Page 1 ™ QuantStudio 6 Pro Real-Time PCR System ™ and QuantStudio 7 Pro Real-Time PCR System USER GUIDE Publication Number MAN0018045 Revision G.0 For Research Use Only. Not for use in diagnostic procedures.
Page 2 Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256 For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition. The information in this guide is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC.
Page 3 Revision Date Description 3 December 2019 • Added Security, Auditing, and E‑signature (SAE) v2.0 module. (continued) • Added instructions to generate and reset an access key for external software to connect to the instrument. • Added instructions to import an Assay Information File. •...
Page 4 Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license. Cy is a registered trademark of GE Healthcare. Amazon, Alexa, and all related logos are trademarks of Amazon.com, Inc. or its affiliates. Windows is a trademark of Microsoft Corporation.
Page 5: Table Of Contents
Contents ■ CHAPTER 1 Product information ..........14 Network and password security requirements .
Page 6 Contents System template file names ........... . . 34 System template file names for the 96-well 0.2-mL block .
Page 7 Contents ™ Set up or remove VeriFlex Zones ......... . . 59 Set up or remove the Auto Delta feature .
Page 8 Contents ■ CHAPTER 7 Calibrate and verify instrument performance ..... 84 Instrument and block calibration ..........84 Calibration and verification schedule .
Page 9 Contents ■ CHAPTER 8 Manage profiles ........... 122 Require sign-in .
Page 10 Contents Enable SAE functions ............143 Workflow: Enable SAE functions .
Page 11 Contents Configure the instrument settings ..........168 Enable or disable demonstration mode .
Page 12 Contents ■ APPENDIX B Connect the instrument to a network ......193 Connect the computer to the instrument directly or to a LAN ..... . . 193 Connect the instrument to a wired network .
Page 13 Contents Control and connection symbols ......... . . 219 Conformity symbols .
Page 14: Chapter 1 Product Information
Product information ■ Network and password security requirements ..........14 ■...
Page 15: Instrument Hardware Description
Chapter 1 Product information Instrument hardware description Instrument hardware description Overview of the instrument ™ ™ The Applied Biosystems QuantStudio 6 Pro and 7 Pro Real-Time PCR Systems use fluorescent- based polymerase chain reaction (PCR) reagents to perform the following functions: •...
Page 16: Features Of Each Instrument
Chapter 1 Product information Instrument hardware description • Smart Help to request technical support or instrument service directly from the instrument ™ • Barcode scanner for tracking plates or TaqMan Array Cards Features of each instrument Feature ™ ™ QuantStudio 6 Pro System QuantStudio 7 Pro System...
Page 17 Chapter 1 Product information Instrument hardware description Wavelength (nm) Emission Spectra Filters x1-m1 x2-m2 x3-m3 x4-m4 x5-m5 x6-m6 ™ ™ ™ ™ ™ x1-m1—FAM dye, SYBR GREEN x4-m4—JUN dye, ROX dye, Texas Red ™ ® ™ x2-m2—VIC x5-m5—Cy 5, MUSTANG PURPLE ™...
Page 18: Overview Of Data Collection
Chapter 1 Product information Instrument hardware description Overview of data collection The instrument collects raw fluorescence data at different points during the PCR cycle, depending on the type of run performed. When you create a plate file, you can customize the optical filter channels through which the instrument collects data.
Page 19: Autodelta Settings
Chapter 1 Product information Instrument hardware description ™ Figure 1 Three VeriFlex Zones Figure 2 Six VeriFlex ™ Zones ™ ™ Note: Plate files are not compatible between the QuantStudio 6 Pro System and the QuantStudio Pro System. For more information, see “Compatibility of plate files” on page AutoDelta settings AutoDelta enables an incremental increase or decrease in the temperature or time in a PCR cycle.
Page 20: Parts Of The Instrument
Chapter 1 Product information Instrument hardware description Parts of the instrument Figure 3 Front of the instrument Cameras Proximity sensor Touchscreen Access door for block change Microphones Speakers USB port Drawer Indicator light QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™...
Page 21 Chapter 1 Product information Instrument hardware description Figure 4 Back of the instrument USB ports RS-232 port (service use only) Wi-Fi dongle port ON/OFF switch Ethernet port Power inlet receptacle Note: The instrument recognizes only one external storage device at a time for data transfer. The USB ports at the rear of the instrument can be used for external devices, for example, a mouse or a keyboard.
Page 22: Instrument Status Indicator
Chapter 1 Product information Hands-free features Instrument status indicator Indicator Instrument status Powered off Sleep mode Blue light changing brightness slowly Powering on Blue light changing brightness Standby Blue light moving inwards towards middle of Drawer opening instrument Blue light moving outwards towards side of Drawer closing instrument Blue light moving back and forth...
Page 23: Indicators For The Hands-Free Features
Chapter 1 Product information Hands-free features Indicators for the hands-free features Indicators for facial authentication Display Status of facial authentication The Sign In screen displays Facial authentication for the instrument is enabled. • Facial authentication for the instrument is disabled. The Sign In screen does not display •...
Page 24: Software Description
Chapter 1 Product information Software description Software description Parts of the home screen Figure 5 Home screen Instrument name Block installed Instrument calendar Current user Microphone Connectivity icons Help Buttons to access plate files Eject Instrument settings Status dial Table 1 Parts of the home screen Element of the home Function screen...
Page 25 Chapter 1 Product information Software description Table 1 Parts of the home screen (continued) Element of the home Function screen • When the instrument is not in use—Displays Set up run. Status dial • When the instrument is in use—Displays the sample block temperature, the elapsed run time, and the run status.
Page 26: Connect And Cloud Definitions
Chapter 1 Product information Software description Connect and Cloud definitions The terms Connect, Cloud, Thermo Fisher Connect, and Thermo Fisher Cloud are used interchangeably on the instrument touchscreen. The term Connect is used in this document. The following icons are used interchangeably on the instrument touchscreen: •...
Page 27: Overview Of File Locations And Files
Chapter 1 Product information Software description (continued) Feature Instrument Desktop Connect View analysis of results — Set calibration reminders — Review exported calibration or RNase P — verification results (RNase P only) Overview of file locations and files ™ Note: The term plate file is applicable to both plates and TaqMan Array Cards.
Page 28 Chapter 1 Product information Software description (continued) File location Description and function • In endpoint PCR, the pre-read data is saved in this folder for post-read Post-read analysis. Files IMPORTANT! Plate files and data files are not included in a back-up of the instrument and are not restored when a backup of the instrument is restored.
Page 29 Chapter 1 Product information Software description (continued) Item Description and function Supported in • The plate file associated with the last run for the profile. Plate File Instrument • Can be edited and saved. From (Run last) • Can be edited and saved as a separate plate file. •...
Page 30: Components Of The Files
Chapter 1 Product information Software description Components of the files Component Instrument Desktop Connect • Data file name • Experiment file name Properties • Reagent information • Plate barcode or TaqMan ™ Array Card barcode – Name • User name –...
Page 31: Third-Party Software
Chapter 1 Product information Types of runs Third-party software Before installing third-party software on the computer running the desktop software, confirm that the third-party software will not do the following: • Restrict Ethernet communication. • Interfere with instrument or computer operation. Network connection options You can connect an instrument to a network or computer in the configurations listed below.
Page 32: Relative Standard Curve Run
Chapter 1 Product information Types of runs Relative standard curve run A relative standard curve runs determines the relative target quantity in samples. 1. The software measures amplification of the target of interest and of an endogenous control target in a standard dilution series, in a reference (calibrator) sample, and in test samples. The endogenous control is a target that is expressed equally in all samples;...
Page 33: Genotyping Run
Chapter 1 Product information Types of runs Genotyping run A genotyping runs detects the single nucleotide polymorphism (SNP) variants of a target nucleic acid sequence. ™ Genotyping runs use preformulated TaqMan SNP Genotyping Assays that include the following components: • Two sequence-specific primers for amplification of sequences containing the SNP of interest ™...
Page 34: System Template File Names
Chapter 1 Product information System template file names System template file names ™ The first part of the file name varies, based on the instrument (QuantStudio 6 Pro System or ™ QuantStudio 7 Pro System). The instrument will display the system templates applicable to the block that is installed. System template file names for the 96-well 0.2-mL block System template name Run type...
Page 35: System Template File Names For The 96-Well 0.1-Ml Block
