To establish control of the MS from the data system computer, use the Thermo Foundation Instrument Configuration window to configure the instrument.

Procedure

  1. From the Windows taskbar, select Start > Thermo Scientific Foundation x.x > Instrument Configuration.
  2. The Thermo Foundation Instrument Configuration window appears.
  3. Add the MS icon to the Configured Devices list.
  4. Highlight the MS icon and select Configure or double-click on the MS icon.
  5. The Instrument Configuration dialog box appears.
  6. Specify the configuration parameters for the MS, as applicable.
  7. Select OK to close the Instrument Configuration window.
  8. Select Done to close the Thermo Foundation Instrument Configuration window.
  9. Restart the data system computer when prompted.

 

Parameters in the Instrument Configuration window

Parameter

Description

System Information

Model

Displays the instrument model.

Serial Number

Displays the instrument serial number.

If you did not specify the serial number during the software installation process, a red box will appear. You can enter or update the serial number in the field, if applicable.

Inlet

Divert valve

Select the divert valve configuration from the dropdown list.

  • None (default): Select this option for a system without a divert valve
  • A: Select this option for a system with one divert valve
  • A and B: Select this option for a system with two divert valves

Syringe pump

Select the syringe pump configuration from the dropdown list.

  • Not configured (default): For a system that does not include a data-system controlled syringe pump.
  • Configured: For a system that includes a data-system controlled syringe pump.

Input Contact Closure

Select which type of event triggers contact closure from the dropdown list.

  • Transition close-to-open (default)
  • Transition open-to-close

Wait for Gas Flows to Stabilize

When enabled, the method is cancelled if the sheath, auxiliary, or sweep gas flow rates vary by more than 10 percent of the maximum and the collision-induced dissociation (CID) gas varies more than 3 percent of the setting during five consecutive measurements.

Default: Selected

Wait for Temperatures to Stabilize

When enabled, the method is cancelled if the ion source temperature varies by more than 3 percent during five consecutive measurements.

Default: Selected

Keep Last Method Settings

Select this option to copy the ion source and scan settings from the last instrument method into the Tune setup. The instrument continues to run with these settings until you make a change or run another method with new settings.

Default: Selected

Ion Source

Default Source

Select the default type of ion source that is installed on the MS from the dropdown list:

  • Heated ESI
  • NSI (optional)
  • APCI (optional)
  • ESI

NOTE: Although atmospheric pressure photoionization (APPI) is not a configuration option, the MS automatically detects if the ion source contains the APPI vacuum ultraviolet (VUV) lamp through the lamp’s USB connection.

Default Source Type

(H-ESI and APCI only)

Select either of these ion source types from the dropdown list:

  • Dedicated Heated ESI (or Dedicated APCI)
  • Combination Source
  • Dedicated Heated ESI PLUS (or Dedicated APCI PLUS)

Enable Sweep Gas For NSI Source

This option enables sweep gas flow to the NSI source.

Sweep gas can aid in the desolvation of the nanospray, but excessive sweep gas can deflect the nanospray from the orifice of the ion transfer tube, which decreases sensitivity. You must have the sweep cone installed for the sweep gas to work.

Default: Selected

Enable Minimum Gas Flow Requirement for Sealed Sources
(H-ESI, ESI, APCI, and APPI)

This option enables a minimum gas flow (2, arbitrary units) for the Sheath gas, Aux gas, and Sweep gas in the Tune application and Method Editor.

When this option is unchecked, the minimum gas flow requirement is removed and the gas flow levels can reach zero (0, arbitrary units).

Default: Selected

Analog Inputs

Channel 1 in Use

Select this checkbox to read the 0–10 Vdc analog input signal from an external device and write the data into the raw data file.

Default: Unselected

For the pin-out assignments, refer to the Operation Manual.

Channel 1 Label

Specify a name for Channel 1.

Default: Channel 1

Channel 2 in Use

Select this checkbox to read the 0–2 Vdc analog input signal from an external device and write the data into the raw data file.

Default: Unselected

For the pin-out assignments, refer to the Operation Manual.

Channel 2 Label

Specify a name for Channel 2.

Default: Channel 2

Instrument Warnings

Low Convectron Gauge Pressure

Select this checkbox to be warned if the pressure in the RF lens region of the vacuum manifold, which the convection gauge measures, is below 20 Pa (0.2 Torr).

If the Convectron™ gauge pressure is low, the ion transfer tube might be blocked or removed. Refer to the Maintenance chapter in the Operation Manual.

Default: Selected

Low Sheath Gas Flow

Select this checkbox to be warned if the gas pressure available from your nitrogen tank is not sufficient to maintain the sheath gas flow.

Default: Selected

IMPORTANT: If you specify not to be warned, you might inadvertently run experiments with less than the optimum sheath gas flow rate. Doing so might adversely affect the quality of your data.

Low Aux Gas Flow

Select this checkbox to be warned if the gas pressure available from your nitrogen tank is not sufficient to maintain the auxiliary gas flow.

Default: Selected

IMPORTANT: If you specify not to be warned, you might inadvertently run experiments with less than the optimum auxiliary gas flow rate. Doing so might adversely affect the quality of your data.

Low Sweep Gas Flow

Select this checkbox to be warned if the gas pressure available from your nitrogen tank is not sufficient to maintain the sweep gas flow.

Default: Selected

IMPORTANT: If you specify not to be warned, you might inadvertently run experiments with less than the optimum sweep gas flow rate. Doing so might adversely affect the quality of your data.

Low Collision Gas Flow

Select this checkbox to be warned if the gas pressure available from your helium tank is not sufficient to maintain the collision gas flow.

Default: Selected

IMPORTANT: If you specify not to be warned, you might inadvertently run experiments with less than the optimum collision gas flow rate. Doing so might adversely affect the quality of your data.

Historical Data Retention

Once a week on the specified day and time, the data purging process will initiate. This process only occurs if the instrument is in an idle state. In addition to these settings, automatic purging managed by the TNG database service can occur nightly at 11pm if the instrument is in an idle state.

Day

Specify your preferred day to start the data purging process.

Default: Sunday

Time

Specify your preferred time to start the data purging process.

Default: 11 PM

Service

Disable Ion Gauge Check

When enabled, the instrument ignores the state of the ion gauge during the vacuum check. However, there are additional interlocks in the hardware that prevent any high voltages from turning on, even if you disable the ion gauge check.

Default: Unselected

Disable Board Identification Check

When enabled, the instrument does not confirm communications with the enabled high-speed serial bus (HSSB) boards upon start up.

Default: Unselected

Disable Ion Source Identification Check

When enabled, the instrument does not automatically identify the type of ion source. The system assumes that the default source is installed

Default: Unselected

Buttons

OK

Saves the settings and closes the Instrument Configuration window.

Cancel

Closes the Instrument Configuration window without saving the changes.

Apply

Applies the changes in the Instrument Configuration window.