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Thermo Fisher Scientific

Re-Establishing Lost Communication with Single Quad MS


No communications with Single Quad Mass Spec instrument


  • Single Quad Mass Spec, specifically ISQ EC, ISQ EM, and MSQ Plus
  • Chromeleon 7


Re-establishing lost communication with a Thermo Single quad MS can be multifaceted problem that has multiple solutions depending on the root cause.  Troubleshooting these issues involves obtaining a considerable amount of information from the attached PC as well as the MS itself.  In the context of this discussion, we will focus on the MSQ, ISQ EC, and ISQ EM and their connection to a Chromeleon 7.X PC.  It is important to take note that the majority of our MS systems ship with a factory computer with the ideal software package preloaded, with appropriate Tune/Calibration files housed in the correct locations.  Any disruption of those files or software configuration can hinder connectivity.

  1. First priority is to gain as much information as one can from the customer (or onsite) as to what changes (if any) the PC has undergone prior to losing connection.  This can be a hardware change, upgrade, Windows update, or network connectivity.
  2. Verify that all USB/LAN ports are configured to not fall asleep via the Windows Control Panel.  Access the Control Panel > Device Manager and then access the appropriate port.  Right click on the port > Properties > Choose the Power Management Tab.  Make sure the “Allow computer to turn off this device to save power” is unchecked.
  3. Take note of the software packages loaded onto the system.  Both the MSQ and ISQ have very specific driver, firmware, and software requirements based on the Windows Operating systems installed on the PC.  All appropriate configurations can be found in the most recent Chromeleon release’s Supported Instruments Document.  Failure to adhere to these requirements will disrupt communication or operation.  Other configurations were not tested fully and are not supported by the factory.
    Manufacturer - System / Family   Type Model  Firmware  Interface Type  Instrument Class  Options Required   Required Chromeleon Version
    Thermo Scientific LC-MS/IC-MS  Single Quad MS MSQ Plus VI Driver 2.0 SP4 [11] USB   1 LC-MS   7.2 SR1
     Thermo Scientific LC-MS/IC-MS Single Quad MS ISQ EC ICMS/LCMS Digital Board
    Controller Interface FPGA 64; Controller Interface MCU 19; Lens Driver Base 21; Lens Driver HV 3; Pressure Controller 18; Display Board 1; RF 9; Rod Driver 3 
    LAN   LC-MS  7.2.6
     Thermo Scientific LC-MS/IC-MS Single Quad MS  ISQ EM ICMS/LCMS Digital Board
    Controller Interface FPGA 64; Controller Interface MCU 19; Lens Driver Base 21; Lens Driver HV 3; Pressure Controller 18; Display Board 1; RF 9; Rod Driver 3 
     LAN  LC-MS 7.2.9 
  4. Important to note that the ISQ utilizes a pre-configured LAN network card to connect to instrument.  The MSQ utilizes a USB connection to the PC.  Both instruments are configured into Chromeleon via the Instrument Configuration Manager available in the Chromeleon CDS software package.  The “Required Chromeleon Version” column denotes the minimum version required to control the Instrument. If a Service Release (SR) or Maintenance Update (MU) is required, the SR or MU number is mentioned in the table.

Verifying correct configuration in Chromeleon

As stated before, the PC should arrive with the correct Tune/Calibration files for the specific model purchased.  Please follow the steps as outlined below to ensure proper configuration of the MS within Chromeleon 7.X.  Prior to evaluating the configuration of any MS, make sure that the MS is on with the appropriate cable plugged into the PC.

