Simoa™ Quick Start Guide

Prepare Instrument

01. Start

  1. Start the day with the PC off, wait 15 seconds, then turn on.
  2. Start the HD-1 Analyzer (instrument), then the Simoa™ software.
  3. Ensure system is finished initializing and is in the ‘Ready’ state before proceeding.

01. Instrument Startup

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This video describes the startup procedure of the Simoa Analyzer.

01.01 — Turning the Instrument Computer On and Off

The instrument computer is inside of the system bay. Complete all assay operations and log out of the Simoa software before you turn off the computer.

To turn the computer on

Press the on/off power switch at the top of the computer. The power switch lights up.

To turn the computer off

Press the on/off power switch at the top of the computer.

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01.02 — Turning the Instrument On and Off

To turn the instrument on

Move the power switch to the on position: Push down the end of the switch with the dash (-). The instrument initializes itself over the next three minutes.

To turn the instrument off

Move the power switch to the off position: Push down the end of the switch with the circle (o).

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01.03 — Logging In To and Out of the Simoa Software

To log in to the software, you need a user name and a password. Only a user with administrative privileges can add users to the system. For information on managing users, see "Managing Users" on page 171.

To log in to the software

  1. Double-touch the Simoa software icon on the instrument desktop.
  2. Enter your user name and password > touch Enter.
  3. Allow HD-1 to enter "Ready" state before proceeding.

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02. Check Fluids

  1. Check/fill system fluids in bottom of cabinet, empty solid waste if necessary, and empty liquid waste if necessary.

02. Check Fluids

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02.01 — Refilling the System Fluid Containers

Refill the secondary system fluid containers (system wash buffer 1, system wash buffer 2, and deionized water) before the first run of the day and whenever the container alert icons at the bottom of the software screen turn red.

Note that you only need to fill the secondary containers, not the primary containers. The primary containers passively refill themselves from the secondary containers.

To refill a secondary system fluid container


  1. Remove the container, as described below. As you lift the front end of the container, the plug connecting it to the primary container disconnects.
    • To remove the secondary containers for the deionized water and the system wash buffer 1, lift the containers out of their seats.
    • To remove the system wash buffer 2 secondary container, with one hand pull out the spring-loaded handle on its seat and with the other hand lift the container out of its seat.
  2. Unscrew the cap and refill the container with the correct fluid. Screw the container cap back on when you are finished.
  3. Replace the container, as described below. Do not force a container into its seat. The connectors should mate easily. If you experience resistance, remove the container and try again.
    • To replace the deionized water and the system wash buffer 1 secondary containers, tip the connector end of the container down slightly and insert it into the seat.
    • To replace the system wash buffer 2 secondary container, with one hand pull out the spring-loaded handle on its seat and with the other hand insert the container into the seat, being sure to tip the connector end of the container down slightly.

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02.02 — Emptying the Solid Waste Container

Empty the solid waste container whenever the solid waste alert icon at the bottom of the software screen turns yellow or red.

The solid waste container holds discarded cuvettes, disposable pipettor tips, and Simoa Discs.

To empty the solid waste container

  1. Pull the solid waste drawer out of the system bay.
  1. Remove the waste bag > insert a new waste bag. Dispose of the waste bag according to the waste disposal policies of your organization.
  1. Touch the System Resources tab > touch one of the disc diagrams to view the Solid Resources screen (for information on reading the Solid Resources screen, see page 127).
  2. Push the solid waste drawer into the system bay.
  3. When the system prompts you, touch Yes to confirm.

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02.03 — Emptying the Liquid Waste Containers

The instrument discards liquids into only one liquid waste container at a time. When a container is in use, a light in its cap turns on.

Empty both liquid waste containers before the first run of the day.

During a run, the instrument senses the fluid level in the containers with a floating sensor inside the containers. When both containers are full, the liquid waste icon at the bottom of the software screen turns red.

To ensure decontamination of liquid waste, follow the instructions below to clean the waste container with the cleaner specified in your in-house decontamination procedures.

To empty the liquid waste container

  1. Disconnect the fluid tubing and the container sensor by pulling them straight up.
  2. Remove the container and dispose of the liquid waste according to the waste disposal policies of your organization.
  1. Place cleaner into the container as specified by your in-house cleaning procedures and replace it in the system bay.
  2. Reconnect the tubing and the container sensor. When done correctly, you hear a click when you reinsert each container.

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03. System Resources Tab

  1. System Resource Tab: Load > 200 cuvettes, tips (two per sample), and discs, if required.

03. System Resources Tab

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03.01 — Loading Instrument Consumables

Loading Cuvettes

Single Cuvette


Cuvette Stack

The instrument uses 1-mL plastic cuvettes as reaction vessels. Cuvettes are snapped together into stacks of 50 to make them easy to load.

The cuvette holder has 10 chutes into which you insert stacked cuvettes. The instrument monitors the number of cuvettes in each chute. When a chute contains only five cuvettes, the instrument rotates the chute to the front of the cuvette holder and the software notifies you to load a new cuvette stack.

To determine whether you need to load cuvettes

Touch the System Resources tab. If there are no cuvettes, the cuvette diagram is red.

To load cuvettes

  1. Touch the System Resources tab > touch the cuvette diagram. The Solid Resources screen appears. For information on reading this screen, see page 127.
  2. Add cuvettes until the count is at least 200:
    • Unwrap a stack of cuvettes and insert it into the cuvette holder, as illustrated below, with the point down. The cuvette number in the Solid Resources screen updates.

The loader rotates to a new position. Wait for the rotation to finish before loading a new stack.

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03.02 — Loading Disposable Pipettor Tips

Each of the two System Resources drawers holds up to three disposable pipette tip rack. A full rack holds 96 tips, so the maximum number of tips that may be loaded at one time is 576, or 6 full racks.

When you load tips, you indicate in the software the position of each loaded tip. Doing so specifies the number of loaded tips and allows the software to count down from this number and to notify you if you need to load more tips.

To determine whether you need to load disposable pipettor tips

  1. Touch the System Resources tab > touch one of the Tip diagrams to view the Solid Resources screen (for information on reading the Solid Resources screen, see page 127.)
  2. If the System Resources drawer is locked, touch the Unlock button located under the System Resources Drawer diagram (see page 127).
  3. Pull out both System Resources drawers and verify that enough tips are loaded to complete the next planned assay run.
  4. Double the total number of tests to be run in the assay to determine the number of tips required.

