the active steps, change its value in the Step Default Injection Parameters table on the Configuration screen.
  • Page 52 ProteOn XPR36 System | Protocol Design added rack or plate. Analyte concentrations must be added before performing an analysis • Click Protocol in the navigation panel, and then click Steps. Edit the protocol in the Protocol Steps screen. An empty sample panel...

  • Page 53: Creating A Protocol From Rack/Plate Contents

    Creating and Saving Protocols Note: You cannot edit protocol steps while running an experiment. You can, however, pause the run and then edit any steps that have not yet been performed. 8. To add steps to a protocol, select a step group or step and drag it into the Protocol Steps list.
  • Page 54 ProteOn XPR36 System | Protocol Design To create a protocol from rack/plate contents: 1. Select the Protocol tab, and then select the Samples screen. 2. In the Step Creation area, select Create Protocol. The Create Protocol From Samples dialog box appears, in which you can build a cycle of steps.

  • Page 55: Creating Sample Data From A File

    1. Open an experiment. 2. In the Data tab, select File Export > Sample data. The sample data are exported as a text file in a format that can be imported into ProteOn Manager software. 3. Delete the data from the file and use the basic format to enter your tab-...

  • Page 56: Configuring Protocols

    ProteOn XPR36 System | Protocol Design Configuring Protocols On the Protocol Configuration screen you can edit the protocol name and description, view chip information, specify autosampler configuration (microplate or rack), and specify sample volumes to use in an experiment. To access the Protocol Configuration screen: •...
  • Page 57 Configuring Protocols When a chip is loaded, Chip ID, Expiration Date, and Date Used are automatically populated for the chip. For experiments, the inserted chip must be the same type that is specified in the protocol. If they do not match, a warning appears. If the chip type is not changed, the software updates the Chip panel;...
  • Page 58 ProteOn XPR36 System | Protocol Design or well volume. If the sample panel volume exceeds the well volume, the Required Volume box on the Samples screen turns red as a warning. Note: After you select Start on the Run screen, the autosampler parameters cannot be changed.

  • Page 59: Editing Protocol Sample Details

    Editing Protocol Sample Details Needle Pre-Wash menu — controls the setting and volume of needle washes performed before sample injection Setting Inside of Needles Outside of Needles Minimum 0.5 ml 0.5 ml Medium 0.5 ml 1.0 ml Maximum 0.5 ml 1.5 ml Needle Post-Wash menu –...

  • Page 60: Importing And Adding Racks/Plates

    ProteOn XPR36 System | Protocol Design Importing and Adding Racks/Plates For more information about importing sample data, see Creating Sample Data From a File on page 37. In the Racks/Plates area you can import, add, and delete racks and plates.
  • Page 61 Editing Protocol Sample Details 2. In the Sample Data Import dialog box, click Browse to find a sample rack or plate configuration file, and click Open. When the data appear in the Sample Data Import table, click Import. 3. If the file contains descriptive headers in the first row instead of sample information, select the Contains header row box to remove the first row.

  • Page 62: Creating Protocol Steps From Sample Panels

    ProteOn XPR36 System | Protocol Design To delete racks or plates: • Click Delete to remove a rack/plate from the sample panel browser. A rack or microplate can be deleted only if no sample is associated with it Note: A single sample cannot be removed using this option.

  • Page 63: Sample Panel Browser

    Editing Protocol Sample Details Sample Panel Browser The Sample Panel browser on the Samples screen shows the following for each sample panel. • Rack/Plate ID — displays an identification number assigned to the rack or microplate. Racks and plates appear in the order they are created •...

  • Page 64: Changing Sample Positions Or Copying Samples

    ProteOn XPR36 System | Protocol Design across the sensor chip. You can add a sample panel to more than one step The following table describes the panel types in the read-only box. Panel Types Description Activator Reagents used in an activation step...

  • Page 65: Autosampler Layout

    Editing Protocol Sample Details To drag a sample panel: • Drag the selected panel to a new position. An alert asks if you want to proceed. The dropped panel overwrites the panel in the new position To copy and paste a sample panel: 1.

  • Page 66: Creating And Editing Protocol Steps

    ProteOn XPR36 System | Protocol Design Creating and Editing Protocol Steps On the Protocol Steps screen you can build a protocol by adding, deleting, and modifying protocol steps and step groups. The Protocol Steps screen consists of the Protocol Editor panel and the Steps Details panel. In the Protocol Editor panel you can view and link these steps together to create a protocol.

  • Page 67: Setting Injection Steps

    Creating and Editing Protocol Steps Setting Injection Steps Interaction analysis protocols consist of up to 12 types of steps. Use the Protocol Editor panel to add or delete steps and step groups. View and link these steps together to create a protocol. If you use a template, the step list populates, and you can edit the steps as needed.

  • Page 68: Protocol Editor

    ProteOn XPR36 System | Protocol Design To reposition a step or step group: • Drag it to the new location To navigate the Protocol Steps list: • Use the keyboard arrow keys or the arrow buttons located at the top of the Protocol Steps listTo delete a step: •...

  • Page 69: Copying And Pasting Protocol Steps

    Creating and Editing Protocol Steps The following step types can be dragged from the Step list. Step Type Description Activate Activation of the sensor chip surface (for amine coupling GLC, GLM, and GLH sensor chips only) Ligand Control of ligand flow across the sensor chip for immobilization Deactivate Deactivation of the sensor chip surface (in amine coupling GLC, GLM, and GLH sensor chips only)

  • Page 70: Editing Injection Step Details

    ProteOn XPR36 System | Protocol Design Paste Regenerate always uses the same sample location. This option notifies you when you have overdrawn the sample. To copy and paste protocol steps: 1. In the Protocol Steps list, select a step or step group.
  • Page 71 Creating and Editing Protocol Steps • Show the interaction layout View and edit injection step parameters Assign sample panels Interaction layout If you want your sample to be drawn from a specific location on the rack, you can specify where you want it to be drawn from in the pull-down list in the Step Details area on the Protocol Steps screen.
  • Page 72 ProteOn XPR36 System | Protocol Design Protocol Step Details — lists protocol types, some of which can be changed. The appearance changes depending on the type highlighted. If a step group is highlighted, the name and type appear. If a step is highlighted, the details in the following table appear (depending on the step type).

  • Page 73: Setting The Buffer Step

    Creating and Editing Protocol Steps Interaction viewer — located at the bottom of the Step Details panel, displays the orientation of the current injection and the flow direction for sample application, and indicates how the samples are to interact with each other.

  • Page 74: Setting The Temperature Step

    Setting the Temperature Step Use the Set Temperature step to change the chip/flow cell temperature in the ProteOn™ XPR36 system during an experiment when the instrument is unattended. When the temperature change request is sent, the protocol pauses until the chip reaches the new temperature.

  • Page 75: Setting The Change Rack Step

    Creating and Editing Protocol Steps To set the temperature step: 1. In the Protocol Editor, select Set Temperature in the Step list. The setting appears in the Protocol Steps list and its details appear in the Step Details panel. 2. You can enter a step name that is up to 32 characters long. The default name is Set Temperature.

  • Page 76: Setting A Pause Step

    ProteOn XPR36 System | Protocol Design When a rack change executes, the protocol pauses until the pause time runs out or until you click Start on the Run screen. Setting a Pause Step Use a Pause step to stop the instrument for buffer changes or for other reasons.

  • Page 77: Protocol Check

    Protocol Check Protocol Check Protocol Check displays a combined view of the entire protocol in tabular form. This table format makes it easy to double-check large protocols quickly before running experiments. Steps are color coded so you can easily identify their status and view the cycle of steps.
  • Page 78 ProteOn XPR36 System | Protocol Design To close the Column Chooser: • Click Close To filter a column on a single entry: 1. In the column head, click the Funnel icon to display the list values for that column. 2. Select a value. The column now displays only the value you selected.

  • Page 79: Protocol And Sample Reports

    Protocol and Sample Reports Protocol and Sample Reports The protocol report documents how the experiment is to be run. This report lists all protocol steps, instrument configuration, chip information, and sample panels associated with each step. The sample layout report lists all samples used in the protocol and the quantity of material required in each vial or microplate well.
  • Page 80 ProteOn XPR36 System | Protocol Design To generate a protocol or sample report: • In the Protocol panel, click Protocol Report or Sample Report. To print a protocol or sample report, do one of the following: • Select Print in the File menu, and then click the report you want to print •...