Chapter 1 Product information System template file names (continued) System template name Run type • Comparative C QS7Pro-96-Well-0-2ml_RQ_Std.edt • 96-well, 0.2-mL Standard plate • Standard cycling mode • Relative standard curve run QS7Pro-96-Well-0-2ml_RSC_Fast.edt • 96-well, 0.2-mL Standard plate • Fast cycling mode •...
Page 36 Chapter 1 Product information System template file names (continued) System template name Run type • Presence/absence run QS7Pro-96-Well-0-1ml_PA_Fast.edt • 96-well, 0.1-mL Standard plate • Fast cycling mode • Presence/absence run QS7Pro-96-Well-0-1ml_PA_Std.edt • 96-well, 0.1-mL Standard plate • Standard cycling mode •...
Page 37: System Template File Names For The 384-Well Block
Chapter 1 Product information System template file names System template file names for the 384-well block System template name Run type • Genotyping run QS7Pro-384-Well-GT-Fast.edt • 384-well plate • Fast cycling mode • Genotyping run QS7Pro-384-Well-GT-Std.edt • 384-well plate • Standard cycling mode •...
Page 38: System Template File Names For The Taqman
Chapter 1 Product information System template file names (continued) System template name Run type • Relative standard curve run QS7Pro-384-Well-RSC-Fast.edt • 384-well plate • Fast cycling mode • Relative standard curve run QS7Pro-384-Well-RSC-Std.edt • 384-well plate • Standard cycling mode •...
Page 39 Chapter 1 Product information System template file names (continued) System template name Run type • Standard curve run QS7Pro-TAC-SC-Std.edt • TaqMan ™ Array Card • Standard cycling mode • Comparative C run with melt curve QS7Pro-TAC-RQ-Melt-Fast.edt • TaqMan ™ Array Card •...
Page 40: Workflow
Chapter 1 Product information Workflow Workflow Sign in to your instrument profile or your Connect account (PIN or facial authentication) ▼ Open a plate file (System template or saved plate file) ▼ (Optional) Edit the plate file ▼ Load the plate into the instrument ▼...
Page 41: Chapter 2 Get Started
Get started ■ Precautions for use ..............41 ■...
Page 42: Installation And Instrument Verification
Chapter 2 Get started Installation and instrument verification Installation and instrument verification The instrument is installed by a representative from Thermo Fisher Scientific. The following tasks will be performed during the installation process: • Unpack the instrument and the computer •...
Page 43: Power On The Instrument
Chapter 2 Get started Power on the instrument Power on the instrument If left unattended, the instrument automatically enters sleep mode to conserve power. The default time that an instrument is inactive before going into sleep mode is 15 minutes. 1.
Page 44: Sign In With Facial Authentication
Chapter 2 Get started Enable or disable the microphone You are signed in and the home screen is displayed. See “Parts of the home screen” on page Sign in with facial authentication For information on indicators for facial authentication, see “Indicators for facial authentication” page For lighting guidelines, see “Light guidelines”...
Page 45: Use Voice Commands
Chapter 2 Get started Use voice commands If the proximity sensor does not detect a person, the microphone icon will change to gray with a bar ). It will change back to red with a bar when the proximity sensor detects a person. Use voice commands The instrument must accept voice commands (see “Configure the instrument for the hands-free features”...
Page 46: Sign Out
Chapter 2 Get started Sign out Sign out 1. In the home screen, tap (Profile). 2. Tap Sign out, then tap Yes to confirm. You are signed out and the Sign In screen is displayed. QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™...
Page 47: Chapter 3 Create And Run Plates On The Instrument
Create and run plates on the instrument ■ Options to run a plate ..............47 ■...
Page 48 Chapter 3 Create and run plates on the instrument Options to run a plate • USB Drive 3. Tap the template file name in the right column. The Plate Properties screen is displayed. 4. (Optional) In the Plate Properties screen, edit the Data file name. The default file name is the template name appended with the date and time.
Page 49: Repeat The Last Run
Chapter 3 Create and run plates on the instrument Options to run a plate Figure 7 Home screen during a run For options during a run, see Chapter 5, “Options for a run”. Repeat the last run The last run is associated with the profile. It is not the last run for the instrument. 1.
Page 50: Overview Of Customized Data Export
Chapter 3 Create and run plates on the instrument Overview of customized data export If the connection between the instrument and the location that was selected to save the data file is interrupted, the instrument completes the run. The data file is saved on the instrument. The data file must be transferred to another location manually (see “Transfer data files at a later time”...
Page 51: (Optional) Scan A Barcode Using A Barcode Scanner
Chapter 3 Create and run plates on the instrument (Optional) Scan a barcode using a barcode scanner (Optional) Scan a barcode using a barcode scanner The instrument is compatible with an optional Handheld Barcode Scanner (Cat. No. 4488442, purchased separately). The barcode scanner reads Code 128 (alphanumeric), which supports 128 ASCII character barcodes.
Page 52: Load A Taqman ™ Array Card Into The Instrument
Chapter 3 Create and run plates on the instrument Load a TaqMan ™ Array Card into the instrument ™ Load a TaqMan Array Card into the instrument IMPORTANT! The instrument should be used by trained operators who have been warned of the moving parts hazard.
Page 53 Chapter 3 Create and run plates on the instrument Unload a plate or a TaqMan ™ Array Card from the instrument The status dial displays Run complete when the run is finished. If the automatic sign-out feature is enabled and the set time has elapsed, the instrument will display the Sign In screen. 1.
Page 54: Chapter 4 Edit A Plate Before Starting A Run
Edit a plate before starting a run ■ Overview of a template file with restricted editing ........54 ■...
Page 55: Options To Edit The Properties Of A Plate File
Chapter 4 Edit a plate before starting a run Options to edit the properties of a plate file Options to edit the properties of a plate file The following files can be edited: • A system template (see “Create and run a plate from a system template or a saved plate file” page A system template that is edited must be saved as a plate file.
Page 56: Options To Edit The Method Of A Plate File
Chapter 4 Edit a plate before starting a run Options to edit the method of a plate file Options to edit the method of a plate file The following files can be edited: • A system template (see “Create and run a plate from a system template or a saved plate file” page A system template that is edited must be saved as a plate file.
Page 57: Method Elements
Chapter 4 Edit a plate before starting a run Options to edit the method of a plate file Method elements Method tab Number of cycles for the stage Heated cover temperature Temperature for the step Reaction volume Hold time for the step Stage of thermal protocol Data collection point Step within a stage...
Page 58: Add Or Remove Steps
Chapter 4 Edit a plate before starting a run Options to edit the method of a plate file Add or remove steps Add a PCR step or remove a PCR step. 1. In the Method tab, tap Edit4Advanced4Manage steps. Note: Use to navigate through the method if it is not all displayed.
Page 59: Set Up Or Remove Veriflex ™ Zones
Chapter 4 Edit a plate before starting a run Options to edit the method of a plate file 2. Tap (Data collection location) to designate a step as a data collection location or to remove data collection from the step. (Data collection location) button functions as an on-off switch.
Page 60 Chapter 4 Edit a plate before starting a run Options to edit the method of a plate file Figure 8 VeriFlex ™ Zones and Auto Delta settings VeriFlex ™ Zones is selected 2. Tap the temperature field in the appropriate VeriFlex ™...
Page 61: Set Up Or Remove The Auto Delta Feature
Chapter 4 Edit a plate before starting a run Options to edit the method of a plate file Set up or remove the Auto Delta feature Note: The Auto Delta feature is only available in the PCR stage. 1. In the Method tab, tap Edit4Advanced4VeriFlex ™...
Page 62: Configure Ramp Rates
Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file Configure ramp rates The ramp rate is how quickly the temperature changes from one stage or step to another stage or step. The maximum ramp rate for the instrument is 6.5°C/second.
Page 63: Options To View A Plate Layout
Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file The following items can be edited in the Plate tab: • Sample name and sample type (see “Assign or edit a well for a plate” on page 65 and “Assign or ™...
Page 64 Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file Select all button Plate view button Well table view button Color by dropdown list View a 384-well plate The Plate tab displays a 384-well plate if the 384-well block is installed. The plate can be edited in the 384-well view.
Page 65: Assign Or Edit A Well For A Plate
Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file If you selected a full row or column in the 96-well view, only the set of wells that was visible in the 96-well view is selected.
Page 66: Assign Or Edit A Well For A Taqman ™ Array Card
Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file 5. Tap Target/SNP, then select Target or Assay from the dropdown list. 6. Tap a row in the table, then tap Done. Add a target or an assay 1.
Page 67: Apply The Reagents To A Plate
Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file 3. Tap a row in the table, then enter the information. • Reagent name • SKU (Part number) • Reagent type •...
Page 68: Add Or Edit The Reagent Details For A Taqman ™ Array Card
Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file 4. Tap a row in the table, then delete the information in each field. • Reagent name • SKU (Part number) •...
Page 69: Import An Assay Information File (Aif)
Chapter 4 Edit a plate before starting a run Options to edit the well details of a plate file The passive reference dye is displayed under the plate diagram. Import an Assay Information File (AIF) The Assay Information File is provided in TXT format and/or XML and HTML format, depending on the product line and order date.
Page 70: Chapter 5 Options For A Run
Options for a run ■ Screens available during a run ............70 ■...
Page 71: Edit A Plate File During A Run
Chapter 5 Options for a run Edit a plate file during a run Figure 10 Home screen during a run Arrow Actions menu Edit a plate file during a run The targets and samples can be added or edited after a run has started. The method cannot be edited after a run has started.
Page 72: Pause An Instrument Run
Chapter 5 Options for a run Pause an instrument run Pause an instrument run Pause a run to add reagents to the plate or to edit the number of cycles. 1. In the home screen during a run, tap (Actions). See Figure 10 on page 2.
Page 73: View The Method During A Run
Chapter 5 Options for a run View the method during a run View the method during a run 1. In the home screen during a run, swipe left once or tap the right arrow ( ) once. Start time Method, including the current stage End time Time remaining 2.
Page 74: Adjust The Display Of Real-Time Plots During A Run
Chapter 5 Options for a run View the time remaining during a run 2. (Optional) Tap the dropdown list then select the view for the plot. • Linear • Log 10 3. (Optional) Tap Actions4Analyze amp plots. 4. (Optional) Tap Actions4View well details to see the amplification for a specific well. 5.
Page 75: Unlock The Touchscreen During A Run
Chapter 5 Options for a run Unlock the touchscreen during a run Unlock the touchscreen during a run The touchscreen can be unlocked by the user who locked it or an administrator. The touchscreen automatically unlocks when the run is complete. 1.
Page 76 Chapter 5 Options for a run Instrument Schedule 3. Tap the reservation. The Edit Reservation screen is displayed. 4. Tap Cancel Reservation, then tap Yes. QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™ 7 Pro Real-Time PCR System User Guide...
Page 77: Chapter 6 View And Manage Files
View and manage files ■ Manage plate files ..............77 ■...
Page 78: Delete Plate Files
Chapter 6 View and manage files Manage data files Delete plate files System templates cannot be deleted. A plate file that was saved from a system template can be deleted. For descriptions of files, see “Files” on page 1. In the home screen, tap Load plate file or Set up run.
Page 79 Chapter 6 View and manage files Manage data files Figure 11 QC Check passed QC Check Figure 12 Review required for QC Check QC Check 2. See the QC data in the QuantStudio ™ ™ Design and Analysis Software v2 or the QuantStudio Design and Analysis v2.
Page 80: View An Amplification Plot After A Run
Chapter 6 View and manage files Manage data files View an amplification plot after a run The status dial displays Run complete when a run is complete. The amplification plot can only be viewed immediately after a run. After Done is tapped, the amplification plot can no longer be viewed on the instrument.
Page 81: Transfer A Data File Immediately After A Run
Chapter 6 View and manage files Manage data files Transfer a data file immediately after a run This section describes the transfer of a data file immediately after a run. To transfer a data file or a set of data files at a later time, see “Transfer data files at a later time” on page In the home screen, the status dial displays Run complete when a run is complete.
Page 82: View The List Of Data Files On The Instrument
Chapter 6 View and manage files Manage data files 1. Tap (Settings)4Run history. The Run History screen is displayed. It contains a list of the runs performed on the instrument associated with the profile. Administrators can view all of the runs performed. 2.
Page 83 Chapter 6 View and manage files Manage data files 1. In the home screen, tap (Settings)4Run history. The Run History screen is displayed. It contains a list of the runs performed on the instrument associated with the profile. Administrators can view all of the runs performed. 2.
Page 84: Chapter 7 Calibrate And Verify Instrument Performance
Calibrate and verify instrument performance ■ Instrument and block calibration ............84 ■...
Page 85: Calibration And Verification Schedule
Chapter 7 Calibrate and verify instrument performance Calibration and verification schedule Calibration and verification schedule The instrument and block will be calibrated during the installation. To ensure optimal performance, perform calibrations at the recommended frequency. Note: After instrument calibration, we recommend performing instrument verification using the provided RNase P plate.
Page 86: Calibration Descriptions
Chapter 7 Calibrate and verify instrument performance Calibration descriptions (continued) Calibration Recommended frequency • After installing or moving the instrument. RNase P instrument verification • After performing any of the calibrations. • As needed to confirm instrument performance. Note: To prepare custom dye plates and to perform custom calibrations, see “Calibrate custom dyes” on page 113.
Page 87: View The Calibration Status And Set Reminders
Chapter 7 Calibrate and verify instrument performance View the calibration status and set reminders (continued) Calibration description and purpose Pass criteria ™ Normalization (TaqMan Array Card block only) • The software extracts a spectral profile for each normalization standard. Normalization standards have sufficient signals to generate a •...
Page 88: Set Calibration Frequency And Reminders On The Instrument
Chapter 7 Calibrate and verify instrument performance View the calibration status and set reminders Set calibration frequency and reminders on the instrument 1. In the home screen, tap (Settings)4Maintenance and service4Calibration4Status and reminders. The Status and Reminders screen is displayed. 2.
Page 89: Review Calibration Status
Chapter 7 Calibrate and verify instrument performance Export a calibration report Review calibration status ™ The calibration status can be reviewed in the QuantStudio Design and Analysis Software v2. The instrument must be added to the Manage Instruments list. 1. In the home screen, click Manage Instruments. To access instruments from a different screen, click System4Instruments.
Page 90: Calibration Workflow
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations for plate blocks Calibration workflow Perform an ROI/uniformity calibration You are automatically prompted to perform background calibration. ▼ Perform a background calibration Perform any time that ROI/uniformity calibrations are current. ▼...
Page 91: Perform Calibrations
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations for plate blocks Thaw, vortex, and centrifuge a calibration plate IMPORTANT! Keep calibration plates protected from light until you perform the calibration. Do not remove the plate from its packaging until you are ready to use it. Prolonged exposure to light can diminish the fluorescence of the dyes in the wells of calibration plates.
Page 92 Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations for plate blocks Note: You will be prompted to perform a background calibration after a ROI/Uniformity calibration. 3. (System dye calibration only) Select the calibration plate. 4. Follow the instructions on the screen to start the calibration. 5.
Page 93: View The Calibration Images
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations for plate blocks 10. Return the plate to its original packaging. Note: Do not discard the packaging for the calibration plate. Each calibration plate can be used up to three time if the following conditions are met: ·...
Page 94: Transfer Calibration Results
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations for plate blocks (continued) Calibration Example results indicating successful calibration Background Few, if any, signals with abnormally high fluorescence. Signals from each well following a uniform trend, and each dye peaks at the correct filter.
Page 95: Troubleshoot Calibration Failure
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations for plate blocks Troubleshoot calibration failure Observation Possible cause Recommended action Calibration failed The plate was improperly Ensure the following: prepared. • The correct plate was used for the calibration performed.
Page 96: Create A Background Plate (Optional)
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations for plate blocks 3. Determine the location of the failed wells again as in step 1. Position of failed wells Action Identical The sample block is contaminated. Decontaminate the sample block (see page 159).
Page 97: Perform Roi/Uniformity, Background, Dye, And Normalization Calibrations For The Array Card Block
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan ™ Array Card block Perform ROI/uniformity, background, dye, and ™ normalization calibrations for the TaqMan Array Card block To calibrate the plate blocks, see “Perform ROI/uniformity, background, and dye calibrations for plate blocks”...
Page 98: Prepare A Calibration Taqman ™ Array Card
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan ™ Array Card block Prepare a calibration TaqMan ™ Array Card ™ Required materials to prepare calibration TaqMan Array Card Unless otherwise indicated, all materials are available through thermofisher.com. "MLS" indicates that the material is available from fisherscientific.com or another major laboratory supplier.