To load disposable pipettor tips

  1. Open the System Resources drawers > remove empty tip racks.
  2. Remove the cover from new tip racks and place them in the drawer. Fill all rack positions.
  1. In the System Resources tab, touch one of the tip diagrams to open the Solid Resources screen.
  2. In the Solid Resources screen, tap twice in the positions where you loaded new tip racks. The tip positions in the rack diagram turn light blue.

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03.03 — Loading Simoa™ Discs

Simoa Discs are loaded onto mounting poles at the rear of the System Resources drawers. One disc stack contains 16 discs. The maximum disc capacity is 32.

When you load a stack of discs, you scan the package barcode, which tells the software that you have loaded 16 discs. The instrument counts down from this number every time you consume a disc and notifies you if you need to load more discs.

To calculate the number of discs needed for a run

Each disc has 24 arrays, and one array is required per sample. Therefore, divide the number of samples in the run by 24 and then round up to the nearest whole disc. For example: 96 samples/24 = 4 discs; 78 samples/24 = 3.5, round up to 4 discs.

  1. Touch the System Resources tab > touch one of the disc diagrams to view the Solid Resources screen (for information on reading the Solid Resources screen, see page 127).
  2. View the Solid Resources screen to determine if there are enough discs for your run.

To load Simoa Discs onto an empty disc pole

  1. Obtain one package of discs.
  2. When the Solid Resources screen indicates there are zero discs available, touch Unlock to open the appropriate System Resource drawer.
  1. Pull out the System Resources drawer.
  2. Remove the blue base plate from the disc pole. This plate sits at the bottom of every package of discs.
  1. Load one package of discs:
    1. Tap the disc barcode box > scan the package barcode with the barcode scanner. The barcode and the number of discs in the package (16) appear in the disc diagram.
    1. Press the package onto the mounting pole. The package label should be on top.
    1. Pull the red tear strip on the plastic wrapper and remove it.
    2. Remove and discard the top disc, which has a logo sticker on it.
    3. Make sure that the discs are oriented correctly. You should see a shiny black surface with holes in it on the top disc on the stack. If you see the flow cells, the discs are upside down.
  1. Push the drawer into the instrument until it catches.
  2. Verify that the Resources screen reports the correct number of discs in both drawers.
  3. Repeat "To load Simoa Discs onto an empty disc pole" on page 48 if you need to load a second package of discs.

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04. Maintenance Tab Part 1

  1. Maintenance Tab: If first run of day, verify that End of Day task was run the previous night. If not, run this task now (about 20 minutes).

04. Maintenance Tab, Part 1

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04.01 — Understanding the Maintenance Screen

The Maintenance screen shows status information about each maintenance task

Legend Add task filter (Customer Service only)
  Blocking behavior. See "Viewing Task Details" on page 150.
  Touch to show log
  Touch to choose columns
  View task parameters
  Print the task
  Run the selected task

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04.02 — Determining Whether a Maintenance Task Was Performed

The Maintenance screen shows status information about each maintenance task. Two methods are available to do this:

  • Check the Last Run column in the Maintenance tab, which reports the date and time when a task was last performed.
  • In the Maintenance tab, touch Show Log to view a log that lists all completed maintenance tasks.

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04.03 — Viewing Task Details

Use the read-only Task Details screen to display a description of a task, the task interval (when it is run), and its blocking behavior.

To view task details

Touch the checkbox for a task > touch View Details.

Legend Interval – The frequency of the task.
  Time – Time of day the task is performed.
  Blocks sample processing – Prevents assays from running or allow them to run if the task is not complete.
  Resets idle time – Resets/does not reset counter after task is performed
  Blocks shutdown when due – When enabled, the following prompt appears when you shut down the software.

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04.04 — Changing Columns

To change the table columns, touch Configure Columns > touch the arrows to move column names between the Available and the Selected boxes.

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04.05 — Performing the End of Day Task

The End of Day task flushes the pipettor that aspirates reagents and all pipettor and system fluid tubings to prevent the buildup of salts, which can clog the pipettor and instrument tubings.

The task performs these actions:

  • Flushes the pipettor with deionized water, cleans it with system wash buffer 1, and flushes it again with deionized water.
  • Primes the tubing for system wash buffer 1 and 2 with deionized water.

To perform the End of Day task

  1. Fill a clean reagent bottle a little more than half way with system wash buffer 1. Make sure that there are no bubbles in the bottle.
  2. Touch the Maintenance tab > touch the End of Day task checkbox > touch Run Task.
  3. When prompted, place the bottle into position 3 on a reagent rack (fourth position from the handle) and put the rack in the rightmost reagent bay position (lane 4).
  4. Allow approximately 20 minutes for completion. When the task is complete, touch Close, and remove the reagent rack and dispose of the reagent bottle.

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05. Maintenance Tab Part 2

  1. Maintenance Tab: If first run of day, verify that Start of Day task was run earlier in the day. If not, run this task now (about 20 minutes).
  2. Note: If software has been restarted, run Start of Day task again.

05. Maintenance Tab, Part 2

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05.01 — Understanding the Maintenance Screen

The Maintenance screen shows status information about each maintenance task

Legend Add task filter (Customer Service only)
  Blocking behavior. See "Viewing Task Details" on page 150.
  Touch to show log
  Touch to choose columns
  View task parameters
  Print the task
  Run the selected task

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05.02 — Determining Whether a Maintenance Task Was Performed

The Maintenance screen shows status information about each maintenance task. Two methods are available to do this:

  • Check the Last Run column in the Maintenance tab, which reports the date and time when a task was last performed.
  • In the Maintenance tab, touch Show Log to view a log that lists all completed maintenance tasks.

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05.03 — Viewing Task Details

Use the read-only Task Details screen to display a description of a task, the task interval (when it is run), and its blocking behavior.

To view task details

Touch the checkbox for a task > touch View Details.