  • Page 81: Chapter 3. Experiments

    Manager™ software • Ligand and analyte • ProteOn sensor chip • ProteOn amine coupling kit (required for GLC, GLM, and GLH sensor chips) • Immobilization buffer (for example, ProteOn acetate buffer pH 4.0, 4.5, 5.0, or 5.5) • Running buffer (for example, ProteOn phosphate buffered saline with 0.005% Tween 20, pH 7.4)

  • Page 82: Experiment Preparation

    1. Store EDAC and sulfo-NHS powder at –20°C to –80°C before use. 2. Add 75 ml cold deionized or distilled water to ProteOn EDAC (0.575 g) to dissolve it and rinse it out of its bottle. The final concentration will be 40 mM.

  • Page 83: Preparing The Buffers

    To load the buffers: 1. Remove a 2 L bottle of running buffer (for example, ProteOn PBST, pH 7.4) from the refrigerator. 2. Take approximately 15 ml of the buffer, place it in a 50 ml conical...

  • Page 84: Priming The System

    The system can be primed only using ProteOn Manager software. Prime the system under the following conditions: •...

  • Page 85: Flushing The System

    You can flush the system manually using the buffer control buttons on the instrument, or in ProteOn Manager software. See also Flushing and Priming the System on page 27.

  • Page 86: Preparing The Samples

    Samples should be particulate free and degassed. To prepare the samples: 1. Dissolve and aliquot the ProteOn EDAC and sulfo-NHS. See To set up a sample holder: on page 69. 2. Remove the required quantities of EDAC and sulfo-NHS from the freezer and keep them on ice.

  • Page 87: Setting The Autosampler Temperature

    Preparing the Samples To set up a sample holder: 1. Place the vials in the appropriate sample holder, according to the Protocol Samples screen placement. See Sample Panel Browser on page 45. See also Sample Holders on page 203 for an illustration of microplates and sample racks.

  • Page 88: Sensor Chips

    ProteOn XPR36 | Experiments 2. In the Autosampler Temperature area, type a temperature value in the Temperature box. 3. Click Set. To set the default autosampler temperature: • Select Options on the Tools menu and specify the autosampler temperature in the dialog box that appears...

  • Page 89: Sensor Chip Types

    Sensor Chips Sensor Chip Types Type Chemistry Applications (and Color) Compact polymer layer containing easily Kinetic analysis (magenta) activated carboxylic groups for general amine Equilibrium analysis coupling. The compact planar structure yields a Concentration determination ligand capacity of about one monolayer Immobilization scouting Regeneration scouting Analyte screening...

  • Page 90: Storage And Temperature Equilibration

    Opening the Sensor Chip To open the sensor chip: 1. Remove the aluminum pouch containing the ProteOn sensor chip from its box and allow the pouch to come to room temperature before opening. The chip is stored at 4ºC. Allow 0.5–1.0 hr for temperature equilibration.

  • Page 91: Conditioning The Sensor Chip

    A set of conditioning protocols and an example protocol are available at the following location on your computer on the hard drive you selected: \Program Files\Bio-Rad\ProteOn Manager\Chip Conditioning and Example Protocols. You can load and save the protocols as templates by selecting File > Save As Template in ProteOn Manager software.
  • Page 92 ProteOn XPR36 | Experiments Default Injection Quality and Needles Washes μ Step Type Orientation Composition Volume, Regeneration 0.5% SDS Regeneration 50 mM NaOH Regeneration 100 mM HCl Regeneration 0.5% SDS Regeneration 50 mM NaOH Regeneration 100 mM HCl Samples Layout...

  • Page 93: Nlc Sensor Chip Conditioning

    Sensor Chips NLC S ENSOR ONDITIONING Note: Trehalose is used as a protective layer for the dry NeutrAvidin on the chip surface. We believe the trehalose is completely removed by continuous buffer flow over the chip surface. However, adding one or two blank buffer injections using chip conditioning prior to the first expermental injection should ensure complete removal.

  • Page 94: Initializing The Chip

    Inserting and Ejecting the Sensor Chip To insert the chip: 1. Cut open the pouch containing the temperature-equilibrated ProteOn sensor chip and insert it into the instrument chip loader. The chip ID,...

  • Page 95: Chip Loader Leds

    Sensor Chips chip chemistry, and chip expiration date populate the Chip Details area of the Sensor Chip group box. 2. Choose one of the three Initialization options (Air Initialization, Glycerol Initialization, or Use Last Initialization). The initialization process takes a few minutes.

  • Page 96: Setting Sensor Chip Temperature

    To set the default chip temperature: • Select Options on the Tools menu and specify the chip temperature in the dialog box that appears. See ProteOn Manager Software Options on page 7. To set the sensor chip temperature on the Protocol Steps screen: 1.

  • Page 97: Reusing Chips

    Sensor Chips If the temperature is out of range, the actual temperature appears in red. When an experiment starts, the actual temperatures are validated against the protocol temperature and a warning appears if there is a mismatch. This does not prevent the experiment from continuing. Reusing Chips If a chip has had ligand immobilized on fewer than six channels during its previous insertion, you can reinsert the chip and immobilize ligand on the...

  • Page 98: Viewing Chip Information

    ProteOn XPR36 | Experiments • Once a chip is ejected, its ligand surfaces are exposed to air and can dry out, therefore, the activity of these surfaces cannot be guaranteed • Contaminants can collect on the optical faces of the chip, making the chip unusable and potentially contaminating the instrument Using a chip on multiple instruments is not supported.

  • Page 99: Running Experiments

    After you have made protocol and experiment preparations, you can run your experiment. Choose the Run tab to access the experiment controls. For more information on sensor chips and for full recommended protocols, see the booklet, ProteOn Sensor Chip Tips and Techniques. Run Tab Command Description Start begins running the experiment at the first nonexecuted step.
  • Page 100 ProteOn XPR36 | Experiments To run an experiment: 1. Prepare the instrument and chip following the instructions in Experiment Preparation on page 64. 2. Select a protocol to run using the Selected Protocol/Experiment pull- down list in the Run tab.

  • Page 101: Nonspecific Binding

    Running Experiments To select an option for viewing the data while the experiment runs: • To group the data by their associated ligand (vertical) channel, on the Data screen click Group by Ligand • To group the data by their associated analyte (horizontal) channel, click Group by Analyte.

  • Page 102: Experiments With Highly Refractive Cosolvents (Dmso)

    ProteOn XPR36 | Experiments Experiments with Highly Refractive Cosolvents (DMSO) In experiments where analytes are dissolved in highly refractive index cosolvents such as DMSO, the ligand surface produces a smaller bulk solvent response than the reference surface. This is known as the excluded volume (EV) effect.
  • Page 103 Running Experiments Figure 2. CA II/CBS interaction data with excluded volume correction. To run an experiment with highly refractive cosolvent: 1. Flush the instrument with running buffer without the cosolvent in it. Cosolvent should not be used in the running buffer unless it is known that it will not affect ligand immobilization.

  • Page 104: Saving And Exporting Experiment Data

    Processing EV Correction Data on page 115 for information on processing and analyzing EV corrected data. Saving and Exporting Experiment Data ProteOn Manager software automatically saves experiment data to the database. For information about exporting your experiment data, see Saving and Exporting Data on page 141.

  • Page 105: Managing Experiments

    Purging an experiment permanently removes it from the database. Purging experiments can take some time, and you cannot exit ProteOn Manager software while experiments are being purged. Purged experiments cannot be restored. Note: You cannot purge an experiment in the Security Edition.
  • Page 106 ProteOn XPR36 | Experiments 4. Click Yes to confirm purging the experiments. The deleted experiments are purged from the database.

  • Page 107: Chapter 4. Analysis

    ProteOn XPR36 System Analysis ProteOn Manager™ software collects, processes, and displays molecular interaction data in real time. You can view raw sensorgram data in the Run tab during or after an experiment. Next, you can use the data processing tools on the Data tab to align...

  • Page 108: Sensorgram Data Windows

    ProteOn XPR36 System | Analysis Sensorgram Data Windows Raw, processed, and analyzed sensorgrams appear as color-coded traces in separate data windows. Vertical bars indicate the start and stop times of each injection. The header of each data window names the protocol step and data grouping selected.

  • Page 109: Changing Sensorgram Appearance

    Tools for Viewing Data Hovering the mouse over a data window legend item displays an annotation consisting of the sample name and injection step number. Changing Sensorgram Appearance You can change the color and thickness of individual sensorgram lines, including fit lines. You might want to change sensorgram line color to increase print quality or to better distinguish one line from another.