Page 99 Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan ™ Array Card block This procedure explains how to create all of the array cards required to calibrate the block, but not all of them are required for at each calibration.
Page 100: Perform Calibrations
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan ™ Array Card block Perform calibrations 1. In the home screen tap (Settings)4Maintenance and service4Calibration. The Calibration screen is displayed. 2. In the Calibration screen, select a calibration type. Calibration type ROI/uniformity ROI and uniformity...
Page 101: View The Calibration Images
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan ™ Array Card block 8. (For calibrations that pass) Select an option. Option Description Details View the calibration images. Transfer EDS Transfer the calibration file to Connect, a USB drive, or a network drive. Reject results The calibration file is deleted.
Page 102: Troubleshoot Normalization Calibration Failure
Chapter 7 Calibrate and verify instrument performance Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan ™ Array Card block • Calibration name • The operator • Result • Reagent name, part number, lot number, and expiration date • Date •...
Page 103: Perform Verification Using Rnase P Plates
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P plates Observation Possible cause Recommended action Normalization calibration failed 1. Locate the wells with the abnormal signal One or more wells produced (continued) spectra that deviate significantly (see “View the calibration images” from the rest of the array card.
Page 104: Instrument Verification Description
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P plates Instrument verification description Purpose Description Pass criteria Confirms the Quantifies the number of copies of The instrument passes performance specifications performance of the the human RNase P gene in samples if the following inequality is true and the instrument.
Page 105: Performance Specifications Pass Criteria
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P plates Figure 14 384-well RNase P plate NTC (no template control) STD 10,000 copies STD 1,250 copies STD 20,000 copies STD 2,500 copies Unknown A (5,000) STD 5,000 copies Unknown B (10,000) Performance specifications pass criteria After the run, the software calculates average copy number values and standard deviation values.
Page 106: Perform Rnase P Verification
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P plates Thaw, vortex, and centrifuge an RNase P plate IMPORTANT! Expose the RNase P plate to room temperature for no more than 45 minutes, inclusive of thawing and preparation time. After thawing, the RNase P plate cannot be refrozen.
Page 107: Troubleshoot Verification Failure
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P plates 5. When the run is complete and the screen displays Complete, tap View results to confirm the status of the run. Verification status Action Passed Instrument is ready for use. Failed See “Troubleshoot verification failure”...
Page 108: Perform Verification Using Rnase P With A Taqman ™ Array Card
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P with a TaqMan ™ Array Card Observation Possible cause Recommended action Verification failed The plate is damaged or Check for damage, improper plate seal, or (continued) contaminated. contamination. Order a replacement plate.
Page 109: Rnase P Instrument Verification Taqman ™ Array Card
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P with a TaqMan ™ Array Card The instrument and block require valid ROI/uniformity, background, normalization, and dye calibrations to perform verification. For a description of verification, see “Instrument verification description” on page 104.
Page 110: Prepare An Rnase P Taqman ™ Array Card
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P with a TaqMan ™ Array Card Prepare an RNase P TaqMan ™ Array Card ™ Required materials to prepare an RNase P TaqMan Array Card Unless otherwise indicated, all materials are available through thermofisher.com. "MLS" indicates that the material is available from fisherscientific.com or another major laboratory supplier.
Page 111 Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P with a TaqMan ™ Array Card ™ Prepare an RNase P TaqMan Array Card ™ For detailed instructions to prepare a TaqMan Array Card, see Appendix C, “Detailed procedures for preparation of a TaqMan ™...
Page 112: Perform Rnase P Verification
Chapter 7 Calibrate and verify instrument performance Perform verification using RNase P with a TaqMan ™ Array Card 4. Pipet 100 µL of each solution into the appropriate port of the array card. Figure 16 RNase P standards layout Port 1, No Template Control Port 2, Unknown A (800 copies) Port 3, Unknown B (1,600 copies) Port 4, Standard 200 copies...
Page 113: Calibrate Custom Dyes
Chapter 7 Calibrate and verify instrument performance Calibrate custom dyes 3. Load the TaqMan ™ Array Card into the instrument. CAUTION! The instrument should be used by trained operators who have been warned of the moving parts hazard. 4. Tap Start. 5.
Page 114: Use A Dilution Series To Determine An Optimal Custom Dye Concentration
Chapter 7 Calibrate and verify instrument performance Calibrate custom dyes Custom dye calibration workflow Determine the optimal dye concentration for each custom dye. Use this concentration to prepare all subsequent dye calibration plates. Dilute the custom dye Prepare a custom dye dilution plate (page 115) ▼...
Page 115 Chapter 7 Calibrate and verify instrument performance Calibrate custom dyes Prepare a custom dye dilution plate IMPORTANT! Wear powder-free gloves throughout the procedure. 1. Prepare a 2- or 3-fold dilution series of the custom dye. 2. Dispense aliquots of each dilution into the center of a reaction plate, then seal the plate. A full plate is not needed.
Page 116 Chapter 7 Calibrate and verify instrument performance Calibrate custom dyes Run the dilution plate IMPORTANT! Do not run the dilution plate as a calibration. 1. Load the plate into the instrument. CAUTION! The instrument should be used by trained operators who have been warned of the moving parts hazard.
Page 117: Calibrate The Custom Dye
Chapter 7 Calibrate and verify instrument performance Calibrate custom dyes 3. Examine the raw data to identify the wells yielding signals according to the ranges shown in the following table. Plate type Acceptable signal range 96-well 800,000 to 3,200,000 384-well 400,000 to 2,000,000 Signal range for the optical filter where the dye is brightest.
Page 118 Chapter 7 Calibrate and verify instrument performance Calibrate custom dyes Add a custom dye to the instrument 1. In the home screen, tap (Settings)4Maintenance and service4Calibration4Custom dye. The Custom Dye screen is displayed. 2. Tap Add custom dye. 3. Tap the Custom Dye Name field, then enter a name. IMPORTANT! ·...
Page 119 Chapter 7 Calibrate and verify instrument performance Calibrate custom dyes 7. Tap View results4Details. 8. Review the plot. Calibration results that pass show uniform signals with peaks that are aligned with the dye wavelength. Filter wavelength (nm) Peak filter Excitation Emission x1-m1 470 ±...
Page 120: Calibrate For A Custom Melt Curve Run
Chapter 7 Calibrate and verify instrument performance Calibrate for a custom melt curve run 10. Unload the plate from the instrument. CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature can reach 100°C. Allow it to cool to room temperature before handling. Note: Use Smart Help if the instrument does not eject the plate (see “Request technical support with Smart Help”...
Page 121 Chapter 7 Calibrate and verify instrument performance Calibrate for a custom melt curve run 5. Load the plate into the instrument 6. Tap Start. 7. When the run is complete and the screen displays Calibration complete, tap View results4Details. 8. Review the plot. Passing calibration results show uniform signals with peaks that are aligned with the dye wavelength.
Page 122: Chapter 8 Manage Profiles
Manage profiles ■ Require sign-in ..............122 ■...
Page 123: Recommended Order To Set Up Profiles
Chapter 8 Manage profiles Recommended order to set up profiles Recommended order to set up profiles Task Description The first profile on the instrument becomes the instrument administrator. Create a profile for the instrument The first profile is set up during the initial install with a representative administrator.
Page 124: Connect Instrument Profile Roles And Functions
Chapter 8 Manage profiles Connect instrument profile roles and functions – The instrument schedule is available. – Smart Help is available. – The same profile can be used for multiple instruments. Connect instrument profile roles and functions The first user who links their local instrument profile to their Connect account is assigned a Connect profile with administrator role.
Page 125 Chapter 8 Manage profiles Test the connection to the Connect platform 2. Tap Test connection. If the connection can be established, You are able to connect to the Connect platform will be displayed. If the connection cannot be established, Unable to connect will be displayed. 3.
Page 126: Link The Instrument To Your Connect Account
Chapter 8 Manage profiles Link the instrument to your Connect account Link the instrument to your Connect account This section describes using your Connect account when you use the instrument for the first time. The first time you use your Connect account on an instrument, you will be prompted to create a four- digit numerical PIN.
Page 127: Create A New Local Instrument Profile