Legend Interval – The frequency of the task.
  Time – Time of day the task is performed.
  Blocks sample processing – Prevents assays from running or allow them to run if the task is not complete.
  Resets idle time – Resets/does not reset counter after task is performed
  Blocks shutdown when due – When enabled, the following prompt appears when you shut down the software.

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05.04 — Changing Columns

To change the table columns, touch Configure Columns > touch the arrows to move column names between the Available and the Selected boxes.

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05.05 — Performing the Start of Day Task

This task sets up the instrument for a new assay run as follows:

  • Washes the fixed-tip pipettor.
  • Primes tubes with wash buffer fluid and then discards the cuvettes.
  • Loads 10 cuvettes into the Wash/Incubator rings.

To perform the Start of Day task

  1. Fill a clean reagent bottle a little more than half way with system wash buffer 1. Make sure there are no bubbles in the bottle.
  2. Touch the Maintenance Tab > touch the Start of Day task checkbox > touch Run Task.
  3. When prompted, place the reagent bottle into position 3 on a reagent rack (fourth position from the handle) and put the rack in the rightmost reagent bay position (lane 4).
  4. Allow approximately 20 minutes for completion. When the task is complete, touch Close, remove the reagent rack and dispose of the reagent bottle.

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06. Maintenance Tab Part 3

  1. Maintenance Tab: If Start of Day Task was performed, but system has been idle for over 4 hours, run Idle System Prime (about 10 minutes).

06. Maintenance Tab, Part 3

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06.01 — Understanding the Maintenance Screen

The Maintenance screen shows status information about each maintenance task

Legend Add task filter (Customer Service only)
  Blocking behavior. See "Viewing Task Details" on page 150.
  Touch to show log
  Touch to choose columns
  View task parameters
  Print the task
  Run the selected task

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06.02 — Determining Whether a Maintenance Task Was Performed

The Maintenance screen shows status information about each maintenance task. Two methods are available to do this:

  • Check the Last Run column in the Maintenance tab, which reports the date and time when a task was last performed.
  • In the Maintenance tab, touch Show Log to view a log that lists all completed maintenance tasks.

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06.03 — Viewing Task Details

Use the read-only Task Details screen to display a description of a task, the task interval (when it is run), and its blocking behavior.

To view task details

Touch the checkbox for a task > touch View Details.

Legend Interval – The frequency of the task.
  Time – Time of day the task is performed.
  Blocks sample processing – Prevents assays from running or allow them to run if the task is not complete.
  Resets idle time – Resets/does not reset counter after task is performed
  Blocks shutdown when due – When enabled, the following prompt appears when you shut down the software.

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06.04 — Changing Columns

To change the table columns, touch Configure Columns > touch the arrows to move column names between the Available and the Selected boxes.

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06.05 — Performing the Idle Fluid Prime Task

Prime the system fluids after 240 idle minutes. Idle time is the amount of time since the instrument finished a run, or the time since a task that resets the idle counter was run.

To perform the Idle Fluid Prime Task

  1. In the Maintenance tab, touch the Idle Fluid Prime checkbox > touch Run Task.
  2. The system fluids are primed and the idle time counter is set to zero.

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Setup Assay

07. Vortex

  1. Vortex beads for about 30 seconds before loading reagents. Don’t let beads sit idle > 5 minutes. If this happens, vortex again.

07. Vortex

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07.01 — Loading Reagents and RGP into the Instrument

Loading reagents and RGP involves:

  • Placing reagent bottles into a reagent rack.
  • Identifying in the Simoa software the physical position of reagents in the rack.
  • Scanning reagent label barcodes.
  • Inserting the rack.

Load as follows:

  • Load detector and SBG reagents into any lane of the reagent bay
  • Load beads into the first three (shaking) positions
  • Load RGP into lanes labeled RGP 1 or RGP 2

Occasionally, a barcode may not be scannable because the label has been damaged in some way. When this happens, manually enter the barcode into the appropriate software field (see page 94).

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07.02 — Understanding the Load Reagents Screen

By default, the screen shows a reagent rack diagram, as shown below. When you touch one of the RGP lanes, the screen changes to show an RGP rack diagram. To view an example of the RGP rack diagram, see page 102.

Legend Diagram of reagent bay lanes 1 to 4 Green box shows selected lane
  Diagram of sample bay lanes RGP1 and RGP 2
  Touch to view screen information as a graphic or table
  Displays barcode number and data for the reagent in the highlighted position in the reagent rack diagram
  Reagent rack diagram: Green box shows selected rack position
  Rack position numbers: Position 1 is farthest from rack

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08. Load Reagents Part 1

  1. Load reagents into reagent rack. Make sure beads are in one of the three shaking positions to continue mixing beads.

08. Load Reagents, Part 1

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08.01 — Understanding the Load Reagents Screen

By default, the screen shows a reagent rack diagram, as shown below. When you touch one of the RGP lanes, the screen changes to show an RGP rack diagram. To view an example of the RGP rack diagram, see page 102.

Legend Diagram of reagent bay lanes 1 to 4 Green box shows selected lane
  Diagram of sample bay lanes RGP1 and RGP 2
  Touch to view screen information as a graphic or table
  Displays barcode number and data for the reagent in the highlighted position in the reagent rack diagram
  Reagent rack diagram: Green box shows selected rack position
  Rack position numbers: Position 1 is farthest from rack

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08.02 — Loading Reagents

Loading reagents involves identifying the rack positions of the bead, detector, SBG, and sample diluent reagents in the Load Reagents screen and then scanning their barcodes. The software associates the barcodes with the identified positions so that the instrument pipettors can be directed to the correct bottles in the loaded rack. The barcode data also allows the software to calculate running reagent volume and count down to reagent expiration dates.

Make sure that the bead reagent is well mixed when you load it. If the bead reagent is left sitting stationary for more than five minutes before you load it, remix the beads according to the instructions in the assay package insert.