  • Page 110: Changing Sensorgram Appearance In A Dataset

    ProteOn XPR36 System | Analysis 3. Click a color to select it or click More Colors to select a custom color. 4. When you have finished selecting colors, click Apply. The sensorgram lines appear in the colors you selected for them.
  • Page 111 Tools for Viewing Data 2. Right-click a sensorgram and choose Set Sensorgram Appearance in the menu that appears. The Color Chooser appears. 3. (Optional) To select colors for each step individually, clear the Apply for all steps checkbox. 4. In the Color Chooser, right-click a step, open the drop-down list, and select a color.

  • Page 112: Changing Sensorgram Views

    ProteOn XPR36 System | Analysis Changing Sensorgram Views By default, all sensorgram data windows appear above the data table. You can change the sensorgram view with the Expand/Collapse buttons below the sensorgram display. To view only the data table: •...

  • Page 113: Showing Interspot Data

    Tools for Viewing Data The following View menu options also change the appearance of sensorgrams. These options do not affect the analysis data. HOWING NTERSPOT Interspots are areas where there is no ligand on the channel of the chip. Showing interspots lines up the interspot data with the interaction data. To show interspot data: •...

  • Page 114: Viewing Kinetic Data In An Isoaffinity Graph

    ProteOn XPR36 System | Analysis IEWING INETIC ATA IN AN SOAFFINITY RAPH The isoaffinity graph enables you to visualize kinetics by plotting together the association and dissociation values in such a way that conclusions can be drawn from viewing all the different molecules. The x-axis displays association ), and the y-axis displays dissociation (k ).

  • Page 115: Visually Comparing Tabular Data In Screening Graphs

    Tools for Viewing Data To change x- or y-axis scale in the graph: • Select settings from the drop-down lists at the bottom of the isoaffinity graph dialog box. The graph refreshes each time you select a setting. To change the label of a scale value in the graph: •...
  • Page 116 ProteOn XPR36 System | Analysis 3. In the sensorgram display click Expand to view the data table. 4. In the data table, right-click in a data column and select Screening Graph. The graph appears in a separate window. To view a screening graph from the Analysis tab: 1.

  • Page 117: Excluding Sensorgrams From Manual Processing

    Tools for Viewing Data You can view information about the displayed points by hovering the mouse over them. Entering a value in the Threshold box displays the threshold as a red line across the graph. Click Apply to make the change. When the response level (or other value used for screening) on the different channels represents replicates, it is possible to display the averaged values across the channels.

  • Page 118: Comparing Data In Multiple Sensorgram Data Windows

    Sensorgrams added to the dataset pick up the automatic processing that has already been applied to the dataset. Manual processing does not apply to deselected data. In previous ProteOn Manager software versions, when new steps were added to a dataset, processing steps did not apply to them. In the current version, all the automatic processing steps you perform apply to all the sensorgrams in the dataset.

  • Page 119: Undo

    Tools for Viewing Data Use the Undo option on the Edit menu to undo actions. The Undo option maintains a history of actions. Select Undo and choose the action you want to undo. Undo works only with processing data. Use the Redo option on the Edit menu to redo actions. The Redo option maintains a history of actions.
  • Page 120 ProteOn XPR36 System | Analysis To update data in saved datasets in the Analysis Dataset screen: 1. Select the saved dataset in the Analysis Dataset screen. 2. Change the steps, data grouping, or sample information as needed. 3. Click Create dataset to save the dataset with the changes.

  • Page 121: Data Filters And Display Controls

    Tools for Viewing Data Data Filters and Display Controls Use the controls in the navigation panel to view and organize datasets for processing and analysis. The buttons on the Data tab (Panel Type, Protocol Step, Data Grouping, and Interaction) organize sensorgram data in the data windows. Data windows are redrawn when the selections in these controls are changed and Apply is selected.
  • Page 122 ProteOn XPR36 System | Analysis Window Grouping radio button options enable grouping of data as follows: • Group by Analyte — groups sensorgrams associated with one analyte channel into a single window • Group by Ligand — groups sensorgrams associated with one ligand channel into a single window •...
  • Page 123 Tools for Viewing Data Across Steps groups these data into six data windows, each showing a composite of all three protocol steps...
  • Page 124 ProteOn XPR36 System | Analysis • Combine and Concatenate Steps — displays data from multiple protocol steps chronologically in one window. For example, if Activator, Ligand, and Deactivator panel types (and their associated protocol steps) are selected, Combine and Concatenate Steps displays these immobilization steps from left to right in each window.

  • Page 125: Interaction Display Options

    Tools for Viewing Data Interaction Display Options Interaction options control the display of interaction data and whether or not to select sensorgrams for processing and analysis. To open the Interaction Display Chooser: • Click Interaction in the Data tab ISPLAY ONTROL The Display control grid represents the available interaction between the analytes (one analyte per row) and ligands (one ligand per column) in an...

  • Page 126: Processing Data

    ProteOn XPR36 System | Analysis • Select the Apply for all steps checkbox to apply the view state changes to the data of all protocol steps displayed in the Interaction Display Chooser • Clear the Apply for all steps checkbox to apply the view state...

  • Page 127: Data Processing Tasks

    Processing Data Data Processing Tasks SING THE OOLBAR The procedures that follow describe data processing actions using menu options. Alternatively, you can click the appropriate button in the toolbar. Data processing buttons on the toolbar are available in the Data tab. Note: For Report Points, see Specifying Report Points on page 121.

  • Page 128: Processing Multiple Tasks

    ProteOn XPR36 System | Analysis ROCESSING ULTIPLE ASKS Choose Auto Process on the Process menu to automatically perform the following tasks simultaneously: • Injection alignment • Baseline alignment • Artifact removal You can also set each option individually. LIGNING THE...

  • Page 129: Moving A Sensorgram

    Processing Data • Selected — removes all data in selected regions and draws a black line from the start and end points. The operation is applied only to sensorgrams that are selected and only in the selected graph windows. To remove artifacts: 1.
  • Page 130 The typical double referencing approach when using the ProteOn system is to collect double reference data in real time as part of the analyte injection itself (Row Reference).

  • Page 131: Displaying Real-Time Data

    Processing Data • Injection Reference — opens a wizard for double reference selection. In the Select Double Reference Injection Step wizard, select the data to be used as a double reference and click Finish ISPLAYING On the Run screen, you work with data being processed in real time using the following options in the Process menu: •...

  • Page 132: Remove Processing

    ProteOn XPR36 System | Analysis Keep in mind that the zero line in the sensorgram data window is not a marker. To hide markers: • Cancel Show Markers in the View menu or in the Markers menu that appears when you click Markers on the toolbar...

  • Page 133: Processing Ev Correction Data

    Processing Data Processing EV Correction Data Use the controls on the Data screen to select and group the analyte data for processing. See Data Filters and Display Controls on page 103. On the Data screen a wizard guides you through selecting reference types, excluding data points, and choosing calibration steps.
  • Page 134 ProteOn XPR36 System | Analysis 3. (Optional) To exclude data points, maximize the calibration plot with the erroneous data point by double-clicking it. Note: At least three data points (solid) must be selected from each calibration plot. 4. On the plot, click the data points you want to exclude. The excluded data point is represented by an empty circle.

  • Page 135: Working With Evc Calibration Plots

    Processing Data reference to a different excluded volume corrected channel reference and to launch the wizard • Do Not Change Reference — Select this option to cancel the channel reference change EVC C ORKING ALIBRATION LOTS Once you have excluded data points, use the context menu, available when you right-click in a plot, to work with the plot data: •...

  • Page 136: Creating A Dataset

    ProteOn XPR36 System | Analysis Creating a Dataset All input to the data screen is temporary until it is saved to a dataset. If you attempt to leave the data workspace without saving the data to a dataset, a message warns you that the data will be lost. To save the data to the database you must create a dataset.

  • Page 137: Deleting A Dataset

    Processing Data 2. Enter a name for the dataset in the dialog box. If the name is new and valid, OK becomes active. Click OK. Deleting a Dataset You can delete unsigned datasets and their associated unsigned analyses to organize and clean up your data as you move through different experiments. Note that deleting a dataset removes the affected data permanently.

  • Page 138: Analyzing Data

    ProteOn XPR36 System | Analysis Analyzing Data Interaction analysis consists of a numerical fit of multiple sensorgrams to a biochemical interaction model or other equation. Use processed datasets and the options available under the Analysis Datasets tab to perform an interaction analysis from an analysis set.