Chapter 8 Manage profiles Create a new local instrument profile 5. (Optional) Tap the Confirm PIN field, enter the four-digit numerical PIN again, then tap Enter. 6. Tap Done. Create a new local instrument profile A local instrument profile is not compatible with Connect-enabled features. A local instrument profile can be linked to Connect at a later time.
Page 128 Chapter 8 Manage profiles Link a local profile to a Connect profile (Optional) Test the connection (see “Test the connection to the Connect platform” on page 124). 1. In the home screen, tap (Profile). The My Profile screen is displayed. 2.
Page 129: Unlink A Connect Account
Chapter 8 Manage profiles Unlink a Connect account Unlink a Connect account Unlinking a Connect is done from the Connect platform on your computer. For more information about unlinking a Connect account, see “If you link when you are signed in to the instrument”...
Page 130: If You Link When You Are Not Signed In To The Instrument
Chapter 8 Manage profiles If you link when you are not signed in to the instrument (continued) Phase Steps that occur • Your local instrument profile (UserABC) is displayed in the home screen of the If your Connect account is instrument.
Page 131: Manage Individual Instrument Profiles
Chapter 8 Manage profiles Manage individual instrument profiles (continued) Phase Steps that occur • Your local instrument profile (User G.) is displayed in the home screen of the If your Connect account is instrument. unlinked: • Plate files and data files that were saved under your Connect instrument profile are accessible under your local instrument profile.
Page 132: Add Facial Authentication To An Existing Instrument Profile
Chapter 8 Manage profiles Manage individual instrument profiles 3. Center your face within the green frame, then tap Start. Note: You must position yourself close enough to the instrument so that the green frame shows only your face without any of the surrounding background. This position is closer to the instrument than when you sign in with facial authentication.
Page 133: Change The Pin For An Instrument Profile
Chapter 8 Manage profiles Manage all instrument profiles as an administrator Change the PIN for an instrument profile This section describes changing a PIN for a local instrument profile. To change a PIN for a Connect profile, see “Change the PIN for a Connect profile” on page 133.
Page 134: Reset The Pin For A Profile
Chapter 8 Manage profiles Manage all instrument profiles as an administrator 3. (Optional) Tap a column in the table to sort by that parameter. 4. Tap Done. Reset the PIN for a profile 1. In the home screen, tap (Profile). The My Profile screen is displayed.
Page 135: Enable Or Disable Administrator Privileges
Chapter 8 Manage profiles Manage all instrument profiles as an administrator Enable or disable administrator privileges Administrator privileges can only be enabled or disabled on the instrument for local instrument profiles. Connect instrument profiles can only have instrument administrator privileges enabled or disabled on the Connect platform.
Page 136 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module ■ Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components ..137 ■ Overview of the instrument features when the SAE module is enabled ..... 137 ■...
Page 137: Chapter 9 Use The Instrument With The Security, Auditing, And E-Signature (Sae) V2.0 Module
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components The Security, Auditing, and E‑signature (SAE) v2.0 module includes three components: •...
Page 138: Security, Auditing, And E-Signature (Sae) V2.0 Module Functions
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Security, Auditing, and E‑signature (SAE) v2.0 module functions Security, Auditing, and E‑signature (SAE) v2.0 module functions Functions that are controlled The following functions are controlled, depending on the user role: •...
Page 139: Functions That Can Be Audited
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Security, Auditing, and E‑signature (SAE) v2.0 module roles Functions that can be audited Certain instrument functions can be audited. This depends on how the SAE administrator has configured the audit settings.
Page 140: Dialog Boxes In The Sae Module
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Dialog boxes in the SAE module Dialog boxes in the SAE module Some of the features and functions described might not be accessible to you. The features and functions that are available depend on the way that the SAE administrator has configured them.
Page 141: Profiles When The Sae Module Is Enabled
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Profiles when the SAE module is enabled Profiles when the SAE module is enabled After the SAE module is enabled on the instrument, the local instrument profiles and the Connect cloud-based platform profiles will not be available.
Page 142: Compatibility Between Sae-Enabled And Sae-Disabled Components
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module SAE-enabled system components Compatibility between SAE-enabled and SAE-disabled components We recommend enabling SAE for all system components (for more information, see “Enable SAE functions” on page 143).
Page 143: Enable Sae Functions
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Enable SAE functions Enable SAE functions Workflow: Enable SAE functions Configure SAE Administrator Console application profiles (page 143) ▼ Enable SAE on the instrument and specify the SAE server (administrator only) (page 143) ▼...
Page 144: Connect To The Sae Server
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Enable SAE functions 3. Tap the Server IP field, then enter the IP address of the SAE server. 4. Tap the Port field, enter the port, then tap Next. 5.
Page 145: Enable Sae Functions In Quantstudio ™ Design And Analysis Software V2
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Disable SAE on the instrument (administrator only) Enable SAE functions in QuantStudio ™ Design and Analysis Software v2 This procedure requires an SAE administrator account. ™ Before you enable SAE functions in the QuantStudio Design and Analysis Software v2, you must complete the following tasks:...
Page 146: Sign In As A Local Administrator With Sae Enabled
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Sign in as a local administrator with SAE enabled Sign in as a local administrator with SAE enabled Sign in as a local administrator to access the instrument settings. Plate files are not accessible if you are signed in as a local administrator.
Page 147: Sign In With Sae Enabled
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Sign in with SAE enabled Sign in with SAE enabled You must create a profile on the SAE Administrator Console before you sign in when SAE is enabled on the instrument.
Page 148: Sign Out With Sae Enabled
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Sign out with SAE enabled Figure 20 Home screen Sign out with SAE enabled 1. In the home screen, tap (Profile). The My Profile screen is displayed. The SAE button is selected and the profile that is signed in is listed.
Page 149: Change Your Sae Account Password On The Instrument
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Change your SAE account password on the instrument Change your SAE account password on the instrument ™ The QuantStudio Design and Analysis Software v2 and the instrument must be connected to the same SAE server in order for the SAE account password to be updated for both the software and the instrument.
Page 150: Sign A Plate Setup
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Sign a plate setup Figure 23 Edit My Profile screen 3. Tap the Old password field, enter the current SAE account password, then tap Enter. 4. Tap the New password field, enter a new SAE account password, then tap Enter. (Optional) Tap the Show password checkbox to show or hide the password.
Page 151: Enter An Audit Reason
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Enter an audit reason 4. In the Plate Properties screen, tap Actions. The Actions screen is displayed. 5. Tap Sign plate. The Sign Plate screen is displayed. 6.
Page 152: View Signing Records For A Plate File
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module View signing records for a plate file View signing records for a plate file 1. In the home screen, tap one of the following options: • (Load plate file) •...
Page 153: View Audit Records
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module View audit records 6. Tap a row to view the details. 7. Tap Close to return to the Signing records screen. View audit records The audit records cannot be viewed on the instrument touchscreen. The audit records are viewed on ™...
Page 154: Use The Instrument When The Sae Server Is Offline
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Use the instrument when the SAE server is offline Use the instrument when the SAE server is offline If your SAE administrator has configured your instrument to allow use when the SAE server is offline (Client offline login System setting in the SAE module), you can use the instrument for the period of time specified by the SAE administrator for Client offline login.
Page 155: Signing In After Automatic Screen Locking
Chapter 9 Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module Signing in after automatic screen locking Signing in after automatic screen locking Depending on the way your SAE administrator has configured your instrument, the instrument touchscreen may automatically lock after a specified duration. An Administrator role or a Scientist role can sign in after automatic screen locking.
Page 156: Chapter 10 Maintain The Instrument
Maintain the instrument ■ Install a block ............... 156 ■...
Page 157: Change The Block