To load reagents

  1. Mix the bead reagent according to instructions in the assay package insert. If the bead reagent is left sitting stationary for more than five minutes before you load it, repeat this step.
  2. Remove and set aside the caps from the reagent bottles. For a Homebrew assay: Make sure that the reagent bottles are labeled, as described in the package insert so that each bottle has the correct barcode.
  3. Insert the bead reagent into reagent rack position 1, 2, or 3.
  4. Insert the other reagents into any other reagent rack position, including unoccupied shaking positions (1, 2, or 3).
  5. Turn the bottles so that the reagent label barcodes are centered in the notch of the bottle holder. The barcodes must be unobstructed so that they can be scanned accurately.
  6. Touch the Load Reagents tab > touch a reagent bay lane in the screen. This step identifies the lane into which you will load the reagent rack.
  7. Legend Reagent bay lane 1 has been selected
  8. Scan the bottle barcodes:
    1. In the reagent rack diagram, touch the position that corresponds to the position of the bead reagent bottle in the reagent rack.
    2. Legend Position 1 has been selected
    3. Scan the bead reagent barcode with the barcode scanner. The barcode and data about the bead reagent appear in the green box in the screen. If a barcode does not scan, enter it manually (see “Manually Entering a Reagent Barcode” on page 94).
    4. Repeat these two steps for the rest of the reagents in the rack.
  9. Insert the rack in the reagent bay lane that you selected in step 6 until it clicks into place. The rack diagram updates to show the short name of each loaded reagent in its identified rack position. The lane diagram updates to show the positions of reagents in the selected lane. The Reagent Barcode box shows barcode data for the position that is highlighted in the reagent rack diagram.

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09. Load Reagents Part 2

  1. Load Reagent Tab: Select reagent lane and use barcode reader to assign positions of reagents in reagent rack. Insert reagent rack. Select an RGP lane (RGP 1 or RGP2) and use the barcode reader to assign RGP. Insert RGP rack. Touch Done

09. Load Reagents, Part 2

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09.01 — Understanding the Load Reagents Screen

By default, the screen shows a reagent rack diagram, as shown below. When you touch one of the RGP lanes, the screen changes to show an RGP rack diagram. To view an example of the RGP rack diagram, see page 102.

Legend Diagram of reagent bay lanes 1 to 4 Green box shows selected lane
  Diagram of sample bay lanes RGP1 and RGP 2
  Touch to view screen information as a graphic or table
  Displays barcode number and data for the reagent in the highlighted position in the reagent rack diagram
  Reagent rack diagram: Green box shows selected rack position
  Rack position numbers: Position 1 is farthest from rack

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09.02 — Loading RGP

RGP must be loaded into an RGP rack and placed in sample bay RGP 1 or RGP 2 only (the substrate lanes).

The RGP racks are customized to hold the short RGP reagent vials at optimum position for the instrument pipettors.

One bottle of RGP is equal to 96 samples.

To load RGP

  1. Mix the RGP vials, as described in the assay package insert.
  2. Remove and set aside the caps from one or more RGP vials > insert the RGP vials into the RGP rack.
  3. Touch the Load Reagents tab > touch lane RGP 1 or RGP 2 in the screen. This step identifies the lane into which you load the RGP rack. The Load Reagents screen shows an RGP rack diagram.
  4. Legend RGP Loading into Lane 1 shown in the Rack Diagram of the Load Reagents screen.
  5. Scan the vial barcodes:
    1. In the RGP rack diagram, touch the position that corresponds to the position of the RGP vial in the reagent rack.
    2. Legend Position 1 has been selected
    3. Scan an RGP vial barcode with the barcode scanner and insert the vial in position 1 of the rack. The barcode and data about the scanned vial appears in the Load Reagents screen.
    4. Repeat these two steps for the rest of the RGP vials.
  6. Insert the rack into the lane that you selected in step 3 until it clicks into place. The RGP rack diagram updates to show each RGP vial in its identified rack position. The lane diagram updates to show the RGP vial positions in the selected lane.

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Load Reagents (button)

10. Setup Run Tab

  1. Setup Run Tab: Enter plate or rack barcode. Use Assign Calibrators screen for calibrators and Assign Samples screen for samples. When setup is complete, insert plate rack or tubes. Touch Done with Setup.

10. Setup Run Tab

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10.01 — Setting up a Run

Setting up the run involves identifying calibrators and samples in the Setup Run tab.

In this tab, you can toggle between the Assign Calibrators and Assign Samples screen.

In this chapter, the examples describe a single plate that contains all of the calibrators. You can also set up your assay calibrators on multiple plates.

Once you have set up a run, you can export the assignments to a file and import the mappings the next time you run the assay.

If an experiment requires multiple assay runs, you can assign a Batch Name to all the plates or tube racks that you run for the experiment. This procedure allows you to group the experiment’s results in the Run History screen.

Assigning calibrators and samples involves:

  • Selecting an assay.
  • Identifying in the software the physical location of calibrators and samples in the plates or tubes that you will be loading into the instrument.
  • Associating each calibrator with one of the calibrator concentrations in the assay definition.
  • Selecting the number of replicates to run. See “Preparing Calibrators and Samples” on page 95 for a complete explanation.
  • Naming each sample and, depending on the assay, selecting the number of replicates to run and a dilution factor for the replicates.
  • Selecting the sample processing order (Rows or Columns).

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10.02 — Understanding the Assign Calibrators Screen

The Assign Calibrators screen shows a plate diagram or a tube diagram depending on how you have set up the instrument (see “Preparing the Instrument for the Run” on page 96).

For information on using the well selection tools, see “Selecting Plate Wells and Removing Assignments” on page 106.

The plate view appears below. See page 186 for the tube rack view.

Use Multi Select to assign replicates for multiple calibrators.

Legend Batch name and plate barcode batch
  Process in row or Plate position diagram Displays ID, concentration, and column order
  Multi‐select non‐adjacent wells
  View screen information as a graphic or table
  Plate position diagram. See page 106 for explanation.
  Slide to view all assay definitions or loaded definitions only
  Displays ID, concentration, and replicates for highlighted wells
  Select number of replicates per well
  Touch to select a calibrator value (assay must be selected first)
  Touch one to automatically assign all calibrators
  Displays sample volume for highlighted wells
  Touch to switch between Assign Calibrators and Assign Samples views
  Import saved calibrator and sample plate assignments

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10.03 — Understanding the Assign Samples Screen

The plate view appears below. See page 186 for the tube rack view.