  • Page 139: Specifying Report Points

    Analyzing Data • Global — calculates one value for all sensorgrams • Local — calculates a different value for each sensorgram • Grouped —calculates one value for each sensorgram group (all the sensorgrams within a data window) Fit/Constant define how values are assigned: •...

  • Page 140: Specifying Report Points On Concatenated Data

    ProteOn XPR36 System | Analysis 3. Type a report point name. 4. (Optional) Adjust the report point range by selecting the Specify report point range checkbox and changing the start and end times in the From and To boxes. 5. If you want the report point to apply to all viewers, select Apply to all viewers.

  • Page 141: Viewing Report Points From A Dataset

    Analyzing Data IEWING EPORT OINTS FROM A ATASET Note that the analysis table displays the average of report point values for all sensorgrams in a group. The average is calculated by adding the report point values together and dividing them by the number of entries in the group. The report point average appears above the report point column.

  • Page 142: Saving Report Points To An External File

    ProteOn XPR36 System | Analysis AVING EPORT OINTS TO AN XTERNAL To save report points to an external file: • Copy and paste the data into an Excel file DDING A EPORT OINTS OLUMN At the end of each analysis wizard, you can add report points to the results tables.

  • Page 143: Deleting A User-Defined Column

    Analyzing Data To add a user-defined column: 1. Once a data table appears in the analysis wizard, right-click the table and choose Add user defined column. A dialog box appears. 2. In the User defined column name box, specify a name for the table column.

  • Page 144: Deleting An Analysis Set

    ProteOn XPR36 System | Analysis The following rules apply to renaming an analysis set: • Analysis set owners can rename their own analysis sets • The analysis set owner can be different from the experiment owner or dataset owner •...

  • Page 145: Kinetic Analysis Wizard

    Analyzing Data • Concentration analysis – determines the concentration of analyte in samples based on a set of standard samples If you want to exit a wizard, click Save to save the analysis data. Saving the data saves a partial analysis, which appears as a gray underlined title under the corresponding dataset.
  • Page 146 ProteOn XPR36 System | Analysis When you select Langmuir, you can choose whether to analyze both the on-rate (k ) and off-rate (k ) or to analyze just the off-rate: • Langmuir mass transfer — simple 1:1 biomolecular interaction, but where analyte diffusion to the surface is slower than the interaction.
  • Page 147 Analyzing Data In the latter instance, the two analytes compete and the higher affinity analyte replaces the data with the lower affinity • Heterogeneous ligand — interaction where one analyte binds two different ligand species. When ligands are bound to the surface of the chip, it is possible that they may be bound in different orientations, resulting in multiple ligands.
  • Page 148 ProteOn XPR36 System | Analysis Step 2: Regions and Parameter Setting Select a region for analysis by selecting a sensorgram, and then click Next. The default association and dissociation regions appear shaded on the graph. You can change the Begin and End times of the association and dissociation (the fit regions) by typing the values in the table.
  • Page 149 Analyzing Data It is possible to change the starting parameters for the fit calculation by typing the desired values in the table. When you want to use a pre-determined value for one of the fit parameters, change the Fit Type of this parameter to Constant, and type the requested value in the table.

  • Page 150: Equilibrium Analysis Wizard

    ProteOn XPR36 System | Analysis To save the analysis data: • Click Finish. The analysis is saved in the experiment and appears listed under its corresponding dataset. To save the data to a file: • Copy and paste or export the data.
  • Page 151 Analyzing Data A table displays the starting analysis parameters to be used in the calculation: • — maximum number of binding places in RU units • (Equilibrium dissociation constant) — affinity of the interaction, expressed in M units Select the Scope on the Global, Local, or Grouped pull-down list. Select the Fit Type on the Fitted or Constant pull-down list.

  • Page 152: Concentration Analysis Wizard

    ProteOn XPR36 System | Analysis To save the analysis data, click Finish. The analysis is saved in the experiment and appears under its corresponding dataset. ONCENTRATION NALYSIS IZARD Concentration analysis determines the concentration of analyte based on a set of samples of different known concentrations. For each standard sample, the sensorgram is analyzed to determine its slope at the start of the injection.
  • Page 153 Analyzing Data • Unknown: Samples whose concentration will be calculated from the standard curve To perform a concentration analysis of selected sensorgrams, use the Concentration Analysis wizard. To begin the wizard, select a processed dataset for analysis and then choose Concentration.
  • Page 154 ProteOn XPR36 System | Analysis Step 1: Region Selection and Analysis Parameters Select a region in a sensorgram for analysis by double-clicking a sensorgram and moving the vertical bars in the graph. The parameters are calculated for groups. Parameters include R...
  • Page 155 Analyzing Data Expanding an item in the table displays the sample names, sample types, and concentrations of the standards and controls. When you are satisfied with the selections, click Next to continue the Concentration Analysis wizard. Step 2: Results Preview Preview the results of the analysis.

  • Page 156: Ungrouping Analysis Results

    ProteOn XPR36 System | Analysis Go back to previous steps to make any necessary changes. To save the analysis data: • Click Finish. The experiment analysis is saved and appears under its corresponding dataset. To save the data to a file: •...
  • Page 157 Analyzing Data To write a filter query: 1. Hover over the column heading and select Filter Editor in the menu that appears. The Filter Editor opens. The column heading is already filled in. 2. Right-click Equals in the query shown to open a list of operators. 3.

  • Page 158: Sorting Analysis Results

    ProteOn XPR36 System | Analysis Sorting Analysis Results You can sort analysis data in ascending or descending order. In grouped views, sorting applies only within the groups. To sort analysis data in ascending or descending order: • Right-click in a column heading and select Sort Ascending or Sort Descending.

  • Page 159: Saving And Exporting Data

    ProteOn Manager software automatically saves data to the database. ProteOn Manager software provides several ways to export analysis data, depending on the kind of data you want to save and how you want to view it. You can export analysis data to a word processing file and sensorgram data into a Microsoft Excel file as a table or graph.

  • Page 160: Exporting Analysis Data

    ProteOn XPR36 System | Analysis 2. On the File menu, select Export, and choose the type of data to export. 3. In the Export dialog box, browse to the file location where you want to export data. Exporting Analysis Data When you export analysis data, the system exports a folder named for the experiment.

  • Page 161: Copying And Pasting Data To A File

    Saving and Exporting Data 5. Click Export. The system exports the data to the location you selected. Copying and Pasting Data to a File In addition to exporting the data stored in the database, you can copy and paste data and graphs to a Microsoft Excel file. When you paste data to an Excel file, it lines up in columns, and the column heads correspond to the sensorgram legends.

  • Page 162: Exporting Experiments To A File

    ProteOn XPR36 System | Analysis 3. Open an Excel file and paste the data or graph directly into the file. Exporting Experiments to a File You may want to export entire experiments for archival purposes, to analyze them on another computer, or to publish the results. The experiment file includes all data and all protocol settings and injection steps connected with the experiment.

  • Page 163: Reports

    Reports Reports You can print and save three types of analysis reports: • Kinetic analysis • Equilibrium analysis • Concentration analysis These report types are defined in Analysis Wizards on page 126. Reports can also be exported to a variety of file formats. Every report displays a header and footer.

  • Page 164: Customizing And Printing Reports

    ProteOn XPR36 System | Analysis Customizing and Printing Reports When you print a report, you can select the sections to include in it in the Report Options dialog box. Appropriate report options appear for each type of analysis (kinetic, equilibrium, or concentration).

  • Page 165: Exporting A Report

    Reports 3. Select the sections you want to include in the report and click OK. The system displays a preview of the report. 4. (Optional) In the Report Preview, select View > Report Options and add or remove sections of the report. The system displays a preview of your selections.
  • Page 166 ProteOn XPR36 System | Analysis...

  • Page 167: Chapter 5. Maintenance

    ProteOn XPR36 Maintenance Maintenance procedures are performed using a set of wizards operated within ProteOn Manager™ software, along with procedures the user performs on the instrument. They include a Prime, Weekly, Postexperiment, Clean MCM, Syringe maintenance/replacement, and the optional OQ procedure.

  • Page 168: Maintenance Chips (Mnt)

    When using a maintenance chip it is important to keep it clean. Before inserting a maintenance chip into the ProteOn™ XPR36 instrument, it should be removed from its cartridge and inspected to ensure it is clean. Never insert a dirty maintenance chip into the instrument.

  • Page 169: Cleaning Chips (Cln)

    Use a cleaning (CLN) chip to clean the multichannel module (MCM). A cleaning chip should be used at least once every three months for moderately used ProteOn XPR36 systems. Store cleaning chips at 4°C and allow the chip to warm to room temperature before use.

