In the Settings area, there are global MS settings to specify the infusion mode, and how to perform the internal mass calibration.

An internal calibrant is one that is analyzed during the same MS experiment as your sample and is detected at the same time as your analytical ions. Internal calibration provides the most accurate corrections to the data. When you perform an internal calibration with the user-defined lock mass correction option, you must use the mass list table to define or import a list of lock masses. You can import the settings from (or export them to) a .csv, a .txt, or a .xml file.

When you perform a standard internal calibration, the system uses the reagent ion from the EASY-IC or EASY-ETD source, instead of user-specified ion masses. However, you must activate internal calibration on each Orbitrap scan by selecting the Internal Mass Calibration option in the Settings area. This activates a scan-by-scan calibration. The EASY-IC or EASY-ETD source injects reagent ions into each calibrated scan.

NOTE

  • The EASY-IC source is compatible with all Orbitrap Tribrid Series instruments.
  • The EASY-ETD source is only compatible with the Orbitrap Apex, Orbitrap Ascend, Orbitrap Eclipse, Orbitrap Fusion Lumos, and Orbitrap Fusion instruments.
  • To use the standard internal calibration setting, your instrument must have the optional EASY-IC or EASY-ETD source and you must enable the internal calibration under the Optional Hardware area in the Thermo Scientific Foundation Instrument Configuration window.

 

The following table describes the parameters in the Settings area.

Parameter

Description

Infusion Mode

Specify the infusion mode from the following options:

  • Liquid Chromatography: Select this option when the sample is introduced by an LC system (i.e. precursors and precursor intensities change with time). This parameter is used for a variety of features including Dynamic AGC mode (with Desired Minimum Points Across the Peak), Auto Dynamic Exclusion, and scheduling AGC prescans.
  • Infusion: Select this option when the sample is introduced by either a direct manual injection or delivered by a syringe pump (i.e. precursors and precursor intensities do not change with time).

Expected LC Peak Width(s)

It is recommended that you measure/determine the Expected LC Peak Width(s) from previous runs. It is taken at 10% valley (FWTM) - please use Peak width as a first approach. The Expected LC Peak Width(s) has a direct influence on AGC and filter properties (Dynamic Exclusion and Apex Detection).

The Expected LC Peak Width(s) measure is used to ensure proper calculations for AGC measures, i.e. the scheduling of periodic AGC pre-scans and receiving scan-to-scan AGC info.

FWTM: Full Width at 10% maximum. FWHM: Full Width at half maximum.

Range: 1–1,000; Default: 30

Advanced Peak Determination

Select to apply the advanced peak determination (APD) algorithm.

The APD algorithm is an advanced algorithm that improves the determination of the charge states and monoisotopic m/z values of isotopic envelopes.

Default: Selected

Default Charge State

Charge state used when the charge state is undetermined. For example, when setting the value for normalized collision energy.

Range: 1–5; Default: 2

Enable Xcalibur AcquireX method modifications

Select this box to use this method as part of the Xcalibur AcquireX workflow.

Default: Deselected

Lock Mass Correction

A list of predefined Lock mass Correction selections, which are:

  • Off: The feature is not enabled.
  • EASY-IC: The EASY-IC source is ON and applied throughout the entire run. By default it is on for all scans, when it is selected under the Settings menu. It can be set on/off scan-type dependent.
  • RunStart Easy-IC™: Select this option if you want to apply the EASY-IC source early in the run only. The early-on performed internal calibration of a single scan is applied throughout the run and internal calibration settings are remembered until the raw file is closed.
  • User-defined Lock Mass: Enter a user-defined lock mass. The lock mass is applied to the entire run. If the lock mass is not found in a given scan, the system will remember the last successful locking for this scan.

When the "User-defined Lock Mass" option is selected, the lock mass table appears. The following options are available in the table:

  • Add: Select Add to create a user-defined lock mass in the table. By default, Positive polarity mode is enabled. To change the polarity from Positive to Negative, select the cell and choose Negative from the drop-down list.
  • Delete: Highlight a row, then select Delete to remove a user-defined lock mass from the table.
  • Import: Use this feature to import a file (csv, txt, or xml) into the lock mass table.
  • Export: Use this feature to export the lock mass table to a file (csv, txt, or xml).

NOTE: For the User-defined Lock Mass option, the Orbitrap mass analyzer calibrates only if it finds the scanned ions listed in the mass table. The lock mass option calibrates the Orbitrap MS full-scan type only.