Legend Batch name and plate barcode batch
  Process in row or column order
  Multi‐select non‐adjacent wells
  Touch to view screen information as a graphic or table
  Plate position diagram. See page 106 for explanation.
  Slide to view all assay definitions or loaded definitions only
  Touch to select sample replicates and dilutions
  Displays sample volume for highlighted wells
  Autoname tool
  Touch to switch between Assign Calibrators and Assign Samples views
  Export calibrator and sample assignments

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10.04 — Understanding the Plate Position Diagram

The plate position diagram identifies the lanes into which a plate is loaded and the position of a plate in those lanes. Plate rack 1 may only be loaded into lanes 1–4, and plate rack 2 into lanes 5–8. There are two plate positions for each plate rack.

Selections in the diagram apply to both the Assign Calibrators and the Assign Samples screens. For example, if you select plate 2 in the Assign Calibrators screen and then switch to the Assign Samples screen, the plate remains selected.

Legend Loads into instrument in this direction
  Position 1 in plate rack 1 has been selected
  Plate rack 1
  Plate rack 2

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10.05 — Selecting Processing Order

You can process your samples within a given plate by Row (left to right) or Column (top to bottom). If you have multiple plates, they are processed in ascending numerical order from 1 to 4.

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10.06 — Selecting Plate Wells and Removing Assignments

You must select plate wells to assign calibrators or samples to them. After you have made assignments, you can deselect or select wells without changing their assignments.

  • To select a block of wells, touch the plate and draw a marquee around the wells.
  • To select individual, nonadjacent wells, turn on Multi Select > touch the wells.
  • To remove specific selections, touch the plate and draw a marquee around the wells > touch Clear Selected.
  • To remove all selections and assignments on a plate, touch Clear Rack.
  • To remove assignments from specific wells, select the wells > touch Clear Contents.

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10.07 — Understanding the Required Sample Volume Field

The Required Sample Volume field reports the total amount of sample that will be consumed by all assignments that you have made. This field can help you monitor sample consumption so that you do not assign more sample volume than you have placed in a plate or a tube.

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10.08 — Understanding the Autoname Tool

Use the Autoname tool to quickly name a range of plated samples. This tool creates names of the following format:

[alphanumeric prefix up to nine characters long][first number in series] 

For example: PSA02Mar1, PSA02Mar2, PSA02Mar3

Autonames are applied to a set of selected samples in row order or column order.

To generate sequential IDs

  1. Enter a text or numeric prefix in the Prefix field.
  2. Touch Row Order or Column Order.
  3. Optionally, change the Start Number.
  4. Touch Generate Now.

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10.09 — Assigning Calibrators

To assign calibrators, you identify in the software the physical location of all calibrators in a plate or tube rack, and then you associate each calibrator with a calibrator concentration in the assay definition.

Assigning Calibrators in Plates

Make sure that you have plated the calibrators correctly. You can assign multiple calibrators to a plate up to the capacity of the plate well. See "Preparing Calibrators and Samples" on page 95.

  1. Open the Assign Calibrators screen:
    • If you are in the Assign Samples screen, touch Assign Calibrators.
    • If you are not in the Assign Samples screen, touch the Setup Run tab > touch Assign Calibrators.
  2. Recommended: Place prepared plates of calibrators and samples in plate racks and put the racks into the sample bay, but do not fully insert them.
  3. Name the plate that contains the calibrators:
    1. Touch the plate position that matches the location of the plate that contains the calibrators. For information on reading the plate position diagram, see page 106.
    2. Enter a name for the batch and a plate name > touch Enter. You can use any combination of letters and numbers.
  4. Perform the following steps to associate each set of calibrator replicates with the calibrator values in the assay definition, in ascending or descending order.
    1. Identify the first of the plated calibrators:
      • If you have plated only one set of calibrators: Touch the well that contains the first calibrator in the set.
      • If you have plated two or more replicates: Touch the first calibrator for one of the replicates. (You will repeat the entire assignment procedure to assign the remaining replicates.)
    2. Identify the assay:
      • If you have already loaded reagents: Set the Assays Loaded only button to On. The instrument selects the correct assay, based on the reagents that you have loaded, so you do not need to manually select an assay.
      • If you are performing a Homebrew assay and you have already loaded reagents: Set the Assays Loaded only button to Off > touch a Homebrew assay.
      • If reagents loaded For Homebrew assay
    3. Touch the highest or lowest calibrator > touch OK. The well that you selected turns red and a checkmark appears on it, signifying that an assay has been assigned to the well.
    4. Touch Ascending or Descending under Assign All Calibrators. The software assigns all calibrators that are defined for the assay in the specified order, beginning with the selected well. The plate diagram shows the assignments. To view the concentration that is assigned to a well, touch the well and view the Calibrator box.
    5. Repeat to assign all sets of calibrator replicates.
  5. Select the processing order.
    • Select Row to process the calibrators within a given plate from left to right
    • Select Column to process the calibrators within a given plate or rack from top to bottom.
  6. If you have multiple plates, they are processed in ascending numerical order from 1 to 4.

  7. If the plates contain samples, assign them now. See "Assigning Samples in Plates" on page 117. If you are finished, see "Loading Calibrators/Samples into the Instrument" on page 123.

Assigning Calibrators in Tubes

  1. Open the Assign Calibrators screen:
    • If you are in the Assign Samples screen, touch Assign Calibrators.
    • If you are not in the Assign Samples screen, touch the Setup Run tab > touch Assign Calibrators.
  2. Recommended: Place prepared plates of calibrators and samples in plate racks and put the racks into the sample bay, but do not fully insert them.
  3. In the tube position diagram, touch the lane that contains the calibrators.
  4. Legend Sample bay lane 1 has been selected
  5. Enter a batch name and a tube rack name > touch Enter. You can use any combination of letters and numbers.
  6. Perform the following steps to associate tubes of calibrators with the calibrator values in the assay definition, in ascending or descending order.
    1. In the tube rack diagram, touch the position that holds the first calibrator in the rack.
    2. Legend Tube 1 has been selected
    3. Identify the assay:
      • If you have already loaded reagents: Set the Assays Loaded only button to On. The instrument selects the correct assay, based on the reagents that you have loaded, so you do not need to manually select an assay.
      • If you are performing a Homebrew assay and you have already loaded reagents: Set the Assays Loaded only button to Off > touch a Homebrew assay.
      • If reagents loaded For Homebrew assay
    4. In the Select Calibrator dialog, touch the position that contains the highest or lowest calibrator > touch OK.
      In the rack position diagram, the tube position that you selected turns red and a checkmark appears on it, signifying that an assay has been assigned to the tube.
    5. Touch Ascending or Descending under Assign All Calibrators. The software assigns all calibrators that are defined for the assay in the specified order, beginning with the selected tube position. The tube position diagram shows the assignments.
      To view a calibrator assignment, touch a tube in the tube rack diagram. The calibrator and concentration appear in the Calibrator box.
  7. If you have loaded tubes of samples, assign them now. See "Assigning Samples in Tubes" on page 121. If you are finished, see "Loading Calibrators/Samples into the Instrument" on page 123.