  • Page 170: Scheduled Maintenance Wizards

    ProteOn XPR36 | Maintenance • Dispose of solutions according to the instructions on their labels Scheduled Maintenance Wizards It is necessary to run the following maintenance wizards to keep the instrument in proper working order and ensure consistent results.The maintenance wizards are available on the Maintenance screen: •...

  • Page 171: Maintenance Protocol Solutions

    Instrument Maintenance Maintenance Protocol Solutions The following table lists all solutions needed for the wizards: Maintenance/Cleaning Purpose Chip Used Solutions Used Protocols Prime Pumps selected buffer through Selected buffer instrument fluids and through flow cell Weekly Wizard Detergent, base, sanitizing and rinse 2% Contrad 70 of instrument fluidics 70% Isopropyl alcohol*...

  • Page 172: Maintenance Wizard Instructions

    MNT chip and the Prime button on the Instrument Maintenance screen of ProteOn Manager software. To prime the system: 1. Load the running buffer. 2. Click Prime on the Instrument Maintenance screen of ProteOn Manager software. 3. Follow the prompts in the wizard. Weekly The Weekly wizard removes stubborn residues from the entire fluidics system.

  • Page 173: Postexperiment

    Maintenance Wizard Instructions Postexperiment This wizard provides routine detergent and acidic cleaning of the needles and sample lines. After cleaning, the whole fluidics system is flushed with DDW. This process is recommended whenever switching sensor chips is necessary. It is an injection-based protocol run with cleaning solutions. This wizard requires approximately 46 min to run.

  • Page 174: Syringe Maintenance

    ProteOn XPR36 | Maintenance 3. Click Clean MCM on the Instrument Maintenance screen of ProteOn Manager software. 4. Follow the prompts in the wizard. 5. Insert the CLN chip in the instrument when the wizard prompts you. Syringe Maintenance The following syringe cleaning and maintenance procedures are recommended to ensure optimum performance of the ProteOn XPR36 protein interaction array system.

  • Page 175: Starting The Syringe Wizard

    Maintenance Wizard Instructions TARTING THE YRINGE IZARD The Syringe Maintenance wizard is accessed on the Maintenance screen. 1. Click Syringe to start the wizard. The first screen appears: 2. Click Next to continue. The instrument lowers the syringes and the second screen appears:...
  • Page 176 ProteOn XPR36 | Maintenance The next screen directs you to remove the syringe pump compartment cover and inspect the syringes. Buffer syringes Sample syringes Syringe pump compartment Loosen thumbscrews Loosen thumbscrews Note: Your system may have hex nuts instead of thumbscrews. If so, your accessory kit contains the proper hex wrench to remove the hex nuts.
  • Page 177 Maintenance Wizard Instructions 3. Click Next to continue. The next screen displays instructions on how to remove the syringes. Refer to this illustration for part names: Metal Luer-Lok fitting Glass barrel Seal Plunger Knurled thumbscrew...
  • Page 178 ProteOn XPR36 | Maintenance 4. Click Next to continue. The next screen tells you what signs of wear to look for, and displays instructions for replacing worn syringes. You can also choose to clean the syringes that do not require replacement.

  • Page 179: Cleaning Syringes

    Maintenance Wizard Instructions Recommendations Syringes with Discard syringes that have rust stains on the plungers or rust stains glass barrels. Syringes leaking Discard syringes if liquid leaks onto the outside of the liquid syringe or if liquid drops under the syringe onto the compartment tray.

  • Page 180: Resuming The Wizard

    ProteOn XPR36 | Maintenance 4. Place the knurled thumbscrew through the plunger opening and turn it clockwise by hand or until it is finger tight. Caution: Hand tighten the syringes only. The use of tools can damage the syringe or the instrument.
  • Page 181 Maintenance Wizard Instructions 3. Check the connection between the metal Luer-Lok fitting and the polypropylene Luer fitting for leaks. Make sure all of the air in the syringes is replaced by fluid. 4. If you see leakage from any syringe, correct it by tightening the metal Luer-Lok.
  • Page 182 ProteOn XPR36 | Maintenance 6. When priming is complete, the Finish screen appears. Click Finish to exit the wizard. 7. Replace the cover to the syringe pump compartment. Slide the right edge of the cover into the rear of the instrument first, then slide the left edge of the cover into the side of the instrument, so that the slots align.

  • Page 183: Oq Protocol

    The OQ protocol can be run after the required quarterly maintenance to minimize instrument downtime. Quarterly Maintenance Schedule Multichannel module (MCM) cleaning Operation Qualification (OQ) Protocol For complete instructions on running the OQ Protocol, refer to the ProteOn XPR36 IQ/OQ Software User Manual, 100005737.

  • Page 184: Shutdown Procedures

    ProteOn XPR36 | Maintenance Shutdown Procedures The ProteOn XPR36 instrument and ProteOn Manager software do not need to be shut down as part of normal operation. Shutdown is only required when: • Switching users (close ProteOn Manager without instrument shutdown) •...

  • Page 185: Long-Term Shutdown

    • When restarting ProteOn Manager software and the ProteOn XPR36 instrument after an involuntary shutdown, the instrument goes into fault mode, and the chip inserted dialog box does not open when a chip is inserted •...

  • Page 186: Software-Only Shutdown

    Exiting ProteOn Manager Software and the Instrument The last option enables you to choose whether to close the software. Select the box to close ProteOn Manager software after any of the preceding shutdown procedures.

  • Page 187: Emptying The Collection Tank

    Shutdown Procedures Emptying the Collection Tank After shutting down the instrument, it is a good idea to check the collection tank. When the collection tank is full, dispose of the contents according to the rules of your facility.
  • Page 188 ProteOn XPR36 | Maintenance...

  • Page 189: Chapter 6. Proteon System Troubleshooting

    ProteOn XPR36 System ProteOn System Troubleshooting The ProteOn™ XPR36 instrument cannot be serviced by the user. This chapter helps you diagnose and prevent problems. If you find it necessary to seek help, download the Instrument Log described on page 4 to provide Technical Support with a complete history of the ProteOn instrument and application events.

  • Page 190: Nonspecific Binding

    Knowing the properties of an analyte can help assess the NSB source. The Quality Control procedures used in the manufacture of ProteOn sensor chips contain a standard test for NSB. However, certain molecules, such as those described above, may still cause NSB. This is because NSB can also come from inadequate cleaning of the ProteOn fluidics, running an inappropriate buffer, and a number of other causes.

  • Page 191: Addressing The Causes Of Nsb

    Nonspecific Binding DDRESSING THE AUSES OF There are a number of methods to prevent NSB. These are specific to the nature of each NSB and listed in order of importance. • Optimize the appropriate running and sample buffer for your application (see the effects of working with positively charged proteins, above) •...

  • Page 192: Firewall Settings

    The files that must be able to run in order for ProteOn to Manager™ software to communicate with its computer controller are ProteOn.exe, TCPCommunicationService.exe, and MySQLd-NT.exe.

  • Page 193: High Throughput Screening Analyses

    High Throughput Screening Analyses High Throughput Screening Analyses ProteOn Manager software can collect and process a maximum of 1,500 protocol steps or analyte samples in a large screening study. However, there are a few temporary recommendations for the number of analytes that should be analyzed simultaneously within these large datasets.
  • Page 194 ProteOn XPR36 System | ProteOn System Troubleshooting...

  • Page 195: Chapter 7. Security Edition

    Professional operating system to provide a secure environment for the maintenance, verification, and tracking of all electronic records generated by the application. These records include experiments, processed data, analyzed data, report points, and ProteOn Manager software logs. The tools provided in the software include: •...

  • Page 196: Standard Mode Vs. Secure Mode

    21 CFR Part 11. Standard Mode vs. Secure Mode ProteOn Manager software, Security Edition can run in Standard mode, in which the security and audit trail features are disabled, or it can run in Secure mode, with the security functions enabled. When in Standard mode, the...

  • Page 197: Enabling And Disabling Secure Mode

    5. Enter your ProteOn administrator user name and password and click OK. Secure mode is enabled. 6. When the ProteOn Manager login dialog box appears, enter a user name and password to continue using ProteOn Manager software or click Cancel to exit the software.

  • Page 198: Users, Passwords, And User Levels

    Note: Contact your Windows system administrator about issues regarding your user name and password. Each user is assigned to a user level. There are five user levels in ProteOn Manager software, Security Edition, and each level gives the user access to specific features and functions of the software.

