Intensity filter - Intensity filter - Orbitrap Tribrid Apex Small Molecule Method Editor Help - Orbitrap Apex Small Molecule MS - Orbitrap Tribrid Apex Small Molecule Method Editor Help - Filter types - Intensity filter - topic

Filter Type

Using the Intensity filter restricts data-dependent scans to precursors that fit the specified intensity requirements.

Select from the following filter types:

• Intensity Threshold: To define only a minimum intensity required to trigger a data-dependent scan.
• Relative Intensity: To define a minimum relative intensity required to trigger a data-dependent scan. The threshold is relative to the base peak (the most intense ion in the spectrum).
• Intensity Range: To define a specific range of precursor intensities that will trigger data-dependent scans.

Dependence on master scan analyzer type: Intensity thresholds for data-dependent scans triggered from Orbitrap master scans have a much higher recommended intensity thresholds than data-dependent scans triggered from ion trap master scans, because the two analyzers use different intensity scales. The MS intensities are in units of ions / second for the ion trap analyzer. The Orbitrap intensity unit is about 10x higher than the ion trap, requiring a proportionately higher intensity threshold. The reason for this different scaling is that the ion trap electron multiplier requires calibration, and the conversion factor between signal and number of ions is determined during this process.

Dependence on dependent scan analyzer type: Intensity thresholds for data-dependent scans detected in the Orbitrap mass analyzer have a much higher recommended intensity threshold than the ion trap mass analyzer because the ion trap mass analyzer is the more sensitive detector.

Intensity Threshold

(Available when the Intensity Threshold filter type is selected.)

Specify the minimum intensity required to trigger a data-dependent scan.

Range: 0 to 1.0 × 10²⁰; default: 5.0e3

Intensity threshold is most often used to prevent data-dependent scans from triggering on low intensity species that will require long injection times and may not provide high quality spectra.

NOTE: The optimal threshold setting depends both on the master scan analyzer type and the dependent scan analyzer type.

Dependence on master scan analyzer type: Intensity thresholds for data-dependent scans triggered from Orbitrap master scans have a much higher recommended intensity thresholds than data-dependent scans triggered from ion trap master scans, because the two analyzers use different intensity scales. The MS intensities are in units of ions / second for the ion trap analyzer. The Orbitrap intensity unit is about 10x higher than the ion trap, requiring a proportionately higher intensity threshold. The reason for this different scaling is that the ion trap electron multiplier requires calibration, and the conversion factor between signal and number of ions is determined during this process.

Dependence on dependent scan analyzer type: Intensity thresholds for data-dependent scans detected in the Orbitrap mass analyzer have a much higher recommended intensity threshold than the ion trap mass analyzer because the ion trap mass analyzer is the more sensitive detector.

Relative Intensity Threshold (%)

(Available when the Relative Intensity filter type is selected.)

Specify the minimum relative signal intensity required to trigger a data-dependent scan.

Range: 0–100; default: 20

Minimum Intensity

(Available when the Intensity Range filter type is selected.)

Specify the minimum signal intensity required to trigger a data-dependent scan.

Range: 0–1.0 × 10²⁰; default: 5.0e3

Maximum Intensity

(Available when the Intensity Range filter type is selected.)

Specify the maximum signal intensity required to trigger a data-dependent scan.

Range: 0–1.0 × 10²⁰; default: 1.0e20