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10.10 — Assigning Samples

To assign samples, you identify the physical location of all samples in a plate or tube rack, and then you specify the number of replicates to run for each sample and dilutions (if the assay definition allows).

Assigning Samples in Plates

  1. Open the Assign Samples screen:
    • If you are in the Assign Calibrators screen, touch Assign Samples.
    • If you are not in the Assign Calibrators screen, touch the Setup Run tab > touch Assign Samples.
  2. Recommended: Place prepared plates of calibrators and samples in plate racks and put the racks into the sample bay, but do not fully insert them.
  3. In the plate position diagram, touch a plate that contains samples. (For informa‐ tion on reading the plate position diagram, see page 106.)
    1. If a name appears in the Plate Barcode field, the plate is already named, and you can skip to step 4. This is true if you touch a plate that contains calibrators that you have previously assigned.
    2. If the Plate Barcode field is empty, enter a batch name and a plate name > touch Enter. You can use any combination of letters and numbers.
    3. Legend Batch name
      Legend Plate name
  4. Select the processing order.
    • Select Row to process the calibrators within a given plate from left to right
    • Select Column to process the calibrators within a given plate or rack from top to bottom.

    If you have multiple plates, they are processed in ascending numerical order from 1 to 4.

  5. Assign an ID to the samples in the selected plate (see page 107 for information on autonames):
    1. Select a range of wells (for information on selecting wells, see page 106).
    2. In the Autoname tool, enter a prefix string, which will apply to every name, and a starting number.
    3. Touch Row Order or Column Order.
    4. Touch Generate Now. The software assigns a name to the selected wells and they turn yellow.
  6. Specify an assay, replicates, and dilutions for samples:
    1. Select plate wells.
    2. Specify an assay (checkmarks appear on the selected wells after you do this):
      • If you have already loaded reagents: Touch On in the Assays Loaded only button. The instrument selects the correct assay, based on the reagents that you have loaded, so you do not need to manually select an assay
      • If you are performing a Homebrew assay and you have already loaded reagents: Touch Off in the Assays Loaded only button > touch a Homebrew assay.
      • If reagents loaded For Homebrew assay
    3. Specify replicates and dilutions:
      • Select a replicate number from the drop‐down list.
      • Touch the dilution that is specified in the assay package insert.
      • Touch any other dilution that has a checkmark to remove the checkmark.
  7. If you have more than one plate of samples, repeat steps 3 to 5 to assign all the samples.
  8. If you need to assign calibrators, see "Assigning Calibrators in Plates" on page 108. If you are finished, see "Loading Calibrators/Samples into the Instrument" on page 123.

Assigning Samples in Tubes

  1. Open the Assign Samples screen:
    • If you are in the Assign Calibrators screen, touch Assign Samples.
    • If you are not in the Assign Calibrators screen, touch the Setup Run tab > touch Assign Samples.
  2. Recommended: Place prepared tubes of calibrators and samples in tube racks and put the racks into the sample bay, but do not fully insert them.
  3. Touch a lane that holds a rack containing sample tubes.
  4. Assign an ID to the samples in the selected rack (see page 107 for information on autonaming):
    1. In the tube rack diagram, select a tube position.
    2. Legend Tube 1 has been selected
    3. Enter a Barcode ID for the tube.
    4. Physically load the rack. See "Loading Calibrators/Samples into the Instrument" on page 123.
    5. Repeat these steps to name all tubes in the rack.
  5. Select an assay for the selected tube:
    • If you have already loaded reagents: Touch On in the Assays Loaded only button. The instrument selects the correct assay, based on the reagents that you have loaded, so you do not need to manually select an assa
    • If you are performing a Homebrew assay and you have already loaded reagents: Touch Off in the Assays Loaded only button > touch a Homebrew assay.
    • If reagents loaded For Homebrew assay
  6. Specify replicates and dilutions for the selected tube:
    1. Select a replicate number from the drop‐down list.
    2. Touch the dilution that is specified in the assay package insert.
    3. Touch any other dilution that has a checkmark to remove the checkmark.
  7. Repeat steps 3 to 6 to assign all tubes of samples.
  8. If you need to assign calibrators, assign them now. See "Assigning Calibrators in Tubes" on page 113. If you are finished, see "Loading Calibrators/Samples into the Instrument" on page 123.

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10.11 — Loading Calibrators/Samples into the Instrument

The final step in assigning calibrators and samples is to load them into the instrument so that the software accepts the assignments.

To load assigned calibrators and samples

  1. Optional: Save the assignment file. In the Assigned Samples screen, touch Export Layout > save the file in the Save As dialog.
  2. If you have not already done so, place the plate racks or tube racks into the sample bay.
  3. Push the plate racks or tube racks into the sample bay until they latch into place.
  4. Touch Done With Setup. The All Resources screen in the System Resources tab opens. See “Starting a Run” on page 124 to initiate the run.

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10.12 — Importing and Exporting an Assignment File

You can export a finished layout of calibrator and sample assignments to a file and then re‐use it the next time you run the assay.

To export an assignments file

In the Assign Samples screen, touch Export Layout > name and save the file. Do not change the specified file extension (.csv).

To import an assignments file

In the Assign Calibrators screen, touch Import Layout > open the file.

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11. System Resources Tab

  1. System Resource Tab: When Start Run button on the All Resources screen becomes active, touch it. If button doesn’t become active, check for red flags on bottom of screen.