  • Page 199: User Authentication

    Perform Service operations Delete files UTHENTICATION ProteOn Manager software, Security Edition requires a user name and password at key points during operation. User authentication creates an electronic audit trail of user activity that cannot be altered or deleted. Users are required to enter their user name and password when they: •...

  • Page 200: File Security And Validation

    When you move secure files from one secure system to another secure system, ProteOn Manager software validates the files to ensure that they have not been damaged or changed. If such a file has been changed in any way, an error message notifies you that the file has failed an integrity check;...

  • Page 201: Signed Files

    Signed Files Experiments, processed data, analysis data, and report point tables become secure files when they are created in Secure mode using a user name and password and are electronically signed. Changes to these documents are tracked in the audit log, and the user must specify a reason for the change.

  • Page 202: Signed Datasets And Analysis Sets

    ProteOn XPR36 System | Security Edition 3. In the Electronic Signature dialog box, the signing party enters their user name and password in the appropriate fields. (The signer may be someone other than the current user.) The reason for signing the document must be entered in the text box.
  • Page 203 Examples of auditable actions include: • Signing a file • Changing Protocol parameters (samples, volumes, concentration, etc.) • Changing document names • Adding or deleting user-defined or Report Point columns to an analysis • Creating or deleting report points Minor changes that affect the display only, such as selecting different columns in the Report Point table, Zoom In/ Zoom Out, or maximizing a view window are not audited.

  • Page 204: Viewing The Audit Trail

    ProteOn XPR36 System | Security Edition IEWING THE UDIT RAIL To view the audit trail for any document: 1. Open the document. 2. Go to the Security menu and select Audit Trail. The audit trail dialog box opens and displays the document’s audit log.

  • Page 205: Protected Directories

    Protected Directories Your Windows system administrator may set up protected directories on your computer or computer network for the secure storage of exported ProteOn Manager software transfer files or other data. These protected directories must be set up using Windows tools and are keyed to your Windows user name and password (which may be different from your ProteOn Manager software user name and password).

  • Page 206: Changing Data Ownership

    ProteOn XPR36 System | Security Edition Changing Data Ownership When the responsibility for specific data moves to another user, it is necessary to change the permissions connected with the secure data. Choose File > Take Ownership to transfer ownership. An Administrator must approve the transfer.

  • Page 207: Proteon Xpr36 Instrument And Peripherals

    Appendix Instrument and Peripherals The main components of the ProteOn™ XPR36 instrument are the chip loader, autosampler, microfluidics system, the optical unit where the surface plasmon resonance (SPA) measurement takes place, and all the supporting peripherals that sustain stable temperatures and facilitate the implementation of an experiment.

  • Page 208: Instrument Front View

    ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals Instrument Front View All components of the ProteOn XPR36 instrument that must be accessed during an experiment are located at the front of the instrument.

  • Page 209: Instrument Side View

    Instrument Side View Instrument Side View The right side of the instrument contains the two sets of syringe pumps. See Syringe Pumps on page 204 for more information.

  • Page 210: Instrument Leds

    ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals Instrument LEDs LEDs indicate (from top to bottom): instrument status, chip temperature, autosampler temperature, autosampler status, and experiment status. Different colors (flashing or steady) indicate different conditions for each component. See Component Status LEDs on page 22 for the key to each...

  • Page 211: Chip Loader And Chip Eject Button

    The sensor chip inside the cartridge is not visible. Note: You can also eject the chip with ProteOn Manager™ software. See Inserting and Ejecting the Sensor Chip on page 76. Buffer Control Buttons Use the buffer control buttons to switch between the left and right buffer bottles.

  • Page 212: Serial Numbers

    ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals respectively. These buttons are not active (the LEDs are off) when an experiment is in progress • Use the Stop button to stop the pumps in the following circumstances: (1) to replace the current buffer bottle, and (2) to change the buffer source bottle (switch the valve) from the buffer A bottle to the buffer B bottle.

  • Page 213: Cables And Power Switch

    Instrument Side View Cables and Power Switch The left side of the instrument contains the power switch, a covered row of ports reserved for service, the power cord connection (plugs into a 100–240 V universal outlet), and a port (above the power cord connection) for the custom communication cable to the controller.
  • Page 214 ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals Warning! Do not put papers or other materials underneath the instrument because they may be sucked up against the intake unit and block air flow.

  • Page 215: Inside The Instrument

    Inside the Instrument Buffer System The two ProteOn buffer bottles can hold either identical or different fluids. At any given time, the fluidics system is connected to a single source. The fluids for both syringe pumps flow from a single bottle.

  • Page 216: Microfluidics System Components

    ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals Microfluidics System Components The ProteOn XPR36 microfluidics system controls the flow of samples (shown here in green) and buffer (blue) over the sensor chip. The primary microfluidics components are the autosampler (to store and load samples) and the syringe pumps and valves (for injecting samples and running buffer over the chip through the multichannel module).

  • Page 217: Autosampler

    The autosampler consists of the needle holder, thermal platform, three sample holder sensors, and needle wash station. Shown below are two ProteOn microplates in the left system, and one ProteOn sample rack in the right system. Lighting in the autosampler compartment works in two different modes: Auto and On.

  • Page 218: Needle Holder With Sampling Needles

    ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals Needle Holder with Sampling Needles The needle arm moves the sampling needles into position for sampling and for needle washing. The needle holder maintains the six sampling needles in the proper configuration and is covered by a safety needle guard.
  • Page 219 Inside the Instrument • Use the 1.5 mm hex wrench to remove and replace the needle safety guard when changing the needle holder • Use the 3.0 mm hex wrench to change between the rack and microplate needle holder • Use the fitting wrench to remove and replace the finger tight fittings on the needle holders when either changing the needle holder or replacing one or more needles...

  • Page 220: Wash Station

    ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals Wash Station Autosampler needles are cleaned at the wash station between successive sample injections. Buffer pumped through and around the needles washes residual sample out of the wells and off the external needle surfaces. The wash station is designed to accommodate both microplate and rack needle holders.

  • Page 221: Sample Holders

    Inside the Instrument Sample Holders The ProteOn XPR36 instrument uses three types of sample holders: • ProteOn Sample Rack — removable rack that fits on the thermal platform and holds ProteOn sample vials. The rack is labeled A–L, left to right, along the front. It is labeled 1–6, front to back, along the left side •...

  • Page 222: Sample Holder Sensors

    ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals Warning! You must use the needle holder corresponding to the type of sample holder you are using. Failure to use the correct needle holder will result in damage to needles and possibly to other components.

  • Page 223: Multichannel Module

    Inside the Instrument ULTICHANNEL ODULE The multichannel module (MCM) is the centerpiece of the ProteOn XPR36 microfluidics system. The MCM has six parallel channels. When pressed on the sensor chip surface, the MCM forms a set of six flow channels. Ligand- containing fluid flows through these channels during the immobilization step.

  • Page 224: Reservoir, Overflow Sensor, And Drain Pump

    Computer and Display The ProteOn XPR36 system is supplied with a computer controller running Microsoft Windows XP operating system, a 19" display, keyboard, mouse, ProteOn Manager software, and Microsoft Office software.

  • Page 225: Hasp Keys

    One Standard Edition or one Security Edition HASP key must be attached to the computer’s USB port to run ProteOn Manager software. The second can be used to run ProteOn Manager software on a separate workstation.
  • Page 226 ProteOn XPR36 System | A ProteOn XPR36 Instrument and Peripherals...

  • Page 227: Specifications And Requirements

    Refractive index range: 1.33–1.37 refractive index units (RIU) • Dynamic range: 1–40,000 response units (RU) • ProteOn XPR36 system is verified to have 1 RU set = 1 x 10 • Baseline noise: <1 RU, 1–20,000 RU <1.5 RU, 20,000–40,000 RU •...

  • Page 228: Working Ranges (Typical Values)

    ProteOn XPR36 | B Specifications and Requirements Working Ranges (Typical Values) • Association rate constant (k ): 3 x 10E to 3 x 10E • Dissociation rate constant (k ): 5 x 10E to 6 x 10E • Equilibrium dissociation constant (K ): 2 x 10E to 1.6 x 10E...

  • Page 229: Installation Requirements

    Installation Requirements Installation Requirements The ProteOn™ XPR36 protein interaction array system is unpacked and installed by a Bio-Rad field service engineer. Please call your local technical support office (see www.bio-rad.com/contact/). In the US, call 1-800- 4BIORAD (1-800-424-6723) to schedule the installation. A preinstallation checklist for the ProteOn XPR36 system will be provided.