Chapter 10 Maintain the instrument Change the block Change the block CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the sample block temperature can reach 100°C. Allow it to cool to room temperature before handling. This section describes changing a block and heated cover when there is already a block installed. To install a block when one is not installed, see “Install a block”...
Page 158: Remove The Block
Chapter 10 Maintain the instrument Remove the block It is recommended to store the block and the heated cover in the provided protective box when they are not installed on an instrument. Remove the block CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the sample block temperature can reach 100°C.
Page 159: Decontaminate The Sample Block
Chapter 10 Maintain the instrument Decontaminate the sample block Decontaminate the sample block Perform this procedure to eliminate fluorescent contaminants from the instrument sample block. Contamination is generally evident in failed background calibrations where one or more wells consistently exhibit abnormally high signals. CAUTION! PHYSICAL INJURY HAZARD.
Page 160: Detailed Procedures For Cleaning The Sample Block
Chapter 10 Maintain the instrument Decontaminate the sample block 4. Rinse the contaminated wells with deionized water (see “Detailed procedures for cleaning the sample block” on page 160). 5. Install the block and heated cover (see “Install a block” on page 156).
Page 161: Replace The Instrument Fuses
Chapter 10 Maintain the instrument Replace the instrument fuses • Clean the sample block with 95% ethanol. a. Pipet a small volume of 95% ethanol solution into each contaminated well. b. In each well, pipet the solution up and down several times to rinse the well. c.
Page 162 Chapter 10 Maintain the instrument Replace the instrument fuses 3. Using a flat‑head screwdriver, unscrew and remove the fuse holder. 4. Remove each fuse from its fuse holder, then inspect it for damage. Carbon typically coats the inside of failed fuses. Good Failed 5.
Page 163: Power On Or Off, Store, And Move
Chapter 10 Maintain the instrument Power on or off, store, and move Power on or off, store, and move Enable and edit sleep mode Sleep mode allows the instrument to use less energy when not in use. The length of time that the instrument is inactive before going into sleep mode can be customized.
Page 164: Power On The Instrument
Chapter 10 Maintain the instrument Power on or off, store, and move Power on the instrument If left unattended, the instrument automatically enters sleep mode to conserve power. The default time that an instrument is inactive before going into sleep mode is 15 minutes. 1.
Page 165: Prepare The Instrument To Store, Move, Or Ship
Chapter 10 Maintain the instrument Power on or off, store, and move Prepare the instrument to store, move, or ship Remove the block and heated cover to store, move, or ship the instrument. It is recommended to store the block and heated cover in the provided protective box when they are not installed on an instrument.
Page 166: Chapter 11 Configure The Instrument Settings
Configure the instrument settings ■ View the instrument details ............166 ■...
Page 167: View The License Agreement
Chapter 11 Configure the instrument settings View the license agreement • Instrument model name • Block type • Wired IP address • Software version • Wired MAC address • Firmware version • Wireless IP address • User interface version • Wireless MAC address •...
Page 168: Configure The Instrument Settings
Chapter 11 Configure the instrument settings Configure the instrument settings 2. Tap Privacy. The privacy policy is displayed. 3. Tap Close. Configure the instrument settings Enable or disable demonstration mode Note: The instrument restarts when demonstration mode is turned on or off. When the instrument is in demonstration mode, the following features apply: •...
Page 169: Configure The Heated Cover Settings
Chapter 11 Configure the instrument settings Configure the instrument settings Configure the heated cover settings The heated cover can be heated when the instrument is idle or it can be left without being heated when the instrument is idle. To save power, configure the settings so the heated cover is left without heating.
Page 170: Select The Region For The Connect Platform
Chapter 11 Configure the instrument settings Configure the instrument settings 4. (Optional) Tap Proxy server to connect the instrument to a proxy server (see “Connect a proxy server” on page 170). 5. Tap Done. Connect a proxy server A proxy server sits between the instrument and the main server. The proxy server intercepts requests to the main server and evaluates if it can complete the request.
Page 171: Select A Disk Storage Management Mode
Chapter 11 Configure the instrument settings Configure the instrument settings Select a disk storage management mode This setting determines how the instrument manages data files when the disk space is full. 1. In the home screen, tap (Settings)4Instrument settings4Disk storage management. 2.
Page 172: Reset The Access Key For External Software To Connect To The Instrument
Chapter 11 Configure the instrument settings Configure maintenance and service settings 3. (Optional) Set the Visible to all users slider. The Visible to all users slider is only displayed if the Enable access slider is set to the On position. 4.
Page 173: Request Instrument Service With Smart Help
Chapter 11 Configure the instrument settings Configure maintenance and service settings 8. (Optional) Tap to record a description of the technical issue. 9. Tap Done. A confirmation email is sent. It is sent even if email was not selected as the preferred contact method. Request instrument service with Smart Help Request instrument service with Smart Help for any instrument service request.
Page 174 Chapter 11 Configure the instrument settings Configure maintenance and service settings The Hardware Test screen is displayed when the self-verification test is complete. The Hardware Test screen displays the functions that pass and fail. 4. (Optional) Tap Export to export the results. 5.
Page 175 Chapter 11 Configure the instrument settings Configure maintenance and service settings 4. In the Touch Accuracy Test screen, tap the screen in several locations. Green dots appear where you tap. 5. Tap Yes to proceed. 6. In the Speaker Test screen, tap (Play).
Page 176 Chapter 11 Configure the instrument settings Configure maintenance and service settings 8. In the Microphone Test screen, tap to record. 9. Tap Yes to proceed. 10. In the Camera Test screen, tap Yes to confirm that the camera is on. A preview is displayed if the camera is on.
Page 177 Chapter 11 Configure the instrument settings Configure maintenance and service settings 13. In the Camera Test screen, tap Yes to confirm that the depth map is displayed on the screen. QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™ 7 Pro Real-Time PCR System User Guide...
Page 178: View The Instrument Log
Chapter 11 Configure the instrument settings Configure maintenance and service settings 14. In the Proximity Test screen, move forwards towards the instrument and backwards away from the instrument. The distance on the instrument screen changes to show your distance from the instrument. 15.
Page 179: Export The Instrument Log
Chapter 11 Configure the instrument settings Configure maintenance and service settings • Run • Calibration • Change Block • Self-Test • Error • Update • Power • User 2. (Optional) Tap any of the table headings to sort by that parameter. 3.
Page 180: Enable Or Disable Remote Monitoring
Chapter 11 Configure the instrument settings Configure maintenance and service settings Enable or disable remote monitoring The following items can be monitored remotely: • The progress of a run • Instrument events • Instrument statistics 1. In the home screen, tap (Settings)4Maintenance and service4Connect services.
Page 181: Repair The Software
Chapter 11 Configure the instrument settings Configure maintenance and service settings Repair the software If a software update failed, the software can be repaired. The software version installed during a repair is the same version that was previously installed on the instrument, even if a newer version is available.
Page 182: Restore A Backup Of The Instrument
Chapter 11 Configure the instrument settings Configure maintenance and service settings 4. Enter a back up file name. 5. Select the elements to back up. • Instrument settings • User profiles • Calibration records 6. Tap Back up. Instrument back up is complete is displayed on the Back Up Instrument screen when the back up is complete.
Page 183: Overview Of An Instrument Reset (Restore Factory Default)
Chapter 11 Configure the instrument settings Request remote support Overview of an instrument reset (restore factory default) IMPORTANT! Back up the instrument before resetting the instrument (see “Back up the instrument” on page 181). Transfer plate files and data files (see Chapter 6, “View and manage files”). Plate files and data files are not included in a backup of the instrument.
Page 184 Chapter 11 Configure the instrument settings Request remote support 1. In the home screen, tap (Settings)4Remote support. The Remote Support screen is displayed. 2. Tap Start remote session, then enter the PIN provided by Support. Remote Session Text field Remote Session is displayed at the top of the touchscreen when a successful connection is established.
Page 185: Configure The Instrument For The Hands-Free Features
Chapter 11 Configure the instrument settings Configure the instrument for the hands-free features Configure the instrument for the hands-free features The administrator must be signed in with a Connect profile in order to enable voice commands. 1. In the home screen, tap (Settings)4Hands-free operation.
Page 186: View The Notifications