11. System Resources Tab

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11.01 — Start a Run

To start a run

  1. Touch Done with Setup in the Assign Calibrators or Assign Samples screen. The System Resources tab opens.
  2. If the button is active, touch Start Run.

    If the button is inactive, touch Resource Details to display a complete readiness status (including status of beads, detectors, SBG, and RGP). You may need to perform some of the following tasks to activate the Start Run button again:
    • If the Maintenance task icon is red, touch the Maintenance icon and perform any pending mandatory tasks. See Chapter 11, "Maintaining the Simoa HD‐1 Analyzer," on page 147.
    • If the cuvettes, tips, or discs diagrams are red, add more of those resources. See “Loading Instrument Consumables” on page 43.
    • If the system liquid diagram or either wash buffer diagrams are red, refill the container. See “Refilling the System Fluid Containers” on page 51.
    • If the liquid waste diagram is red, empty the liquid waste container. See “Emptying the Liquid Waste Containers” on page 56.
    • If the solid waste diagram is red, push the solid waste container into its correct position. See “Emptying the Solid Waste Container” on page 54.
    • If the sealing oil diagram is red, replace the sealing oil bag. See “Changing the Sealing Oil Bag” on page 53.

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11.02 — Understanding the System Resources Screen

Diagram color indicates status:

  • Green: Adequate amounts
  • Yellow: Low amounts
  • Red: Empty, must be refilled, or container is full and must be emptied.
Legend Cuvette status
  Disc status
  Select type of resource and detail level
  Disposable pipettor tip status
  Fill status of wash buffer containers
  Fill status of deionized water container
  Fill status of solid waste container
  Fill status of liquid waste container
  Fill status of sealing oil bag
  Touch to start a run

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11.03 — Understanding the Solid Resources Screen

Touch the System Resources tab > touch the cuvette diagram or one of the disposable tip or disc diagrams. The Solid Resources screen opens.

Legend Number of loaded cuvettes
  A cuvette chute in the holder
  Number of discs on each mounting pole
  Barcode for disc package
  Select type of resource and detail level
  System resource drawer 1
  System resource drawer 2
  Touch Unlock to open a locked resource drawer
  Number of disposable pipettor tips present in the drawer

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12. Current Run Tab

  1. Current Run Tab: Use this screen to monitor progress of run. Run is finished when this tab reads 00:00 and status line at bottom left corner says READY.

12. Current Run Tab

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12.01 — Monitoring a Run

Touch the Current Run tab to observe the status of sample processing during the run. Each loaded plate or tube is graphically represented on this tab. As samples are processed, they change color. See the color key at the bottom of the screen for an explanation of the meaning of each color.

A sample Current Run screen for plates appears below. To view the Current Run screen for tubes, see page 193.

Legend View screen information as a graphic or table
  Countdown display
  Select a well and click to display the associated Event Log
  Processing status, see the color key below the plate

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12.02 — Checking Instrument Status

During the run, periodically check the instrument status indicators at the bottom of the software to determine whether you need to add any consumables or system liquids, or empty any system waste containers.

The icons for system fluids, consumables, and instrument waste containers change color when any of these components need attention:

  • Green: Adequate amounts
  • Yellow: Low amounts
  • Red: Empty, must be refilled, or container is full and must be emptied

For information about refilling system fluid containers or emptying system waste containers, see Chapter 11, "Maintaining the Simoa HD‐1 Analyzer," on page 147.

When the run finishes, the countdown display says 00:00 and the instrument state notice changes to Ready.

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13. Review Results

Review the results in one of these ways:

  1. From the History & Reports tab, export the data to a CSV file for external analysis.
  2. Analyze the calibrators in the Data Reduction tab.
  3. From Reports subsection of the History and reports tab, Run Batch Curve Report.

13. Review Results

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13.01 — Data Analysis Overview

When the assay run is complete, results appear on the Run History screen. You can perform data analysis on all of the results or a subset.

Results can be exported to an external analysis package or a LIMS system, or you can view and analyze results in the instrument’s software. The following options are available:

  • Export a CSV file for external analysis
  • Export a PDF or Excel file for external analysis
  • Analyze the results in the instrument’s Data Reduction screen

See Simoa HD‐1 Data Analysis (USER‐104‐25) for complete instructions on how to analyze data when your assay run is complete.

Log in to the Quanterix portal and view a data analysis training video, Training – Modifying Calibration and Curves and Recalculating Samples, at www.quanterix.com/customer/training-videos.

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13.02 — Working with Run History

The Run History screen provides options that allow you to select the data and columns to include in the analysis, export the data to a CSV file, and move analysis data between multiple instruments.



The following table explains how to use the Run History screen.

  Element Definition
Add New Filter Adds filter criteria that determine what results appear in the table. Multiple filters are allowed. Touch the Add New Filter (+) button to add a filter. Touch the X on the filter button to remove the filter from the table.
Loading a large amount of data into the results table can decrease responsiveness. To avoid this, add a new filter before removing unwanted ones.
Configure Columns Opens the Configure Columns window that allows you to configure column display and ordering.
Automatic Replicates Selection When enabled, the software automatically selects all related replicates when one of the replicate results is selected.
Select all Results Selects all currently displayed results, as determined by data filters, if any are in place.
Deselect all Selected Results Clears any selection made on results in the table.
Exclude Selected Results from Analysis

Marks selected results for exclusion in analysis. Only results that have been automatically included in analysis can be excluded manually. Isingle is not recalculated when excluding results in the Run History table.

Note: Ensure the Automatic Replicates Selection button is turned off > select the replicates to be excluded from analysis, then touch Exclude Selected Results from Analysis button for result.

Include Selected Results Into Analysis Marks selected results for inclusion in analysis. Only results that have been excluded automatically from analysis can be included manually.
Show Related Flags and Events Displays all flags and event messages for selected results.
Recalculate with Different Curve Allows you to recalculate concentration results by manipulating the default calibration curve or to select a new calibration curve.
Export Exports displayed results to a comma separated value (CSV) file. All columns displayed in the table are exported. If you have not selected a column with Configure Columns, it is not exported. Additionally, if you applied data filters to the table, only results matching the filter criteria are exported.
Archive/Restore Provides ability to move result data between two computers running the Simoa HD‐1 software. Results archived (exported) to an XML file can be restored (imported) into the software running on another computer.