  • Page 230: Environmental Requirements

    15–30ºC is recommended. The recommended ambient humidity range is 10–75% relative humidity. Chemical Compatibility The ProteOn XPR36 instrument is compatible with all ProteOn reagents, solutions, and buffers, and under all conditions using any of the protocols described in this manual.

  • Page 231: Surface Plasmon Resonance

    6 x 6 interaction array for analyzing up to six ligands with up to six analytes. The detection principle of the ProteOn XPR36 system is based on SPR measurement. SPR is an optical effect that, in the ProteOn XPR36 system, occurs on the surface of a thin layer of gold that coats a high refractive index glass prism (the sensor chip).

  • Page 232: Interaction Analysis

    Interaction Analysis For interaction analysis with the ProteOn XPR36 system, one interactant (the ligand) is immobilized on the sensor chip surface, and the other interactant (the analyte) is passed in solution over that surface. The analysis consists of a series of steps and the requirement for each of these steps depends on sensor chip chemistry.

  • Page 233: Ligand Immobilization Process

    Amine coupling uses primary and secondary amine groups in the ligand for coupling with carboxy-coated sensor chips. The carboxylic groups on the sensor chip surface (for example, ProteOn GLC, GLH, and GLM chips) form amide bonds with the ligand. ONCOVALENT...

  • Page 234: Activation Step (Amine Coupling)

    Activation Step (Amine Coupling) ProteOn GLC, GLM, and GLH sensor chips are used for amine coupling, which requires activation of the carboxylic groups on the chip surface. The ProteOn NLC sensor chip, which is precoated with NeutrAvidin, does not require activation.
  • Page 235 The concentration, flow rate, and injection times for the activating agents all influence the extent of activation. ProteOn GLC sensor chips have easily activated carboxylic groups and a binding capacity of approximately one protein monolayer, while GLM sensor chips have easily activated...
  • Page 236 ProteOn XPR36 System | C Surface Plasmon Resonance carboxylic groups and moderately enhanced binding capacity. GLH sensor chips have a polymer matrix layer with high binding capacity, and are used for general amine coupling. The following table provides general guidelines for ligand immobilization levels,...

  • Page 237: Determining The Optimum Ph For Immobilization

    Determining the Optimum pH for Immobilization • Contact time — Increasing the contact time of ligand with the chip surface increases immobilization levels up to the point that saturation is reached, or the intermediate active ester groups have decayed away. Limit contact time to what is necessary to preserve ligand samples.

  • Page 238: Deactivation And Stabilization Steps

    Stabilization of the sensor chip surface can be accomplished by performing one or more blank injections or by using reagents from the ProteOn regeneration kit. In applications that use high ligand densities, such as small-molecule interactions, the high ligand...

  • Page 239: Determining The Extent Of Ligand Immobilization

    Determining the Optimum pH for Immobilization Determining the Extent of Ligand Immobilization Changes in the SPR signal are monitored during immobilization. Immobilization levels are determined by the signal and measured in response units (RU), observed as the difference between the level before ligand injection and the level after deactivation is complete.

  • Page 240: Analyte Interaction Process

    Dilution of analyte in running buffer is recommended to minimize bulk effects (refractive index difference between two solutions) ProteOn phosphate buffered saline with Tween 20 (PBST), pH 7.4, is the recommended running buffer for most ProteOn XPR36 system applications. The running buffer should contain salt (ProteOn PBS contains 10 mM sodium phosphate and 150 mM sodium chloride, pH 7.4) and a surfactant, such as Tween 20, to...
  • Page 241 Analyte Interaction Process the MCM. Surfactant is omitted from the running buffer (as in the case of ProteOn PBS, pH 7.4) if the sample or interaction is detergent-sensitive. For DNA-protein interactions, a chelating agent (EDTA, for example) is added to remove any metal ions that may interfere with the interaction.

  • Page 242: Regeneration Step

    Use high flow rates and minimal volumes (100 μl/min and 30 μl, for example) to minimize damage to the ligand. The ProteOn Regeneration Buffer Kit contains nine of the most commonly used regeneration solutions.

  • Page 243: Protocol Development Kits

    Appendix Kits ProteOn™ protocol development kits are designed for use with the ProteOn™ XPR36 protein interaction array system. Each kit provides the reagents and sensor chip needed to complete an interaction analysis experiment. One-shot Kinetics™ (OSK)™ Kit The ProteOn One-shot Kinetics™ kit provides the materials for analyzing the interaction between the cytokine IL-2 and an antibody to IL-2.

  • Page 244: Protein-Small Molecule Kit

    201 Da. The carbonic anhydrase II/CBS interaction not only demonstrates the ability of the ProteOn XPR36 system to detect low molecular weight analytes, but it also highlights the methodology for optimizing system performance.

  • Page 245: Ordering Information

    ProteOn XPR36 System Ordering Information Appendix How to Order For orders, quotations, or information, contact Bio-Rad at: Toll-Free (US and Canada only): 800-4BIORAD (800-424-6723) Toll-Free Fax: 800-879-2289 Email: lsg.orders.us@bio-rad.com Online: discover.bio-rad.com Bio-Rad Laboratories, Inc. 2000 Alfred Nobel Drive Hercules, CA 94547 USA...

  • Page 246: Materials And Supplies

    Number ProteOn™ XPR36 Protein Interaction Array System 176-0100 ProteOn XPR36 interaction array system, 100–240 V: includes ProteOn XPR36 instrument, 2 licensed copies of ProteOn Manager™ software, computer and display, communication cable, sample rack, rack needle set, microplate needle set, collection tank, and instructions...
  • Page 247 ProteOn HTG sensor chip, for capturing of His-tagged proteins, polymer matrix layer contains tris-NTA complexes 176-2500 ProteOn HTG capturing kit, includes 1 ProteOn HTG sensor chip and 1 ProteOn HTG reagent kit 176-5100 ProteOn MNT maintenance chip, for use in maintenance protocols...
  • Page 248 ProteOn deep-well microplates, 96 deep wells, 2.0 ml, 5 176-6040 ProteOn microplate sealing film, 50 sheets 176-6060 ProteOn collection tank, used to collect buffer and solution overflow, 10 L capacity 176-6061 ProteOn collection tank tubing ProteOn Maintenance Kit and Solutions...
  • Page 249 176-4115 ProteOn maintenance solution 1, 0.5% sodium dodecyl sulfate (SDS), 2 L 176-4116 ProteOn maintenance solution 2, 50 mM glycine hydrochloride, pH 9.5, 2 L ProteOn XPR36 System Replacement Syringes for sample and buffer intake 176-6005 1 each, ProteOn Syringe...
  • Page 250 ProteOn XPR36 System | E Ordering Information...

  • Page 251: Security Edition Configuration Guide

    This appendixidentifies these areas and makes policy and procedure suggestions. Standard Mode vs. Secure Mode ProteOn Manager software, Security Edition can run in Standard mode with all security and audit trail features disabled—in which case the software functions like the Standard Edition of ProteOn Manager software—or it can run in Secure mode, with the security functions enabled.

  • Page 252: Proteon Manager Software Users And Groups

    User Accounts To give users access to ProteOn Manager software, Security Edition, create new Windows user accounts or add existing user accounts to the user groups specified in the previous section.

  • Page 253: Configuring Users And Groups On The Local Computer

    Security on page 242 for information on setting passwords for maximum security. • Each user can belong to only one ProteOn Manager software user group. For example, a user cannot belong to both the Administrator group and the Service group. An error is displayed if a user is assigned to more than one group.
  • Page 254 ProteOn XPR36 System | F Security Edition Configuration Guide 2. Fill out all the fields in the New User dialog box: • User Name —The user name must be unique. • Full Name —The Full Name box must be filled out and unique. We recommend using the user’s actual full name, as this name will be...
  • Page 255 Configuring Users and Groups on the Local Computer 2. In the Group name box, enter one of the group names specified on the page. You can also enter a description in the Description box. The group does not require any special operating-system level privileges.
  • Page 256 ProteOn XPR36 System | F Security Edition Configuration Guide 3. In the expanded dialog box, click Find Now to populate the list with all the users on the local computer. 4. Click a user name in the list to select it, or hold down CTRL and click multiple users to select them.