Chapter 11 Configure the instrument settings View the notifications 4. Tap the lines beside an attribute, then drag the attribute above or below the other attributes in the table. Location to tap and drag an attribute The order of the attributes in the table is the order that they will appear in the data file name. 5.
Page 187: Set Up Email Notifications
Chapter 11 Configure the instrument settings Set up email notifications Set up email notifications Email notifications are only available when a user is signed in with a Connect account. The emails notifications will be sent to the email address associated with the Connect account. 1.
Page 188: Appendix A Instrument Specifications And Layout
Instrument specifications and layout ■ Instrument dimensions ............. . 188 ■...
Page 189: Instrument And Computer Clearances
Appendix A Instrument specifications and layout Instrument dimensions Depth: 52.5 cm Instrument and computer clearances During instrument installation and maintenance, it is necessary to access the back of the instrument. If the back of the instrument faces a wall, ensure that there is sufficient clearance on the bench to rotate the instrument for access.
Page 190: Configured System Dimensions
Appendix A Instrument specifications and layout Instrument dimensions Configured system dimensions Allow space for the configured instrument. It is not a requirement to locate the computer next to the instrument. The clearances for the instrument shown in the figures also apply to an instrument without a computer. Top clearance for the instrument: 30.5 cm Width of system: 185 cm Back clearance for the computer: 15.25 cm...
Page 191: Light Guidelines
Appendix A Instrument specifications and layout Electrical requirements Light guidelines Use the following guidelines to ensure that there is proper lighting for facial authentication. • Avoid direct light above or behind the user. • Place the instrument in a position that minimizes backlight. •...
Page 192: Environmental Requirements
Appendix A Instrument specifications and layout Environmental requirements Environmental requirements Condition Acceptable range Installation site Indoor use only Electromagnetic Do not use this device in close proximity to sources of strong electromagnetic radiation (for interference example, unshielded intentional RF sources). Strong electromagnetic radiation may interfere with the proper operation of the device.
Page 193: Appendix B Connect The Instrument To A Network
Connect the instrument to a network ■ Connect the computer to the instrument directly or to a LAN ......193 ■...
Page 194: Connect The Instrument To A Wired Network
Appendix B Connect the instrument to a network Connect the instrument to a wired network 6. Set the Internet Protocol (TCP/IP) Properties for either DHCP or Static IP communication: Network configuration Action DHCP 1. Select Obtain an IP address automatically. 2.
Page 195: Connect The Instrument To A Wireless Network
Appendix B Connect the instrument to a network Connect the instrument to a wireless network 5. Tap Done. The Network Connections screen is displayed. The Status and IP Address fields under the Wired option have the information from the selected wired network. 6.
Page 196: Instrument And Computer Connections
Appendix B Connect the instrument to a network Instrument and computer connections Instrument and computer connections Figure 25 Instrument back panel USB ports Wi-Fi dongle port Ethernet port RS-232 port (service use only) ON/OFF switch Power inlet receptacle QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™...
Page 197: Download And Install The Desktop Software
Appendix B Connect the instrument to a network Download and install the desktop software Figure 26 Instrument‑to‑computer connections (minitower configuration) Detachable power supply cord compatible with local power supply receptacle. Connection between the computer and the instrument. Connection between the computer and the monitor, keyboard, and mouse. Connection between the computer and the (optional) handheld barcode scanner.
Page 198: Install The Desktop Software
Appendix B Connect the instrument to a network Networking Install the desktop software If you ordered a computer supplied by Thermo Fisher Scientific, the Field Service Engineer will configure the computer and install the desktop software during system installation. 1. Use an administrator account to log in to the computer on which you are installing the desktop software.
Page 199 Appendix B Connect the instrument to a network Networking (continued) Connect cloud-based platform connection • Instrument‑to‑Connect platform connection (select an option): – Wired connection to the network using an Ethernet cable – or– – Wireless connection to the network using the instrument Wi‑Fi module Local area network (LAN) connection •...
Page 200: Control And Monitor Networked Instruments
Appendix B Connect the instrument to a network Networking Control and monitor networked instruments The following items apply when the instrument is connected to a network: • Computers on the network that are running the desktop software can control the instrument. Networked instruments can be controlled by only one computer at a time.
Page 201: Ethernet Port Overview
Appendix B Connect the instrument to a network Networking Ethernet port overview The Ethernet port of the instrument supports: • Static IP network service with subnet mask, primary and secondary data network service (DNS), and default gateway settings, or dynamic host configuration protocol (DHCP) network service. •...
Page 202: Appendix C Detailed Procedures For Preparation Of A Taqman
Detailed procedures for preparation ™ of a TaqMan Array Card Guidelines for preparation of a card • Keep the card protected from light and stored as indicated until ready for use. Excessive exposure to light may affect the fluorescent probes of the dried-down assays in the card. •...
Page 203: Taqman ™ Array Card Diagram
Appendix C Detailed procedures for preparation of a TaqMan ™ Array Card ™ TaqMan Array Card diagram • Load the card with PCR reaction mix before centrifuging the card. During centrifugation, the PCR reaction mix resuspends the dried-down assays in each well of the card.
Page 204: Load The Pcr Reaction Mix
Appendix C Detailed procedures for preparation of a TaqMan ™ Array Card Load the PCR reaction mix Fill port Vent port Load the PCR reaction mix Before removing the card from its packaging: • Prepare each sample-specific PCR reaction mix. •...
Page 205 Appendix C Detailed procedures for preparation of a TaqMan ™ Array Card Centrifuge the card d. Place the loaded card holder into the bucket so that the card holder label faces the front of the bucket. ► 2. Configure the centrifuge using its front‑panel controls. a.
Page 206: Seal The Card
Appendix C Detailed procedures for preparation of a TaqMan ™ Array Card Seal the card 4. Run the centrifuge. a. Press The centrifuge will start, then automatically stop after 1 minute. b. Repeat substep 4a so that the cards are centrifuged for a total of two, consecutive, 1‑minute centrifugations.
Page 207 Appendix C Detailed procedures for preparation of a TaqMan ™ Array Card Seal the card c. Ensure that the carriage for the sealer is at the starting position. IMPORTANT! Do not insert a filled card into the sealer if the carriage is not in its starting position.
Page 208 Appendix C Detailed procedures for preparation of a TaqMan ™ Array Card Seal the card IMPORTANT! · Do not use excessive force or speed when pushing the carriage across the card. · Do not move the carriage back across the card. Leave the carriage at the ending position while removing the card from the sealer.
Page 209: Appendix D Parts And Materials
Parts and materials Kits, consumables, accessories, and reagents Unless otherwise indicated, all materials are available through thermofisher.com. Store all calibration and RNase P plates at –20°C. All other items can be stored at 15–30°C. Use all materials by the expiration date on the packaging. 96-well 0.2 mL consumables Consumable Amount...
Page 210: 96-Well 0.1 Ml Consumables
Appendix D Parts and materials 96-well 0.1 mL consumables 96-well 0.1 mL consumables Consumable Contents Cat. no. MicroAmp ™ Optical 8-Cap Strips 300 strips 4323032 ™ MicroAmp Fast 8-Tube Strip, 0.1 mL 125 strips 4358293 ™ MicroAmp Fast Reaction Tube with Cap, 0.1 mL 1000 tubes 4358297 MicroAmp...
Page 211: Taqman ™ Array Card Consumables
Appendix D Parts and materials TaqMan ™ Array Card consumables Calibration or instrument verification plate Cat. no. ™ TaqMan RNase P Instrument Verification Plate, 384-well 4455280 Region of Interest (ROI) and Background Plates, 384-well 4432320 ™ QuantStudio 5 10-Dye Spectral Calibration Kit, 384-well A26341 (contains the 2 spectral calibration plates listed below) QuantStudio...
Page 212: Accessories
Appendix D Parts and materials Accessories Accessories Item Amount Cat. No. MicroAmp ™ 96-Well Tray/Retainer Set 10 trays 4381850 ™ MicroAmp Multi Removal Tool 1 tool 4313950 ™ MicroAmp Cap Installing Tool (handle style) 1 tool 4330015 MicroAmp ™ Optical Adhesive Film 25 films 4360954 100 films...
Page 213: Appendix E Safety
Safety ■ Symbols on this instrument ............213 ■...
Page 214: Standard Safety Symbols
Appendix E Safety Symbols on this instrument Standard safety symbols Symbol and description CAUTION! Risk of danger. Consult the manual for further safety information. CAUTION! Risk of electrical shock. CAUTION! Hot surface. CAUTION! Potential biohazard. CAUTION! Ultraviolet light. Symbole et description MISE EN GARDE ! Risque de danger.
Page 215: Additional Safety Symbols
Appendix E Safety Symbols on this instrument Additional safety symbols Symbol and description CAUTION! Moving parts. Symbole et description MISE EN GARDE ! Parties mobiles. Location of safety labels The instrument contains warnings at the locations shown in the figures below. Figure 27 Labels on the back of the instrument (QuantStudio ™...