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13.03 — Exporting Results in CSV Format

Export a CSV file from the Run History screen to create a file for external analysis. To export data for troubleshooting analysis, include the Extended Properties column.

To export results in CSV format

  1. In the History & Reports tab, touch Run History.
  2. Clear all filters on the results table.
  3. Touch the Add New Filter button > select a filter from the drop‐down list > touch Next.
  4. Specify the filter criteria. Some filters provide drop‐down lists and others provide a text entry field that sets the filter.
  5. Touch OK. The results are filtered and the filter name appears above the results table.
  6. Touch Configure Columns.
  7. Select the columns you want to export and move them to the Selected column with the right arrow key.
  8. Touch Done.
  9. Touch Select All.
  10. Touch Export > specify a file name > touch Save.

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13.04 — Exporting Results in PDF or Microsoft Excel Format

Export a file in PDF or Microsoft Excel format from the Reports window to create a file for external analysis.

To export results in PDF or Microsoft Excel format

  1. In the History & Reports tab, touch Reports.
  2. Touch a report in the displayed list.
  3. Select individual reports or touch Select All for all reports.
  4. Touch Preview Report > touch Export.
  5. Save the data in PDF or Excel format.

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13.05 — Analyzing Results in the Data Reduction Tab

The instrument plots a Calibration Curve representing the selected results on the Data Reduction tab.

Curves are batch‐based. All the samples in the batch have the same calibration curve applied to them, regardless of processing order.

The calibration data table contains all calibration data points used in curve fitting. The table includes aggregated replicates data. If calibrators were run as replicates, their averages are used.

Curves are specific to the assay and the plex. All samples of the same assay, plex, and batch will initially have the same calibration curve, but they can be assigned to a different curve, if calibration data points are included in the batch or Curve Selection Strategy is set to None.

Following is a sample Data Reduction tab and a table that explains its components.

To review results in the Data Reduction tab

  1. In the Data Reduction tab, select the relevant fields in Assay, Plex, Calibration Curve, Curve Fit Algorithm, and Weighting.
  2. Use the tools described in the following table to analyze the data.


The following table explains how to use the Data Reduction tab.

  Element Definition
Selection Controls which calibration curve is displayed and the fitting algorithm and weighting used to generate the curve.
Plot Style Controls how the data is plotted.
Pan/Zoom Pan across the graph or zoom in on a selected area for more detail.
Reset Axes Use this to reset the graph axes to their original values.
Curve/Residuals Use the Curve and Residuals buttons to toggle between the calibration curve and fitting errors.
Calibration Means/Calibration Replicates Calibration Means shows the replicates’ summarized information in the main table. Calibration Replicates shows individual replicate concentrations.
Configure Columns Select the columns to include in the calibration data table.
Include To exclude individual replicate results from analysis uncheck the Include checkbox in the row you want to exclude. For detailed instructions, see Simoa HD‐1 Data Analysis Guide (USER‐104‐25).
Recalculate and View Results After selecting a different calibration curve, recalculates results and displays them in the Run History table.
Cancel Recalculate Results Cancel recalculation and return to the History and Reports tab.
Save As Saves the calibration curve. When you modify an existing curve, you must save it before it can be used to recalculate the results.
Cancel Curve Changes Resets any changes made to the existing calibration curve.

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End of Day

14. Maintenance Tab

  1. Maintenance Tab: Perform End of Day Task (about 20 minutes).

14. Maintenance Tab

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14.01 — Understanding the Maintenance Screen

The Maintenance screen shows status information about each maintenance task

Legend Add task filter (Customer Service only)
  Blocking behavior. See "Viewing Task Details" on page 150.
  Touch to show log
  Touch to choose columns
  View task parameters
  Print the task
  Run the selected task

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14.02 — Determining Whether a Maintenance Task Was Performed

The Maintenance screen shows status information about each maintenance task. Two methods are available to do this:

  • Check the Last Run column in the Maintenance tab, which reports the date and time when a task was last performed.
  • In the Maintenance tab, touch Show Log to view a log that lists all completed maintenance tasks.

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14.03 — Viewing Task Details

Use the read-only Task Details screen to display a description of a task, the task interval (when it is run), and its blocking behavior.

To view task details

Touch the checkbox for a task > touch View Details.

Legend Interval – The frequency of the task.
  Time – Time of day the task is performed.
  Blocks sample processing – Prevents assays from running or allow them to run if the task is not complete.
  Resets idle time – Resets/does not reset counter after task is performed
  Blocks shutdown when due – When enabled, the following prompt appears when you shut down the software.

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14.04 — Changing Columns

To change the table columns, touch Configure Columns > touch the arrows to move column names between the Available and the Selected boxes.

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14.05 — Performing the End of Day Task

The End of Day task flushes the pipettor that aspirates reagents and all pipettor and system fluid tubings to prevent the buildup of salts, which can clog the pipettor and instrument tubings.

The task performs these actions:

  • Flushes the pipettor with deionized water, cleans it with system wash buffer 1, and flushes it again with deionized water.
  • Primes the tubing for system wash buffer 1 and 2 with deionized water.

To perform the End of Day task

  1. Fill a clean reagent bottle a little more than half way with system wash buffer 1. Make sure that there are no bubbles in the bottle.
  2. Touch the Maintenance tab > touch the End of Day task checkbox > touch Run Task.
  3. When prompted, place the bottle into position 3 on a reagent rack (fourth position from the handle) and put the rack in the rightmost reagent bay position (lane 4).
  4. Allow approximately 20 minutes for completion. When the task is complete, touch Close, and remove the reagent rack and dispose of the reagent bottle.

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15. Shutdown Software

  1. Shut down software when End of Day Maintenance task is complete. Turn off instrument.

15. Shutdown Software

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15.01 — Shutting Down the Instrument After the Last Run of the Day

After the last run of the day:

  • Remove any leftover reagents and samples from the instrument. Recap the reagents and store at 2–8° C or as instructed in the assay package insert.
  • Empty the solid and liquid system waste containers (see page 54).
  • Perform the End of Day task (see page 154).

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