  • Page 257: Configuring Users And Groups On A Network Domain

    Configuring Users and Groups on a Network Domain ProteOn Manager software, Security Edition has been tested on servers running the Windows 2003 server operating system. Since it is impossible to describe every network configuration, it is necessary for the network administrator to know how users and groups are set up using their particular server software.
  • Page 258 ProteOn XPR36 System | F Security Edition Configuration Guide To create a new user on a Windows server: 1. With the Users folder open, select New User on the Action menu or the right-click context menu. 2. Fill out all the fields in the New User dialog box: •...
  • Page 259 Configuring Users and Groups on a Network Domain 2. In the New Object - Group dialog box Group Name box, enter one of the group names specified in ProteOn Manager Software User Groups on page 234. Be careful to type the name exactly as specified. You can also enter a description in the Description box.

  • Page 260: Password Security

    ProteOn XPR36 System | F Security Edition Configuration Guide 3. In the expanded dialog box, click Find Now to populate the list with all the users. 4. Click a user name in the list to select it, or hold down CTRL and click multiple users to select them.

  • Page 261: Password Policy Setting Examples

    Password Security To locate the password policy settings on your local computer, go to the Windows Control Panel and select Administrative Tools, then select Local Security Policy. Password Policy Setting Examples • Enforce password history: 12 passwords remembered • Minimum password age: 5 days •...

  • Page 262: Auditing Windows Event Logs

    However, by default, Windows systems automatically remove this data without warning. No ProteOn Manager software information is stored in the Windows Event Logs. All instrument and application events are saved continuously within the ProteOn Instrument Log, described on page 4 of this manual.

  • Page 263: Miscellaneous Security Measures

    Miscellaneous Security Measures Miscellaneous Security Measures Bio-Rad recommends taking advantage of the built-in protections that Windows XP Professional offers in order to protect the computer when the user is absent. It should be standard operating procedure for users to lock the computer when they step away by pressing CTRL+ALT+DELETE and then clicking Lock computer or Windows-L.
  • Page 264 ProteOn XPR36 System | F Security Edition Configuration Guide...

  • Page 265: Glossary

    (for example, biomolecules) that causes them to form a complex (see Avidity) Analyte Chemical substance that is the subject of analysis. In the ProteOn™ XPR36 protein interaction array system, the analyte is the interaction partner that flows over the immobilized ligand...
  • Page 266 Interaction model in which the analyte has two binding sites for the ligand Bubbles In the ProteOn XPR36 protein interaction array system, air gaps that are intentionally introduced to separate sample from the running buffer in the microfluidics system, to minimize sample dilution/mixing...
  • Page 267 Uninterrupted stream of running buffer over the chip surface required Buffer by the ProteOn XPR36 fluidics system Crisscross Pattern of orthogonal, intersecting lines. In the ProteOn XPR36 system, it refers to the six parallel ligand flow channels and their intersection with six parallel analyte flow channels Critical Angle...
  • Page 268 Upper and lower bounds on the ability of a system (that is, instrument, reagents, etc.) to measure. In the context of interaction analysis, it refers to the range of SPR signals which the ProteOn XPR36 system can measure. Dynamic range is expressed in...
  • Page 269 An experiment file is saved with a *.pxf extension To adjust (a smooth curve of a specified type) to a given set of points Flow Cell For the ProteOn XPR36 system, the fluidic channels formed when the multichannel module is pressed onto the chip surface Flow Rate...
  • Page 270 ProteOn XPR36 instrument Interaction Spot One of up to 36 sites on the ProteOn XPR36 sensor chip surface where a biomolecular interaction is measured Intercept Intersection of the data with either axis (X or Y) of the graph Interspot Reference One of 42 spots within the analyte channels used for referencing.
  • Page 271 Langmuir with Drift Langmuir model with an extra parameter for fitting data with linear baseline drift Ligand In the ProteOn XPR36 system, the biomolecule immobilized on the sensor chip surface. In general, ligand can refer to any molecule that covalently binds to the chip surface (for example, EDAC, sulfo-NHS, ethanolamine, protein, DNA, etc.)
  • Page 272 Optical Detection The light source, the collection lenses, the polarization optical System element, the biosensor chip (prism), and the detector in the ProteOn XPR36 instrument Orthogonal Intersecting perpendicularly Panel Set of up to six samples or reagents applied to the sensor chip in a single injection.
  • Page 273 Running State ProteOn XPR36 instrument mode in which an experiment is being executed Sample Holder Generic term referring to the microplates or sample rack used to hold...
  • Page 274 Phase preceding the injection of analyte Delay Standby State ProteOn XPR36 instrument mode entered after it has been in the Ready state for four hours with no activity. Standby may be requested from the Instrument Control screen also. In this mode,...
  • Page 275 Thermal Block Component of the autosampler that supports the sample holder and regulates its temperature Total Internal Condition where light incident on an interface between a medium of Reflection high optical density and a medium of lesser optical density is totally internally reflected for all angles greater than the critical angle Verification Calibration of the SPR response using a set of solutions of known...
  • Page 276 ProteOn XPR36 System | Glossary...

  • Page 277: Index

    ProteOn XPR36 System | Index Index ungrouping 138 Analysis wizard Accessing database browser 7 concentration 134 Activation step (amine coupling) 51 equilibrium 132 Active buffer position kinetic 127 changing 33 Analyte Adding bivalent 128 column to Report points 124 concentrations, best results 223...
  • Page 278 ProteOn XPR36 System | Index Buffer Collection tank 169 bottle selection 30 Color control buttons 28 changing sensorgram lines 91 flow rate 151 sensorgram, changing 91 preparing 65 Combine data across steps 106 recommended 65 Communication cable 195 running 222...
  • Page 279 7 Excluding saving templates 32 sensorgram 99 Datasets 118 Exiting creating 118 Fault state 27 deleting 119 ProteOn Manager 21 navigating between 114 Experiment renaming 118 defined 31 Deactivating chip surface 64 sealing 83 Deactivation step 51 Experiment workflow 1...
  • Page 280 ProteOn XPR36 System | Index reports 145 by steps 104 reports to a file 147 data for analysis 103 Extent of ligand immobilization 221 Guidelines of experiment 218 Fans, cooling 195 Hand tools 200 Fault state 26 HASP key 11...
  • Page 281 Index Inserting a chip 76 data 95 Installing Ion removal, metal 65 ProteOn Manager 11 Isoaffinity graph 96 syringe 161 installing 11 Instrument buttons 30 capturing log file 9 KD 133 components 190 Kinetic flushing 67 analysis 126 hand tools 200...
  • Page 282 ProteOn XPR36 System | Index Maintenance chips 149 Panel type 45 flow rate 151 Parameters instrument 151 analysis 120 protocol solutions 153 in equilibrium wizard 132 state 26 protocol values 54 wizards 154 scopes 120 Manual artifact removal 110 steps 52...
  • Page 283 Region selection concentration calculation 136 Sample kinetic calculation 130 information 46 Req calculation 132 interaction viewer 55 Reinstalling ProteOn Manager software 18 layout report 61 Removing preparing 68 artifacts 110 protocol screen 41 chip from instrument 193 rack and needle holder 200...
  • Page 284 ProteOn XPR36 System | Index changing data ownership 188 report points 121 configuring 233 selecting a range 108 file security 182 selecting all 109 log files 182 showing or hiding 89 logging off 187 Serial overview 177 cable 195 passwords 180...
  • Page 285 Index Stop to Ready instrument state 25 sensor chip 78 Status LEDs 192 step 56 Step details panel 52 Template Step name 54 defined 31 Step parameters 52 Templates Steps creating from protocol 35 activation for amine coupling 216 creating protocol from 32 analyte interaction 214 editing 32 buffer 55...
  • Page 286 ProteOn XPR36 System | Index Warnings v Weekly maintenance 154 Window grouping 104 Windows Event Logs 244 Wizards concentration analysis 134 equilibrium analysis 132 kinetic analysis 127 Workflow, experiment 1 Working ranges 210 Wrenches 200 Yellow sensor chip 71...
  • Page 288 Bio-Rad Laboratories, Inc. Web site www.bio-rad.com USA 800 424 6723 Australia 61 2 9914 2800 Austria 01 877 89 01 Belgium 09 385 55 11 Life Science Brazil 55 31 3689 6600 Canada 905 364 3435 China 86 21 6169 8500 Czech Republic 420 241 430 532 Group Denmark 44 52 10 00 Finland 09 804 22 00 France 01 47 95 69 65 Germany 089 31 884 0 Greece 30 210 777 4396 Hong Kong 852 2789 3300 Hungary 36 1 459 6100 India 91 124 4029300 Israel 03 963 6050 Italy 39 02 216091...

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