Page 216 Appendix E Safety Symbols on this instrument Figure 28 Labels on the back of the instrument (QuantStudio ™ 7 Pro Real-Time PCR System) Electrical rating label RFID label Safety label Figure 29 Labels on the drawer Moving parts label QuantStudio ™...
Page 217 Appendix E Safety Symbols on this instrument Figure 30 Labels on the top of the block Hot surface label Figure 31 Labels on the bottom of the block QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™ 7 Pro Real-Time PCR System User Guide...
Page 218 Appendix E Safety Symbols on this instrument Figure 32 Labels on drawer and the installed block Hot surface label Moving parts label Figure 33 Labels on the top of the heated cover Hot surface label QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™...
Page 219: Control And Connection Symbols
Appendix E Safety Symbols on this instrument Figure 34 Labels on the bottom of the heated cover Control and connection symbols Symbols and descriptions On (Power) Off (Power) Conformity symbols Conformity mark Description Indicates conformity with safety requirements for Canada and U.S.A. Indicates conformity with China RoHS requirements.
Page 220: Safety Information For Instruments Not Manufactured By Thermo Fisher Scientific
Appendix E Safety Safety information for instruments not manufactured by Thermo Fisher Scientific (continued) Conformity mark Description Indicates conformity with the WEEE Directive 2012/19/EU. CAUTION! To minimize negative environmental impact from disposal of electronic waste, do not dispose of electronic waste in unsorted municipal waste.
Page 221: Physical Injury
Appendix E Safety Instrument safety Physical injury CAUTION! Moving and Lifting Injury. The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparation guide. Improper lifting can cause painful and permanent back injury. Things to consider before lifting or moving the instrument or accessories: ·...
Page 222: Electrical Safety
Appendix E Safety Instrument safety Electrical safety WARNING! Fuse Installation. Before installing the instrument, verify that the fuses are properly installed and the fuse voltage matches the supply voltage. Replace fuses only with the type and rating specified for the unit. Improper fuses can damage the instrument wiring system and cause a fire.
Page 223: Laser Safety
Appendix E Safety Instrument safety Laser safety ™ ™ WARNING! LASER HAZARD. The QuantStudio 6 Pro System and the QuantStudio 7 Pro System are compatible with an optional Handheld Barcode Scanner. Lasers can burn the retina, causing permanent blind spots. To ensure safe laser operation: ·...
Page 224: Cleaning And Decontamination
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards Cleaning and decontamination CAUTION! Cleaning and Decontamination. Use only the cleaning and decontamination methods that are specified in the manufacturer user documentation. It is the responsibility of the operator (or other responsible person) to ensure that the following requirements are met: ·...
Page 225: Safety Standards
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards Safety standards Reference Description EU Directive 2014/35/EU European Union “Low Voltage Directive” IEC 61010-1 Safety requirements for electrical equipment for measurement, control, and laboratory use – Part 1: General requirements EN 61010-1 UL 61010-1 CAN/CSA C22.2 No.
Page 226: Environmental Design Standards
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards Environmental design standards Reference Description Directive 2012/19/EU European Union “WEEE Directive”—Waste electrical and electronic equipment Directive 2011/65/EU European Union “RoHS Directive”—Restriction of hazardous substances in electrical and electronic equipment SJ/T 11364-2014 “China RoHS”...
Page 227 Appendix E Safety Safety and electromagnetic compatibility (EMC) standards (continued) Reference Description ICES (Innovation, This device contains licence-exempt transmitter(s)/receiver(s) that comply with Science and Economic Innovation, Science and Economic Development Canada's licence-exempt RSS(s). Development Canada) Operation is subject to the following two conditions: 1.
Page 228: Rf Transceiver Specifications
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards RF transceiver specifications RFID readers Description ID ISC.MRM102-A RFID module with asynchronous RS232 interface Frequency 13.56 MHz Modulation Transmit power 54.5 dBuV/m at 10m Antenna 3674.000.00 (ID ISC. ANT40/30 HF PCB Antenna) Dimensions: 40 mm x 30 mm (1.57 inches x 1.18 inches) Antenna: 50 Ohm Supply voltage...
Page 229: Chemical Safety
Appendix E Safety Chemical safety Chemical safety WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel read and practice the general safety guidelines for chemical usage, storage, and waste provided below. Consult the relevant SDS for specific precautions and instructions: ·...
Page 230 Appendix E Safety Chemical safety · Veiller à utiliser des récipients à déchets primaire et secondaire. (Le récipient primaire contient les déchets immédiats, le récipient secondaire contient les fuites et les écoulements du récipient primaire. Les deux récipients doivent être compatibles avec les matériaux mis au rebut et conformes aux exigences locales, nationales et communautaires en matière de confinement des récipients.) ·...
Page 231: Biological Hazard Safety
Appendix E Safety Biological hazard safety Biological hazard safety WARNING! Potential Biohazard. Depending on the samples used on this instrument, the surface may be considered a biohazard. Use appropriate decontamination methods when working with biohazards. WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases.
Page 232: Appendix F Documentation And Support
Documentation and support Related documentation Document Pub. No. QuantStudio ™ 6 Pro Real-Time PCR System and QuantStudio ™ 7 Pro Real-Time MAN0018430 PCR System Hands‑Free Features Quick Reference ™ ™ TaqMan Array Plates with RFID for use with QuantStudio 6 Pro and 7 Pro MAN0018436 Real-Time PCR Systems Quick Reference Guide ™...
Page 233: Customer And Technical Support
Appendix F Documentation and support Customer and technical support Customer and technical support Visit thermofisher.com/support for the latest service and support information. • Worldwide contact telephone numbers • Product support information – Product FAQs – Software, patches, and updates – Training for many applications and instruments •...
Page 234: Index
Index plate, prepare 91 Background calibration accessories 212 Description 86 Add assay 66 Frequency 88 Add data collection location 58 Reminders 88 Add facial authentication 132 Run 91, 100 Add pause 62 Status 87 Add PCR stage 58 When to perform 85 Add PCR step 58 Barcode scan 51 Add profile 134...
Page 235 Index Cancel scheduled run 75 Dilution, Guidelines 114 centrifuge the card 204 Dilution plate Certificate, Upload 182 Prepare plate 115 Change block 157 Run 116 Change password Optimal concentration 116 SAE, Change password 149 Perform 118 Change PIN 133 Prepare plate 117 Clean block 159 Workflow 114 Clear notifications 187...
Page 236 Index dye calibration, plate, prepare 91 fluorescence high Dye calibration Functions, SAE 138, 139 Description 86 Fuses Frequency 88 Replace, Materials required 161 Reminders 88 Run 91, 100 Status 87 When to perform 85 Genotyping run 33 Dyes Guest access Edit 122 Custom 17, 113 System 16...
Page 237 Index Workflow 40 Add 58 Instrument calibration 84 Remove 58 Instrument comparison 16 VeriFlex Zone Instrument features, SAE enabled 137 Remove 59 Instrument log Set up 59 Export 179 View during run 73 View 178 Method elements 57 Instrument name 168 Method tab Instrument profile Actions, Edit method 57...
Page 238 Index Unload 52 Plate file Ramp rates, Configure 62 Copy 77 Reaction volume 57 Create and run a plate 47 Reagents Delete 78 Add 66, 68 Layout 63 Apply 67, 68 Method 56 Delete 67 Properties 55 Edit 66–68 Repeat last run 49 Region, Connect platform 170 Plate layout, Edit 65, 66 related documentation 232...
Page 239 Index Run type Software, Repair 181 Comparative Ct 18 Software features 26 Genotyping 18 Speaker volume, Adjust 169 Melt curve 18 Standard 65, 66 Presence/absence 18 Standard curve run 31 Relative standard curve 18 Standard profile 124 Standard curve 18 Statistics, View 179 Run types Stop run 72...
Page 240 Index Unknown 65, 66 View instrument log 178 Unload plate 52 View license agreement 167 Unlock touchscreen, During run 75 View method during run 73 Upload certificate 182 View notifications 186 USB drive 27 View plots during run, Zoom 74 View privacy policy 167 View time remaining during run 74 Voice commands...
Page 241 QS GT_Instrument UG_RUO_MAN0018045-v22-GUID-6E25F81A- D9AF-47D4-873C-29498B895347-2021/02/13 01:49:02 en 23:54:02.06Z thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 17 February 2021...

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Applied biosystems quantstudio 7 pro

Thermo Scientific Applied Biosystems QuantStudio 6 Pro User Manual

CHAPTER 1 Product Information

CHAPTER 2 Get Started

CHAPTER 3 Create and Run Plates on the Instrument

CHAPTER 4 Edit a Plate before Starting a Run

CHAPTER 5 Options for a Run

CHAPTER 6 View and Manage Files

CHAPTER 7 Calibrate and Verify Instrument Performance

CHAPTER 8 Manage Profiles

CHAPTER 9 Use the Instrument with the Security, Auditing, and E-Signature (SAE) V2.0 Module

CHAPTER 10 Maintain the Instrument

CHAPTER 11 Configure the Instrument Settings

APPENDIX A Instrument Specifications and Layout

APPENDIX B Connect the Instrument to a Network

APPENDIX C Detailed Procedures for Preparation of a Taqman

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