  1. The MS instrument should be powered “On”, under vacuum and supplied with nitrogen gas.
  2. Open Chromeleon Service Manager, make sure the Instrument Controller is started, and select the “Configure Instruments” option.
  3. Open the Instrument with the configured MS.  Ensure that the proper family is selected for the configured IC or LC system.
    • Thermo Scientific > Mass Spectrometry > ISQ LCMS Family
    • Thermo Scientific > Mass Spectrometry > ISQ ICMS Family
  4. If a PC was purchased with the mass spectrometer, the instrument will configure automatically and display an IP address.  Verify the correct Instrument is displayed (ISQ EM or ISQ EC)
  5. If the Driver does not load correctly, remove the MS from the configuration, Save the Instrument Configuration and re-add the instrument.  
  6. Verify the correct Instrument is displayed and an IP address is displayed.
  7. If the IP address is not configured correctly and communication cannot be established, manual configure the IP Address by performing the steps on page 125 of the ISQ EC and ISQ EM Operating Manual.
  1. A computer is an automatic part of the MSQ-Plus purchase and comes preinstalled with Thermo Foundation, XCalibur, and MSQ Tune software.  Additionally, the preliminary autotune information for the specific instrument purchased is entered in Tune for the MSQ Plus to start seeing an ion beam immediately upon use.
    • If the computer does not come with Chromeleon 7.2 pre-installed, that installation will have to be performed by the FSE.
  2. Open the Instrument Configuration Manager as previously described in the ISQ notes.
  3. There is no specific MSQ Plus listed amongst the instruments to be added to an instrument in Chromeleon Instrument Configuration,
    • The correct path to add (or re-add) the MSQ > Thermo Scientific >Mass Spectrometry> Legacy Mass Spectrometer (of which, the MSQ Plus is the only one included).
    • In the Open VI Configuration button, verify the correct serial number and asset number is displayed.

Re-establishing Lost Communication

The following actions are to be considered if those previously mentioned do not remedy the issue, or if correct configuration is confirmed in Chromeleon.

  1. Basic Communication with the ISQ is extremely stable due to the nature of the LAN Ethernet connection.
    • Though rarely required, a hard restart of the PC should re-establish communication.
  2. Communication issues can arise specifically when Windows or Thermo Foundation is upgraded.
    • Prior to upgrading any software, be sure to save Tune parameters to the instrument.
    • Make sure to make a back-up copy of the Instrument Configuration to be loaded following reinstallation.
    • Refer to the most recent Xcalibur/TF compatibility matrix to ensure that the software installed is compatible with the new version of Windows.
    • Following the re-installation of all software, be sure to choose the correct ISQ configuration in the Chromeleon Instrument configuration manager (or reload the saved Instrument Configuration.
    • If the IP address is not configured correctly and communication cannot be established, manual configure the IP Address by performing the steps on page 125 of the ISQ EC and ISQ EM Operating Manual.
  3. Verify the correct communication by checking gases and voltages.  Perform ESI positive Autotune (print report) and ESI Diagnostics.
  1. Basic communication can be checked by opening Developer Tune, independent of the Chromeleon software.  
    • It is recommended to stop the Chromeleon Instrument controller while operating Tune to prevent an “argument” between the two software packages.
  2. Initial indication of proper communication can be assessed by checking the upper-right corner of the screen.  The musical notes should be rotating and the dot in the system tray should be one of the colors described below, depending on its state.  A basic function test, BFT, completely demonstrates communication and functionality.  Specifics for a BFT can be found in the MSQ Installation and Commissioning Guide excerpts provided by a qualified Field Service Engineer.
    • The colors of the dot represent the state of the MSQ Plus.
      • Red indicates that it is in the vented state.
      • Blinking yellow dot indicates that it is attempting to reach vacuum.  Solid yellow dot means that vacuum has been achieved.
      • Green dot means that the MSQ Plus is acquiring data.
  3. MS data is large and communication can be lost if too much is trying to be transferred at once.
    • If communication does get lost, the recommendation is to first close both the Chromeleon Instrument Controller and Tune (if it’s open).
    • Take a ball point pen and press the Reset button on the back of the MSQ Plus. A chirp may be heard upon resetting the detector.
    • Reopen the program that is desired to operate the instrument and determine whether or not communication is present by monitoring the Dot and front LED color and performing a BFT.
    • If the above does not reengage communication, the computer may need to be rebooted. The MSQ Plus should not need to be physically turned off through any of this process.


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